Population dynamics of Malassezia species on the skin of HIV-infected patients

Population dynamics of Malassezia species on the skin of HIV-infected patients | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Population dynamics of Malassezia species on the skin of HIV-infected patients Abdourahim Abdillah, Isabelle RAVAUX, Saadia MOKHTARI, Stephane Ranque This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4139174/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Malassezia species are lipid-dependent yeasts of the normal skin mycobiota in humans and some animals, which can cause skin infections. Yet, both the dynamic of Malassezia skin colonization and the associated fungal and bacterial skin microbiome remain unknown in HIV-infected patients. The purpose of this study was to compare Malassezia yeast community structure and associated microbiome on the healthy skin of HIV-infected patients and healthy controls. A total of 23 HIV-infected patients and 10 healthy controls were included and followed-up for a maximum of 5 visits over 10 to 17 months. At each visit, chest, face, nasolabial fold, and scalp skin samples were subjected to both culture and MALDI-TOF MS identification, and ITS/16S metabarcoding. The participants were categorized according to their Malassezia colony forming unit (CFU) abundance. Malassezia were cultured from each participant at each visit. HIV-infected patients were highly colonized on all visits with CFU > 100. M. sympodialis and M. globosa were the most dominant species overall. M. furfur and M. dermatis were more prevalent in HIV-infected than in healthy participants. M. sympodialis prevalence was stable at each sampling sites over time. M. furfur prevalence was stable and more abundant over time on HIV-infected patients’ chest. Although not statistically significant, the metagenomic analysis showed a higher fungal and bacterial diversity and an increased abundance of Cladosporium halotolerans and Streptococcus in HIV-infected patients than in controls. Our data showed a high skin colonization of Malassezia yeasts as well as a dysbiosis of both fungal and bacterial communities in HIV-infected patients. Malassezia skin HIV infection colonization fungal and bacterial microbiome mycobiome dysbiosis Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Introduction Malassezia species are lipid-dependent basidiomycetous yeasts that are part of the skin microbiota of humans and some animals. However, under certain conditions such as high temperature and/or humidity or oily skin, these yeast become opportunistic pathogens and cause skin infections such as pityriasis versicolor, seborrheic dermatitis, and folliculitis (Gaitanis et al., 2012 ; Prohic et al., 2016 ). More rarely, they cause bloodstream infections (Rhimi et al., 2020 ). Malassezia species are also associated with other multifactorial skin diseases such as psoriasis and atopic dermatitis (Baroni et al., 2004 ; Gaitanis et al., 2012 ; Glatz et al., 2015 ; Prohic et al., 2016 ). Seborrheic dermatitis (SD) has a particularly high prevalence, ranging from 30–80%, in immunocompromised HIV-infected patients (Tragiannidis et al., 2010 ). Furthermore, it appears that the onset of SD can be an early sign of CD 4 T cell depletion (Tragiannidis et al., 2010 ), suggesting a control of CD 4 T cell related immunity to cutaneous Malassezia . It may contribute to the early diagnosis of HIV-associated immunodeficiency (Forrestel et al., 2016 ). In a study analysing healthy skin of HIV-infected patients and non-HIV individuals, it was found that HIV-infected patients have a higher Malassezia density than non-HIV individuals (Pechère et al., 1995 ). Recently, it has been reported that HIV-infected patients with SD have a higher Malassezia load than HIV-infected patients without seborrheic dermatitis (Moreno-Coutiño et al., 2019 ). In addition, it is reported that HIV infection is associated with abnormalities in skin surface lipids, particularly by a significant increase in triglycerides and squalenes, and a significant decrease in free fatty acids (Vidal et al., 1990 ). These findings suggest that HIV infection facilitates Malassezia overgrowth. A culture-based study conducted on the healthy skin of 38 HIV-infected and 40 HIV-uninfected persons had reported a high density of Malassezia in the HIV patients (Pechère et al., 1995 ). However, a recent study reported a non-statistically significant difference of 69% and 79% of Malassezia yeast isolation from the healthy skin of 46 HIV-infected patients and 46 healthy controls, respectively, with (Krzyściak et al., 2020 ). In addition, the authors found that HIV-infected patients with high CD 4 T cells had a higher Malassezia colonization. However, the authors of this study did not provide data on the abundance of Malassezia yeasts isolated from the two groups. Also, the fungal and bacterial skin microbiome was not explored, which may provide a better understanding of the skin microbiome associated with HIV infection (Krzyściak et al., 2020 ). On the other hand, the distribution of species varies in epidemiological studies for several reasons such as geographical location, culture media used, sampling and identification methods (Prohic et al., 2016 ; Saunte, Gaitanis and Hay, 2020 ). It is considered, for example, that M. sympodialis is the dominant species in Europe where the culture method is more widely used, whereas M. restricta and M. globosa are more dominant in Asia where molecular methods are more widely used (Saunte, Gaitanis and Hay, 2020 ). Furthermore, it is important to note that most of the studies investigating the cutaneous distribution of Malassezia species have been performed by sampling a single period in time. The question of the dynamics and stability of Malassezia yeasts is rarely addressed on the skin. If Malassezia abundance varies over time or if certain Malassezia species dominate the skin at all times is a question to be answered. The objectives of this study were: 1) to quantify Malassezia yeasts in healthy skin of HIV-infected patients compared to healthy controls, 2) to evaluate the stability of Malassezia species on the skin, and 3) to investigate the fungal and bacterial skin microbiome associated with HIV infection. Patients and Methods Inclusion. Participants of this study were recruited at the Infectious Diseases outpatient ward at the “Institut Hospitalo-Universitaire Méditerranée Infection” (IHU-MI), La Timone University Hospital of Marseille, France. A total of 33 volunteers were included, comprising 23 HIV-infected patients (HIV+) and 10 healthy (non-HIV infected) controls. Inclusion criteria were: age at least 18 years; no history of systemic or local antifungal treatment within the last 30 days. All participants gave informed consent and completed a form with age, sex, and whether they had taken local or systemic antifungal treatment in the previous 30 days. Ethical clearance . This study protocol was conducted in accordance with the Helsinki Declaration and was approved by the ethics committee “Comité de Protection des Personnes Ile de France II” (N19.05.29.69947 RIPH3, dated 21 October 2019). Samples collection. A longitudinal cohort study was conducted from November 2019 to June 2021. At each visit of the 5 visits, samples were collected from 4 body sites, including the chest, scalp, face, and left nasolabial fold, by rubbing for 5–10 s, as previously (Abdillah et al., 2020 ), a sterile gauze (non-woven sterile swabs 10 cm x 10 cm, SYLAMED, Paris, France) for Malassezia species isolation. Dry swab samples were also collected from each body site at 1 or 2 visits and stored in liquid transport medium at -20°C for DNA extraction and further ITS and 16S metabarcoding. Culture medium. The MalaSelect medium (4.3% Schædler agar, 2% peptone, 1% glucose, 1% malt extract, 0.5% ox-bile, 0.5% Tween 60, 0.2% oleic acid and 0.25% glycerol [pH6], each from Sigma-Aldrich, Saint-Quentin Fallavier, France) containing 0.5 g/L cycloheximide (CliniSciences, Nanterre, France) and 4 mg/L rapamycin (CliniSciences, Nanterre, France) was prepared as previously (Abdillah and Ranque, 2021 ), supplemented with 0.5 g/L chloramphenicol (Sigma-Aldrich). After cooling to approximately 56°C, 0.03 g/L colistin (Sigma-Aldrich) and 4 mg/L rapamycin were supplemented before dispensing the medium into Petri dishes. Malassezia isolation and identification. Sterile gauze specimens were directly inoculated onto the MalaSelect medium plates within one hour after collection at the IHU-MI mycology laboratory. Unused sterile gauze were also plated on MalaSelect medium as negative control. All plates were sealed into plastic bags, incubated aerobically at 30°C for 3 to 10 days, and examined daily for the growth of Malassezia species. Malassezia colony forming units (CFU) were counted and identified via MALDI-TOF Mass Spectrometry (MALDI Biotyper, Bruker Daltonics GmbH, Bremen, Germany) with a reference spectra library supplemented with in house (including Malassezia spp.) reference spectra, as previously described (Cassagne et al., 2016 ; Diongue et al., 2018 ). The identification procedure was systematically carried out on 1 to 5 CFU per plate. Malassezia CFU abundance was categorized as follows: negative (0 CFU), low (≤ 20 CFU), intermediate (20 100 CFU). ITS and 16S Metabarcoding. The total DNA from the swab samples was extracted with the EZ1 DNA tissue kit (Qiagen GmbH, Hilden, Germany) following an automated extraction protocol of EZ1 Advanced XL (QIAGEN Instruments Hombrechtikon, Switzerland) with the DNA card bacteria V 1.066069118 QIAGEN. Briefly, 200 µL of samples and 200 µL of G2 lysis buffer were mixed in a 2 mL Eppendorf tube. Glass powders (Sigma-Aldrich, ref. G4649-500g) were added and mechanical lysis was performed with the FastPrep-24 TM 5G V. 6005.1 (M.P Biomedicals, LLC Santa Ana CA, USA) at 6 m/s for 40 s, and then incubated at 100°C for 10 min. After centrifugation at 10,000 g for 1 min, 200 µL of the supernatant was recovered, and 10 µL of proteinase K was added, followed by 2h incubation at 56°C. DNA was then extracted according to the manufacturer's instructions, and eluted in 200 µL. For the fungi, the ITS1 and ITS2 region were amplified in triplicate with hybridization temperatures of either 52°C or 55°C, using a previously described procedure (Hamad et al., 2017 ). The 25 µl amplification reaction mix consisted of 12.5 µl AmpliTaq Gold master mix, 0.75 µl of each primer (Eurogentec, Seraing, Belgium), 6 µl distilled water, and 5 µl DNA template. PCR cycling conditions were: 95°C for 10 min, 40 cycles of 95°C for 30 s, (55°C or 52°C) for 30 s, and 72°C for 1 min, followed by a 5 min final extension step at 72°C. For each sample, the amplicons of each ITS1 and ITS2 PCR replicates at the two temperatures were then pooled. For bacteria, the 16S “V3-V4” regions were amplified using the primers with overhang adapters described herein (Kodio et al., 2019 ). The amplification reaction mix consisted of 12.5 µl de Kapa HiFi HotStart ReadyMix 2x (Kapa Biosystems Inc, Wilmington, MA U.S.A), 0.5 µl of each primer (Eurogentec, Seraing, Belgium), 1.5 µl distilled water and 10 µl DNA template for 25 µl volume. PCR cycling conditions were as follows: 95°C for 3 min, 45 cycles of 95°C for 30 s, 55°C for 30 s, and 72°C for 30 s, followed by a 5 min final extension step at 72°C. PCR products were then purified on AMPure beads (Beckman Coulter Inc, Fullerton, CA, USA), quantified using High sensitivity Qubit technology (Beckman Coulter Inc, Fullerton, CA,USA), pooled and barcoded before sequencing for ITS and 16S rRNA on a MiSeq system (Illumina, Inc, San Diego CA 92121, USA) with paired end strategy as previously described (Kodio et al., 2019 , 2021 ). Bioinformatics and statistical analysis. The bioinformatics analyses of the ITS reads were performed using the PIPITS automated pipeline that was developed for the analysis of ITS sequences from Illumina sequencing (Gweon et al., 2015 ). The obtained OTU table was completed by manually analysing the sequences obtained of the operational taxonomic units (OTU) from the ITS1 and ITS2 regions via the standard Basic Local Alignment nucleotide Search Tool (BLASTN) search as previously described (Kodio et al., 2021 ). The criteria for taxonomic assignment of fungal OTUs were established as follows: PID (percentage of identity) > 97% assignment to species level; PID between 95 and 97%: assignment to genus; PID between 90 and 95%: assignment to the family; PID below 90%: assignment to the kingdom. Sequences that were well assigned taxonomically to the family or genus level and not to the species level, for example, were named unclassified to the species level. For 16S sequences, the reads were analysed by the MetaGX and VSEARCH tools as previously described (Kodio et al., 2019 ). The SILVA database as well as the Culturomics and Diagnostics in-house databases were used for the taxonomic assignments of bacterial OTUs. The criteria for taxonomic assignment of bacterial OTUs were established as follows: 1) presence of one or more BLAST hits associated with a reference sequence (100% coverage; identity > 97% corresponds to the assignment of OTUs to the species associated with the best BLAST hit); 2) presence of less relevant BLAST hits (identity between 95 and 97%: assignment to genus level; between 90 and 95%: assignment to the family; below 90%: assignment to the kingdom) with, in each case, the creation of a putative species; 3) no BLAST hits (creation of putative new bacterial species). We used R software (Version 4.2.1) to computer the alpha and beta diversity. Alpha diversity was estimated by the observed OTU richness and Shannon diversity. The Wilcoxon test was used to test whether there was a difference between HIV-infected patients and healthy controls. Beta diversity was computed using the Bray-Curtis dissimilarity calculated using the vegdist function from R package vegan . Community composition was visualized using non-metric-multidimensional scaling (NMDS). To test whether HIV status explained community composition, Permutational Multivariate Analysis of Variance (PERMANOVA) test was performed using the anosim function from R package vegan . Boxplots were made using the ggplot2 R package. The relative abundance of bacterial and fungal taxa was assessed between the two groups, by combining together OTUs designating the same phylum, genus or species. Because the ITS does not allow precise identification for some fungi, sectional grouping was performed for Aspergillus and Penicillium . The linear discriminant analysis (LDA) effect size (LEfSe) was performed to identify the bacterial and fungal taxa differentially represented between groups at the species level (Segata et al., 2011 ). Correlation analyses between fungal and bacterial genera were performed using the corrplot R package. All statistical tests with a p -value under 0.05 was considered statistically significant. Results Study participants’ baseline characteristics. Of the 33 volunteers included in this study, 10 were healthy controls and 23 were HIV-infected. Of the 23 HIV-infected patients, 10 patients were immunocompromised, as defined by a CD 4 T-cell count below 200, with 105.9 (± 48.8 SD) mean CD 4 T-cell count, and 13 non-immunocompromised patients (as defined by a CD 4 T-cell count above 500), with 701.7 (± 228.6 SD) mean CD 4 T-cell count. The 10 immunocompromised patients had a mean age of 47.5 (± 8.6 SD); 8 were males (2 females); and their HIV load was undetectable in 50%. The 13 non-immunocompromised HIV infected patients had a mean age of 54 (± 9.5 SD); 9 were males (4 females); and their HIV load was undetectable in 46%. All HIV-infected patients were on highly active antiretroviral therapy and none of them had skin lesions on the sampling sites. In the healthy controls, the mean age was 34.6 ± 14.3 years with 8 males and 2 females. None of them complained of disease-related symptoms. Follow-up study . All 10 healthy controls participated in all visits. Because many HIV-infected patients, had an incomplete follow-up (most were lost to follow-up and 2 of the immunocompromised patients died) due to the SARS-CoV-2 pandemic-related crisis, all HIV-infected patients were grouped, irrespective of their CD4 levels, in the follow-up analyses. Malassezia cultivation and abundance. All subjects in this study had at least one culture positive for Malassezia species within visit1. The prevalence of positive cultures varied according to body site and HIV status (Table 1 ). The prevalence of positive cultures on chest samples was high in both immunocompromised patients (100%) and healthy volunteers (80%) while it was high on the nasolabial fold in non-immunocompromised patients (92.3%). Depending on the HIV immune status, the rate of positive culture appeared to have no apparent difference. Considering all HIV-infected patients, the chest and the nasolabial fold were the two most colonized sites with a positive culture prevalence of 91.3% compared to healthy controls (Table 1 ). Table 1 Prevalence of Malassezia -positive cultures at visit1 according to body site. Positive cultures body sites Controls All HIV+ HIV+ > 500 CD 4 < 200 CD 4 (n = 10) (n = 23) (n = 13) (n = 10) Chest – no. (%) 8 (80%) 21 (91.3%) 11 (84.6%) 10 (100%) Scalp – no. (%) 6 (60%) 18 (78.2%) 11 (84.6%) 7 (70%) Forhead – no. (%) 4 (40%) 19 (82.6%) 11 (84.6%) 8 (80%) Nasolabial fold – no. (%) 6 (60%) 21 (91.3%) 12 (92.3%) 9 (90%) When analysing the level of Malassezia abundance, colonization was slightly higher in non-immunocompromised patients with CFU > 100 on the chest (15.4% vs 10%), scalp (7.7% vs 0%) and nasolabial fold (15.4% vs 10%) when compared to immunocompromised patients (Fig. 1 A, 1 B and 1 D). However, immunocompromised patients were more abundantly colonized on the forehead compared to non-immunocompromised patients (Fig. 1 C). On the scalp, 70% of immunocompromised patients had low colonization with ≤ 20 CFU compared to 46.1% in non-immunocompromised patients (Fig. 1 B). Analysis of 4 sampled body sites showed that 52.2% of all HIV-infected patients had CFU > 100 while 70% of healthy controls had CFU ≤ 20, suggesting a high colonization of Malassezia species in HIV-infected patients. Within visit1, 4 Malassezia species were isolated including M. sympodialis (41%), M. globosa (24.7%), M. restricta (21.7%) and M. furfur (12.6%). The frequency of isolation of M. sympodialis , M. globosa and M. restricta was 39.1% vs 30%, 86.9% vs 90% and 78.2% vs 40% in HIV-infected patients and healthy controls, respectively. M. furfur was isolated only in HIV-infected patients (13%) with high colonization on the chest (Fig. 1 E). The distribution of isolated species varied according to site and group (Fig. 1 E- 1 H). M. sympodialis was most abundant on the forehead (84.6%), nasolabial fold (58%) and chest (55.7%) while M. globosa was most abundant on the scalp (69.2%) in healthy controls (Fig. 1 E- 1 H). In contrast, M. sympodialis was most abundant on the scalp (67.5%) and nasolabial fold (51.5%) while M. globosa and M. restricta were most abundant on the chest (42.7%) and forehead (63.2%) in HIV-infected patients. The analysis of all sampled body sites showed 39.9% vs 53.4%, 23.3% vs 42.7%, 23.1% vs 3.8% and 13.6% vs 0.0% abundance for M. sympodialis , M. globosa , M. restricta , and M. furfur in HIV-infected patients and healthy controls, respectively. Depending on the HIV immune status, the frequency of isolation of M. sympodialis , M. globosa , M. restricta , and M. furfur was 50% vs 30.8%, 90% vs 84.6%, 70% vs 84.6% and 20% vs 7.7% in immunocompromised patients and non-immunocompromised patients, respectively. M. restricta appeared to be more abundant in immunocompromised patients on the scalp, face and nasolabial fold compared to non-immunocompromised patients (Fig. 1 F, 1 G and 1 H). Stability of Malassezia skin colonization over time. We sought to determine the stability of Malassezia species in body sites sampled depending on HIV status. All subjects sampled within 5 visits had at least one positive culture for Malassezia species. During the 5 visits, the prevalence of positive cultures varied according to body site and HIV status (Table 2 ). The chest was the site with the highest prevalence of positive cultures on all visits, particularly in HIV-infected patients (Table 2 ). Table 2 Prevalence of Malassezia -positive cultures in 5 visits according to body site. Positive cultures/body sites Chest – no. (%) Scalp – no. (%) Forehead – no. (%) Nasolabial fold – no. (%) Visit1 Healthy (n = 10) 8 (80) 6 (60) 4 (40) 6 (60) HIV+ (n = 23) 21 (91.3) 18 (78.2) 19 (82.6) 21 (91.3) Visit2 Healthy (n = 10) 10 (100) 8 (80) 7 (70) 7 (70) HIV+ (n = 11) 11 (100) 10 (90.9) 11 (100) 10 (90.9) Visit3 Healthy (n = 10) 10 (100) 9 (90) 8 (80) 6 (60) HIV+ (n = 8) 8 (100) 8 (100) 8 (100) 8 (100) Visit4 Healthy (n = 10) 10 (100) 10 (100) 8 (80) 9 (90) HIV+ (n = 8) 8 (100) 7 (87.5) 7 (87.5) 8 (100) Visit5 Healthy (n = 10) 9 (90) 9 (90) 6 (60) 8 (80) HIV+ (n = 7) 7 (100) 6 (87.5) 7 (100) 7 (100) Analysis of Malassezia CFU abundance level showed that HIV-infected patients were highly colonized, and this was stable over time compared to healthy controls (Fig. 2 A). Considering all sites together, the mean percentage of HIV-infected patients with CFU > 100 was 64.6% compared to 38% in healthy controls on all visits. Over the 5 visits, the mean percentage of HIV-infected patients with CFU > 100 was 35.9%, 7.7%, 4.5%, and 18.8% compared with 16%, 4%, 0%, and 0% in healthy controls on the chest, scalp, forehead, and nasolabial fold, respectively. The high colonization levels remained relatively stable on the chest and nasolabial fold of HIV-infected patients (Fig. 2 A). At the species level, the Malassezia community structure was highly heterogeneous according to the sampling site and time (Fig. 2 ). M. sympodialis , M. globosa , M. restricta , and M. furfur were isolated at each visit, while M. dermatis was only isolated at visits 3, 4 and 5. In HIV-infected patients and healthy controls, the mean abundance of M. sympodialis , M. globosa , M. restricta and M. furfur was 39.8% vs 55.7%, 21.3% vs 32.7%, 18.5% vs 8.6% and 16.5% vs 2.8%, respectively. M. dermatis was isolated with 15.6%, 0.05% and 3.3% abundance in HIV-infected patients at visits 3, 4 and 5, respectively. While in healthy controls, M. dermatis was isolated at visit 4 only with 0.5% abundance (Fig. 2 B). M. sympodialis colonization was stable independently of the sampling sites and the HIV status. In HIV-infected patients, M. furfur colonization remained stable at each sampling site, and was particularly abundant on the chest, whereas M. restricta remained stable and relatively more abundant on the forehead and nasolabial fold (Fig. 2 B). In healthy controls, species diversity was low on the chest, a sampling site where M. sympodialis and M. globosa were dominant over time (Fig. 2 B). ITS and 16S Metagenomic sequencing. A total of 10 healthy controls and 13 HIV-infected patients were sampled for metagenomic analysis at all 4 body sites, for a total of 92 samples. One sample from the nasolabial fold of an HIV-infected patient failed ITS bioinformatics analysis. ITS metabarcoding yielded 2,702,739 reads and 1135 single OTUs including 1,423,691 reads and 735 single OTUs from ITS1 and 1,279,048 reads and 400 single OTUs from ITS2, respectively. Although 1002 fungal OTUs (651 in ITS1 and 351 in ITS2) were classified at the genus level, 133 OTUs (84 in ITS1 and 49 in ITS2) were classified as "Unknown" due to missing precise information in the databases. Most OTUs belonged to the phyla of Ascomycota (56.7% in ITS1 and 52.2% in ITS2) and Basidiomycota (38.2% in ITS1 and 42.7% in ITS2). For 16S, 3,124,342 reads and 1639 OTUs were yielded including 720 bacterial OTUs, 6 Candidate phyla radiation (CPR) OTUs and 913 unassigned OTUs. The fungal and bacterial alpha diversity indices, as measured by observed OTUs and Shannon diversity, are summarized in Table 4 . There were no significant differences between HIV-infected patients and healthy controls for either observed OTUs (Wilcox test; p = 1 in ITS1, p = 0.877 in ITS2 and p = 0.1 in 16S) or Shannon diversity (Wilcox test; p = 0.483 in ITS1, p = 0.131 in ITS2 and p = 0.738 in 16S) (Fig. 3 A and 3 B). However, Venn diagrams of detected OTUs showed that fungal and bacterial microbial diversity was increased in HIV-infected patients compared to healthy controls (Fig. 3 C- 3 E). Community composition analysis showed no clustering between HIV-infected patients or healthy controls in either ITS1 (PERMANOVA; p = 0.9968), ITS2 (PERMANOVA; p = 0.3435) or 16S (PERMANOVA; p = 0.7945) (Fig. 4 A- 4 C). Table 4 Alpha diversity of fungal and bacterial communities. Observed OTUs Shannon diversity ITS1 ITS2 16S ITS1 ITS2 16S Mean: HIV + vs HC 175.3 vs 173.3 97.8 vs 96.7 208.8 vs 178.5 3.9 vs 3.6 2.7 vs 2.4 4.5 vs 4.3 Median: HIV + vs HC 163 vs 188 102 vs 92.5 189 vs 168.5 3.9 vs 3.8 2.9 vs 2.6 4.5 vs 4.5 Minimum: HIV + vs HC 90 vs 82 44 vs 79 161 vs 121 3.0 vs 2.1 1.6 vs 1.2 3.4 vs 3.0 Maximum: HIV + vs HC 263 vs 240 146 vs 119 272 vs 293 5.1 vs 4.4 3.4 vs 3.0 5.5 vs 5.3 The relative abundance of Basidiomycota was very high in ITS2 compared to ITS1 but with almost equal proportions between HIV-infected patients and healthy controls (Fig. 5 A). While for 16, the abundance of unassigned reads (71.32%) was very high followed by bacterial phyla (28.67%) and CPR (0.01%). Bacterial phyla were dominated by Actinobacteria, Firmicutes and Proteobacteria with an abundance of 14.0% vs 17.8%, 8.1% vs 6.7% and 4.4% vs 3.3% in HIV-infected patients and healthy controls, respectively (Fig. 5 B). Fungal genera with abundance > 0.1% were dominated by Malassezia , followed by Neocamarosporium and Candida in ITS1 and Debaryomyces and Penicillium in ITS2 (Fig. 5 C and 5 D). The abundance of Malassezia was slightly increased in HIV-infected patients compared to healthy controls in ITS1 (39.4% vs 32.3%) while in ITS2 (91.1% vs 93.4%) the abundance was relatively equal (Fig. 5 C). Remarkably, the abundance of the genus Pichia was high while that of the genus Rhodotorula was low in HIV-infected patients compared to healthy controls in both ITS1 and ITS2 (Fig. 5 C and 5 D). At the 16S level, the genera Cutibacterium/Propionibacterium , Staphylococcus and Corynebacterium dominated with an abundance of 31.3% vs 40.2%, 21.5% vs 19.2% and 7.1% vs 8.4% in HIV-infected patients and healthy controls, respectively (Fig. 5 E). The abundance of Streptococcus , a common skin genus, was increased in HIV-infected patients (1.8%) compared to healthy controls (0.6%) (Fig. 5 E). By analysing fungal species with an abundance > 0.1%, we found in ITS1 that species such as M. globosa (7.5% vs 2.5%), M. dermatis (0.9% vs 0.01%) and Erythrobasidium yunnanense (0.3% vs 0.0%) had a slightly increased abundance in HIV-infected patients compared to healthy controls, respectively (Fig. 6 A). The abundance of M. restricta in ITS1, the most frequently detected Malassezia species in metagenomics, was 26.3% vs 28.9% in HIV-infected patients and healthy controls, respectively (Fig. 6 A). Other Malassezia species were also detected with low abundance. M. sympodialis and M. furfur were detected with an abundance of 0.3% vs 0.5% and 0.04% vs 0.006% in HIV-infected patients and healthy controls, respectively. M. obtusa (1 read only in a healthy control) and M. slooffiae (19 reads only in an HIV-infected patient) were detected with very low abundance. While in ITS2, M. restricta (36.1% vs 16.5%), M. globosa (15.3% vs 9.7%), M. dermatis (2.0% vs 0.03%) and Pichia kluyveri (0.2% vs 0.0%) had a slightly increased abundance in HIV-infected patients compared to healthy controls, respectively (Fig. 6 B). M. arunalokei was detected in ITS2 with a relatively evenness between HIV-infected patients (4.7%) and healthy controls (3.7%). The linear discriminant analysis (LDA) effect size (LEfSe) of fungal and bacterial species that displayed a significantly heterogeneous distribution between HIV-infected patients and healthy controls is presented in Fig. 6 . In ITS1, Cladosporium halotolerans and Erythrobasidium yunnanense were significantly more abundant in HIV-infected patients while Allophoma cylindrispora was more significantly abundant in healthy controls (Fig. 6 C). In ITS2, Aspergillus sydowii was significantly more abundant in HIV-infected patients while Unclassified_Malassezia , Cladosporium oxysporium/tenuissimum/colocasiae and Buckleyzyma aurantiaca were significantly more abundant in healthy controls (Fig. 6 D). In level of bacterial species, Neisseria cinerea , Shingomonas spp ., Corynebacterium aurimucosum and Streptococcus spp . were significantly more abundant in HIV-infected patients while IHU_PS_89_Bacteria_70108 was more significantly abundant in healthy controls (Fig. 6 E). We sought to investigate the correlations between fungal and bacterial genera by analysing ITS and 16S data from the same samples. In general, the negative correlations found between fungal and bacterial genera tended to be stronger (Fig. 7 ). While some genera such as Acinetobacter were strongly negatively correlated to Malassezia , positive correlations were found between Malassezia and the genera Cutibacterium / Propionibacterium , Lawsonella and Neoactinobaculum (Fig. 7 A). We then sought to determine the stability of the skin mycobiome of HIV-infected patients and healthy controls. We performed a second consecutive time sampling (S2) in 9 HIV-infected patients and 10 healthy controls. We determined the prevalence of fungal species in all volunteers, and the fungal species that had a prevalence ≥ 50% are shown in Tables 5 and 6 . Some Malassezia species such as M. globosa and M. restricta were present with a prevalence of 100% on the two successive samples while other species such as M. sympodialis and M. dermatis had a low prevalence (Tables 5 and 6 ). At S2 in ITS1, the abundance of M. restricta , M. globosa and M. dermatis were 24.5% vs 22.2%, 6.2% vs 2.0% and 0.2% vs 0.3% in HIV-infected patients and healthy controls, respectively. While in ITS2, the abundance of M. restricta , M. globosa and M. dermatis was 23.1% vs 13.7%, 12.3% vs 8.8% and 2.2% vs 0.3% in HIV-infected patients and healthy controls, respectively. The other more prevalent non- Malassezia fungal species were mainly filamentous fungi such as Aspergillus , Penicillium , Fusarium and Cladosporium (Tables 5 and 6 ). Interestingly, the prevalence of Cladosporium halotolerans was higher on both samples in HIV-infected patients compared to healthy controls (Table 5 ). The bacterial genera Cutibacterium/Propionibacterium (37.5% vs 42.1%), Staphylococcus (17.0% vs 17.3%), and Corynebacterium (4.6% vs 9.7%) were most abundant in HIV-infected patients and healthy controls, respectively. The genus Streptococcus (1.6% vs 0.6%) was also abundant at S2 in HIV-infected patients compared to healthy controls, suggesting an association with HIV infection. An analysis of the variability of the fungal and bacterial skin microbiota was performed for the two successive time samples by calculating the Bray-Curtis dissimilarity. A comparison was then performed between HIV-infected patients and within HIV-infected patients as well as between healthy controls and within healthy controls. A significant difference in variability was found in ITS2 between HIV-infected patients and within HIV-infected patients (Wilcox test; p = 0.041) (Fig. 8 A). However, no significant difference was found for the other cases in ITS1 and 16S (Fig. 8 A et 8B). Table 5 Fungal species present in ≥ 50% of all volunteers in sample 1 (S1). Sample 1 (S1) Sample 2 (2) Fungal species from ITS1 % of Healthy with species (n = 10) % of HIV + with species (n = 13) % of All volunteers with species (n = 23) % of Healthy with species (n = 10) % of HIV + with species (n = 9) % of All volunteers with species (n = 19) Cladosporium_sp. 100 100 100 100 100 100 Malassezia_globosa 100 100 100 100 100 100 Malassezia_restricta 100 100 100 100 100 100 Alternaria_sp. 90 100 95.6 100 100 100 Aspergillus_sect_Fumigati 90 92.3 91.3 100 100 100 Candida_albicans 80 100 91.3 100 100 100 Neocamarosporium_betae 80 100 91.3 100 100 100 Aspergillus_sect_Nigri 80 92.3 86.9 100 100 100 Penicillium_sect_Fasciculata 90 84.6 86.9 100 100 100 Plectosphaerella_sp. 70 100 86.9 100 100 100 Fusarium_sp. 80 84.6 82.6 100 100 100 Debaryomyces_sp. 70 84.6 78.2 100 100 100 Fusarium_equiseti 80 69.2 73.9 100 100 100 Saccharomyces_cerevisiae 90 61.5 73.9 100 100 100 Fusarium_delphinoides 70 61.5 65.2 100 100 100 Aureobasidium_leucospermi 70 61.5 65.2 100 100 100 Penicillium_sect_Brevicompacta 60 61.5 60.8 100 100 100 Candida_parapsilosis 50 69.2 60.8 100 100 100 Candida_sp. 70 53.8 60.8 100 100 100 Eremothecium_sinecaudum 50 69.2 60.8 100 100 100 Aspergillus_fumigatus 60 53.8 56.5 100 100 100 Penicillium_sect_Cinnamopurpurea 60 53.8 56.5 100 100 100 Aureobasidium_melanogenum/pullulans 60 53.8 56.5 100 100 100 Cladosporium_sphaerospermum 70 46.1 56.5 100 100 100 Cladosporium_langeronii 50 61.5 56.5 100 100 100 Malassezia_sympodialis 70 46.1 56.5 100 100 100 Aspergillus_sp. 50 53.8 52.1 100 100 100 Fusarium_longifundum 50 53.8 52.1 100 100 100 Penicillium_digitatum 40 61.5 52.1 100 100 100 Cladosporium_spp. 60 46.15 52.1 100 100 100 Filobasidium_magnum 70 38.4 52.1 100 100 100 Fusarium_wereldwijsianum 60 46.1 52.1 100 100 100 Malassezia_dermatis 50 53.8 52.1 100 100 100 Plectosphaerella_niemeijerarum 60 46.1 52.1 100 100 100 Table 6 Fungal species present in ≥ 50% of all volunteers in sample 1 (S1). Sample 1 (S1) Sample 2 (S2) Fungal species from ITS2 % of Healthy with species (n = 10) % of HIV + with species (n = 13) % of All volunteers with species (n = 23) % of Healthy with species (n = 10) % of HIV + with species (n = 9) % of All volunteers with species (n = 19) Debaryomyces_prosopidis/vindobonensis/fabryi 100 100 100 100 100 100 Malassezia_arunalokei 100 100 100 100 100 100 Malassezia_globosa 100 100 100 100 100 100 Malassezia_restricta 100 100 100 100 100 100 Penicillium_Sect_Fasciculata 100 100 100 100 100 100 Saccharomyces_cerevisiae 100 100 100 100 100 100 Penicillium_Sect_Chrysogena 90 100 95.6 90 100 94.7 Cladosporium_sp. 100 84.6 91.3 60 77.7 68.4 Aspergillus_Sect_Fumigati 90 84.6 86.9 100 100 100 Cladosporium_austrohemisphaericum/langeronii 100 76.9 86.9 60 77.7 68.4 Malassezia_sympodialis 90 61.5 73.9 80 77.7 78.9 Penicillium_Sect_Roquefortorum 70 69.2 69.5 60 66.6 63.1 Aureobasidium_lini 70 53.8 60.8 40 66.6 52.6 Cladosporium_halotolerans 30 76.9 56.5 40 66.6 52.6 Malassezia_dermatis 60 53.8 56.5 70 55.5 63.1 Penicillium_Sect_Brevicompacta 60 53.8 56.5 30 33.3 31.5 Alternaria_doliconidium/destruens 50 53.8 52.1 50 33.3 42.1 Discussion The culture data from our study showed a prevalence of 100% positive culture for Malassezia yeast in healthy controls and HIV-infected patients at visit1. However, the level of Malassezia CFU abundance was higher in HIV-infected patients, regardless of immune status, compared to healthy controls (Figs. 1 and 2 ). The high abundance was observed during all visits in our study, showing a high colonization of Malassezia yeasts on the skin of HIV-infected patients. Wikler et al ., quantified Malassezia by culture in 21 HIV-infected and 10 non-HIV-infected patients without SD and found similar prevalence of positive cultures. In addition, a recent study analysing 46 HIV-infected patients and 46 healthy controls found no difference in the frequency of isolation of Malassezia yeasts (Krzyściak et al., 2020 ). Our data and those of other studies show that the rate of positive culture cannot be a criterion for comparing the skin colonization of Malassezia yeasts in HIV-infected patients and healthy controls. However, the Malassezia CFU abundance could be used as a more discriminant criterion for Malassezia skin colonization evaluation. By categorizing the CFU counts, we have shown that HIV-infected patients are highly colonized by > 100 CFU Malassezia yeast. Our results are in agree with those of Peche et al. (1995), who quantified by culture the density of Malassezia yeasts on healthy forehead skin in 38 HIV-infected and 40 non-HIV-infected persons. In addition, a culture study conducted by Bergbrant et al (1996), found similar results on the healthy skin of the chest of 21 healthy controls and 41 HIV-infected patients. In this study, 4 Malassezia species were isolated from all groups at the visit1 including M. sympodialis (41%), M. globosa (24.7%), M. restricta (21.7%) and M. furfur (12.6%). The predominance of M. sympodialis and M. globosa is in agree with the results of Krzyściak et al . (Krzyściak et al., 2020 ). In line with our observation, these authors found that M. sympodialis was the dominant species in particular in healthy controls, whereas M. furfur was dominant in HIV-infected patients. Geographically, our results are comparable to those of other European countries where M. sympodialis and M. globosa are found to be the most frequent species in the population (Prohic et al., 2016 ). Noteworthy, the follow-up study showed a trend in HIV-infected patients to have a higher Malassezia species diversity in culture and, notably, M. dermatis and M. furfur were more frequently isolated compared to healthy controls. A similar trend in Malassezia species diversity was observed by other authors (Krzyściak et al., 2020 ). Whether the HIV infection and/or its treatment, alters the skin surface lipids composition and subsequently influences Malassezia species diversity remains to be elucidated. As a high abundance of yeast can be found on healthy skin, it has been hypothesized that the pathogenicity of Malassezia in SD is probably determined by the type of strain colonizing the skin rather than the high abundance of yeast (Pechère and Saurat, 1997 ). Although most species were isolated on all visits, some species were dominant on some sites. M. sympodialis colonization was stable at all sites and regardless of HIV status. In HIV-infected patients, M. furfur colonization was stable at all sampling sites with a high abundance on the chest, whereas M. restricta was stable on the forehead and nasolabial fold (Fig. 2 B). In healthy controls, M. sympodialis and M. globosa dominated on each visit on the chest (Fig. 2 B). Metagenomic sequencing data from our study showed that there was no significant difference in alpha diversity, and no community composition was observed between HIV-infected patients and healthy controls (Figs. 3 and 4 ). However, the number of fungal and bacterial OTUs detected in HIV-infected patients was high compared to healthy controls, suggesting a high microbial diversity on the skin of HIV-infected patients. ITS metabarcoding showed a slightly increased relative abundance of fungal species, including M. restricta , M. globosa , M. dermatis , E. yunnanense , C. halotolerans and P. kluyveri on the skin of HIV-infected patients compared to healthy controls. E. yunnanense , P. kluyveri and C. halotolerans are opportunistic fungal species and are not associated with the skin microbiota. Their presence is probably due to the hazard although C. halotolerans was abundant in HIV-infected patients on both time samples. However, Malassezia species are known to be commensal to the skin. When analysing the second S2 time point sampling, the abundance of M. restricta , M. globosa and M. dermatis was also found to be slightly increased in HIV-infected patients compared to healthy controls, showing an effect of HIV status on the density of skin colonization of Malassezia species. Although Malassezia is commensal to the skin, this fungal genus is often designated as a biomarker for SD (Lin et al., 2020 ). Our culture and metagenomic findings have shown high colonization of Malassezia on the skin of HIV-infected patients. As SD can be a common dermatological condition in both HIV-infected and HIV-uninfected patients, it is possible that the overgrowth of Malassezia in HIV-infected patients promotes more SD in these patient categories. The increased abundance of Malassezia in other body sites has been reported in HIV-infected patients, including the gut (Hamad et al., 2018 ) and oral cavity (Chang et al., 2021 ). As suggested in the introduction, it is possible that HIV infection is a risk factor for Malassezia overgrowth although the physiological conditions are not well known. To explain the prevalence of SD, several hypotheses were suggested regarding the involvement of Malassezia . One hypothesis is the immune deficiency associated with HIV infection. However, the studies are conflicting on this subject (Panjaitan, Pudjiati and Siswati, 2014 ; Forrestel et al., 2016 ; Krzyściak et al., 2020 ). In our study, we did not observe a trend between CD 4 T cell count and Malassezia CFU count on the skin of HIV-infected patients. This is in agreement with other studies that have reported that there is no significant relationship between the CD 4 T cell count and the number of Malassezia CFU in HIV-infected patients (Panjaitan, Pudjiati and Siswati, 2014 ). While other authors demonstrated that there was a trend between numbers of Malassezia yeasts present on lesional skin, severity of seborrheic dermatitis and CD 4 T cell counts in HIV-positive patients (Schechtman, Hay and Midgley, 1995 ). Another possible hypothesis, which is little studied, is the investigation of the composition of skin surface lipids. Two studies have reported an association between abnormal skin surface lipid composition and HIV infection but also an association between abnormal skin surface lipid composition and SD (Vidal et al., 1990 ; Ostlere et al., 1996 ). At the level of bacteria, the abundance of genera Cutibacterium/Propionibacterium and Corynebacterium were decreased while Streptococcus was increased in HIV-infected patients, showing a cutaneous bacterial dysbiosis. Streptococcus is a genus usually found on the skin and its high abundance on both time samplings in HIV-infected patients deserves further investigation. Because many bacterial OTUs were not accurately classified, it is difficult to identify skin-associated bacterial species in HIV-infected patients. In this study, negative correlations between Malassezia and some bacterial genera including Acinetobacter and Streptococcus were found (Fig. 7 ). However, the biological significance of these fungal-bacterial interactions on healthy skin of HIV-infected and HIV-uninfected patients is not known. Our data may provide an opportunity for research to understand the role of skin microbiota interactions in the occurrence of SD in HIV-infected patients. Studies of fungal and bacterial microbiota on healthy skin of HIV-infected patients are infrequent. Our knowledge is limited on the fungal and bacterial skin microbiota associated with HIV infection. Most studies of the cutaneous microbiota have focused on diseased skin of patients with common dermatological conditions such as SD. In this study, by combining culture, ITS1, ITS2 and 16S metabarcoding, our study provided some insights into the dynamics of cutaneous Malassezia as well as the fungal and bacterial skin microbiome in HIV infected patients. Our study showed the advantage of combining several methodical approaches. We detected by metagenomics Malassezia species not isolated in culture such as M. slooffiae , M. obtusa and M. arunalokei . In addition, by targeting both ITS1 and ITS2, we detected many fungal species that would not have been detected with ITS1 or ITS2 only. Targeting both ITS1 and ITS2 might seem fastidious for the analyses but it is important since there is an amplification bias between ITS1 and ITS2 (Hamad et al., 2017 ; Mbareche et al., 2020 ). This study had interesting strengths as it studied the dynamics of the cutaneous Malassezia yeast community over time, which is rarely investigated. In addition, we studied by metagenomics the fungal and bacterial skin microbiota associated with HIV infection. However, our study had some limitations. First, a metagenomic analysis was not performed to test the immune status between HIV-infected patients. Second, the sample collection period and follow-up were not the same for all participants, and many HIV-infected patients were lost to follow-up, due to the pandemic crisis of coronavirus disease 2019 (COVID-19). Third, the size of the participant cohort was not large, due to recruitment difficulties. Fourth, the absence of HIV-infected patients with seborrheic dermatitis, which would have allowed us to compare the evolution of the abundance of Malassezia yeasts over time. Fifth, many of the fungal and bacterial sequences were not well classified, due to incomplete databases. In conclusion, the HIV-infected patients studied here showed an increased colonization of Malassezia on the skin. A fungal and bacterial skin dysbiosis was observed in the HIV-infected patients, characterized by an increase of C. halotolerans and Streptococcus . Future studies, with a large size of the participant cohort and long follow-up time, are needed to understand if there is any relationship between skin surface lipid composition, Malassezia abundance and the type of strain colonizing the skin of HIV-infected patients. This will help to better understand the occurrence of SD in these patients and thus improve their management. Declarations Author Contributions: A.A.: Conceptualization; Data curation; Investigation; Formal analysis; Methodology; Visualization; Writing the original draft. I.R.: Methodology; Investigation. S.M.: Methodology; Investigation. S.R.: Conceptualization; Methodology; Investigation; Formal analysis; Resources; Supervision; Writing - Review & Editing. Data are available at : DOI: 10.13140/RG.2.2.17697.21607. Funding: This research was funded by the Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, the French Government under the program “Investissements d’avenir” managed by National Agency for Research, reference ANR-10-IAHU-03, the Région Provence Alpes Côte d’Azur and European funding FEDER PRIMI. Conflicts of Interest: The authors declare no conflict of interests. References Abdillah, A. et al. (2020) ‘Comparison of three skin sampling methods and two media for culturing malassezia yeast’, Journal of Fungi , 6(4), pp. 1–7. doi: 10.3390/jof6040350. Abdillah, A. and Ranque, S. (2021) ‘MalaSelect : A Selective Culture Medium for Malassezia Species’, J. Fungi , 7(10), p. 824. doi: 10.3390/jof7100824. Baroni, A. et al. 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(1997) ‘Malassezia yeast density in HIV-positive individuals.’, The British journal of dermatology , 136(1), pp. 138–9. doi: 10.1111/j.1365-2133.1997.tb08770.x. Prohic, A. et al. (2016) ‘Malassezia species in healthy skin and in dermatological conditions’, International Journal of Dermatology , 55(5), pp. 494–504. doi: 10.1111/ijd.13116. Rhimi, W. et al. (2020) ‘Malassezia spp. Yeasts of Emerging Concern in Fungemia’, Frontiers in Cellular and Infection Microbiology , 10(July). doi: 10.3389/fcimb.2020.00370. Saunte, D. M. L., Gaitanis, G. and Hay, R. J. (2020) ‘Malassezia-Associated Skin Diseases, the Use of Diagnostics and Treatment’, Frontiers in Cellular and Infection Microbiology , 10(March), pp. 1–11. doi: 10.3389/fcimb.2020.00112. Schechtman, R. ., Hay, R. J. and Midgley, G. (1995) ‘HIV disease and Malassezia yeasts : a quantitative study of patients presenting with seborrhoeic dermatitis’, Br J Dermatol , pp. 694–698. Segata, N. et al. (2011) ‘Metagenomic biomarker discovery and explanation’, Genome Biology . BioMed Central Ltd, 12(6), p. R60. doi: 10.1186/gb-2011-12-6-r60. Tragiannidis, A. et al. (2010) ‘Minireview : Malassezia infections in immunocompromised patients’, mycoses , pp. 187–195. doi: 10.1111/j.1439-0507.2009.01814.x. Vidal, C. et al. (1990) . ‘Seborrheic dermatitis and HIV infection’, Journal of the American Academy of Dermatology . American Academy of Dermatology, Inc., 23(6), pp. 1106–1110. doi: 10.1016/0190-9622(90)70341-E. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4139174","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":284759149,"identity":"0b557202-cc4a-4636-ae30-9029ee12539b","order_by":0,"name":"Abdourahim Abdillah","email":"","orcid":"","institution":"IHU Méditerranée Infection: IHU Mediterranee Infection","correspondingAuthor":false,"prefix":"","firstName":"Abdourahim","middleName":"","lastName":"Abdillah","suffix":""},{"id":284759150,"identity":"cd7c0acc-720f-45c9-87a1-3cc9811f1229","order_by":1,"name":"Isabelle RAVAUX","email":"","orcid":"","institution":"AP-HM: Assistance Publique Hopitaux de Marseille","correspondingAuthor":false,"prefix":"","firstName":"Isabelle","middleName":"","lastName":"RAVAUX","suffix":""},{"id":284759151,"identity":"1f296e39-a696-4d15-8fa7-8b024f191a18","order_by":2,"name":"Saadia MOKHTARI","email":"","orcid":"","institution":"AP-HM: Assistance Publique Hopitaux de Marseille","correspondingAuthor":false,"prefix":"","firstName":"Saadia","middleName":"","lastName":"MOKHTARI","suffix":""},{"id":284759152,"identity":"3f068546-ebd3-4886-8296-c4e1e4f7a3a7","order_by":3,"name":"Stephane Ranque","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABD0lEQVRIie3RMWrDMBSA4QcFdZHJqmCwrqAgcAild3EoxItNOgZaqCCgsVldcoreQEWgLj6AIZ4ayF4onoKp3CRtFjlrB/1g8QZ/+BkB+Hz/MCoArg7TmySfso3siOwTOQkzJ0Lu3ocvUvEj4W6CfsksXQdSTcVFQpdme/9YR0CycUfS1VqgjwrY3PkvEqW8MDsOtIw3gdznRa2ueQZsIlzG4DjESE8FxR1RuajmTZjBnjk3M4MmxK1+EsNV85DbxWiVIEtYD8EoDKROgJTxza1UCbtEmJmNefCsR5Jk8aQo1ei1VpYwN6FLvdviRtOBJeRr0dJoIyxZ9Cx2uIXT2UV+vt4Dzl8+Iz6fz+f76xv7e1iL8z1PxgAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0003-3293-5276","institution":"Aix Marseille University","correspondingAuthor":true,"prefix":"","firstName":"Stephane","middleName":"","lastName":"Ranque","suffix":""}],"badges":[],"createdAt":"2024-03-20 19:08:15","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4139174/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4139174/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":53965396,"identity":"9c19d187-7a64-4c69-92e0-a5e60864bcb8","added_by":"auto","created_at":"2024-04-02 19:21:23","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":795798,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cem\u003eMalassezia\u003c/em\u003e species abundance at Visit1 in HIV-infected patients and healthy controls. Prevalence of patients according to the level of \u003cem\u003eMalassezia\u003c/em\u003e CFU abundance on the chest (\u003cstrong\u003eA\u003c/strong\u003e), scalp (\u003cstrong\u003eB\u003c/strong\u003e), forehead (\u003cstrong\u003eC\u003c/strong\u003e) and nasolabial fold (\u003cstrong\u003eD\u003c/strong\u003e). Distribution of \u003cem\u003eMalassezia\u003c/em\u003e species isolated from chest (E), scalp (F), forehead (\u003cstrong\u003eG\u003c/strong\u003e) and nasolabial fold (\u003cstrong\u003eH\u003c/strong\u003e).\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-4139174/v1/64d0632d27202d10a0d3856b.png"},{"id":53964878,"identity":"3e39709f-f3c6-447f-abc4-35068c00c4ac","added_by":"auto","created_at":"2024-04-02 19:13:23","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":791986,"visible":true,"origin":"","legend":"\u003cp\u003eSee image above for figure legend\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-4139174/v1/ee708a61fec28147211ec3b7.png"},{"id":53965395,"identity":"ad6a25ba-d252-43da-9d30-52ba92f52110","added_by":"auto","created_at":"2024-04-02 19:21:23","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":706856,"visible":true,"origin":"","legend":"\u003cp\u003eSee image above for figure legend\u003c/p\u003e","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-4139174/v1/6bcdcb6cb7a024ec141912fc.png"},{"id":53964877,"identity":"119c7121-5c8c-49cd-99ec-acf4cb8d6e0f","added_by":"auto","created_at":"2024-04-02 19:13:23","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":172582,"visible":true,"origin":"","legend":"\u003cp\u003eSee image above for figure legend\u003c/p\u003e","description":"","filename":"4.png","url":"https://assets-eu.researchsquare.com/files/rs-4139174/v1/182e19d98f5fa51ad17b139d.png"},{"id":53964882,"identity":"8698bbe7-8098-46ae-8d6e-b71a9b0a04c4","added_by":"auto","created_at":"2024-04-02 19:13:23","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":2409271,"visible":true,"origin":"","legend":"\u003cp\u003eSee image above for figure legend\u003c/p\u003e","description":"","filename":"5.png","url":"https://assets-eu.researchsquare.com/files/rs-4139174/v1/c959818f7b0a9f3231f6573f.png"},{"id":53964884,"identity":"fa35dc9d-5fdd-4a45-94ef-031eba260797","added_by":"auto","created_at":"2024-04-02 19:13:23","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":2177298,"visible":true,"origin":"","legend":"\u003cp\u003eRelative abundance of fungal species with an abundance \u0026gt;0.1% in each group in ITS1 (\u003cstrong\u003eA\u003c/strong\u003e) and ITS2 (\u003cstrong\u003eB\u003c/strong\u003e). Linear discriminant analysis (LDA) effect size (LEfSe) of the skin fungal and bacterial community structure at species levels, between HIV-infected patients (red) and healthy controls (green) in ITS1 (\u003cstrong\u003eC\u003c/strong\u003e), ITS2 (\u003cstrong\u003eD\u003c/strong\u003e) and 16S (\u003cstrong\u003eE\u003c/strong\u003e). \"Other\" here represents all species with \u0026lt;0.1% abundance. The comparison was performed on a random time sample noted sample 1 (S1) from each volunteer.\u003c/p\u003e","description":"","filename":"6.png","url":"https://assets-eu.researchsquare.com/files/rs-4139174/v1/020df2c91422bd575ead0016.png"},{"id":53964883,"identity":"e943e636-b1a0-44e9-bb32-36a4f41d85dc","added_by":"auto","created_at":"2024-04-02 19:13:23","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":4493,"visible":true,"origin":"","legend":"\u003cp\u003eSpearman correlations between fungal and bacterial genera. (\u003cstrong\u003eA\u003c/strong\u003e) and (\u003cstrong\u003eB\u003c/strong\u003e) represent the correlations between genera detected in ITS1 \u003cem\u003evs\u003c/em\u003e 16S and ITS2 \u003cem\u003evs\u003c/em\u003e 16S, respectively. Correlations were calculated on genera with \u0026gt;0.05% abundance and \u0026gt;10% prevalence from sample 1 (S1). Only significantly (\u003cem\u003ep\u003c/em\u003e\u0026lt;0.05) positive (blue) and negative (red) correlations are shown.\u003c/p\u003e","description":"","filename":"7.png","url":"https://assets-eu.researchsquare.com/files/rs-4139174/v1/5635370b2b0d7f6b41dabf4d.png"},{"id":53964881,"identity":"e2b1fc0f-ef7b-434d-ad14-6757ce526431","added_by":"auto","created_at":"2024-04-02 19:13:23","extension":"png","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":4493,"visible":true,"origin":"","legend":"\u003cp\u003eVariability of the fungal and bacterial skin microbiota. Comparisons of Bray-Curtis dissimilarity values between samples donated by different HIV-infected patient (between HIV+, n = 9) or different control healthy (between healthy, n = 10) and between samples donated by the same HIV-infected patient (within HIV+) or same control healthy (within healthy) for ITS (\u003cstrong\u003eA\u003c/strong\u003e) and 16S (\u003cstrong\u003eB\u003c/strong\u003e). Bray-Curtis dissimilarity values range from 0 to 1, with 0 being the least dissimilar and 1 being the most dissimilar. *\u003cem\u003eP\u003c/em\u003e \u0026lt; 0.05; ns: not significant; Wilcoxon test.\u003c/p\u003e","description":"","filename":"8.png","url":"https://assets-eu.researchsquare.com/files/rs-4139174/v1/2dc29a8f58380fe2c556970d.png"},{"id":57041132,"identity":"67cd2153-7d46-4b4b-8dd4-cdc765bc1fd3","added_by":"auto","created_at":"2024-05-23 21:16:55","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":9871022,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4139174/v1/17460526-68d7-4ab8-8add-cd02394cd331.pdf"}],"financialInterests":"","formattedTitle":"Population dynamics of Malassezia species on the skin of HIV-infected patients","fulltext":[{"header":"Introduction","content":"\u003cp\u003e \u003cem\u003eMalassezia\u003c/em\u003e species are lipid-dependent basidiomycetous yeasts that are part of the skin microbiota of humans and some animals. However, under certain conditions such as high temperature and/or humidity or oily skin, these yeast become opportunistic pathogens and cause skin infections such as pityriasis versicolor, seborrheic dermatitis, and folliculitis (Gaitanis et al., \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2012\u003c/span\u003e; Prohic et al., \u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e2016\u003c/span\u003e). More rarely, they cause bloodstream infections (Rhimi et al., \u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). \u003cem\u003eMalassezia\u003c/em\u003e species are also associated with other multifactorial skin diseases such as psoriasis and atopic dermatitis (Baroni et al., \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e2004\u003c/span\u003e; Gaitanis et al., \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2012\u003c/span\u003e; Glatz et al., \u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e2015\u003c/span\u003e; Prohic et al., \u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e2016\u003c/span\u003e). Seborrheic dermatitis (SD) has a particularly high prevalence, ranging from 30\u0026ndash;80%, in immunocompromised HIV-infected patients (Tragiannidis et al., \u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e2010\u003c/span\u003e). Furthermore, it appears that the onset of SD can be an early sign of CD\u003csub\u003e4\u003c/sub\u003e T cell depletion (Tragiannidis et al., \u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e2010\u003c/span\u003e), suggesting a control of CD\u003csub\u003e4\u003c/sub\u003e T cell related immunity to cutaneous \u003cem\u003eMalassezia\u003c/em\u003e. It may contribute to the early diagnosis of HIV-associated immunodeficiency (Forrestel et al., \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2016\u003c/span\u003e). In a study analysing healthy skin of HIV-infected patients and non-HIV individuals, it was found that HIV-infected patients have a higher \u003cem\u003eMalassezia\u003c/em\u003e density than non-HIV individuals (Pech\u0026egrave;re et al., \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e1995\u003c/span\u003e). Recently, it has been reported that HIV-infected patients with SD have a higher \u003cem\u003eMalassezia\u003c/em\u003e load than HIV-infected patients without seborrheic dermatitis (Moreno-Couti\u0026ntilde;o et al., \u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). In addition, it is reported that HIV infection is associated with abnormalities in skin surface lipids, particularly by a significant increase in triglycerides and squalenes, and a significant decrease in free fatty acids (Vidal et al., \u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e1990\u003c/span\u003e). These findings suggest that HIV infection facilitates \u003cem\u003eMalassezia\u003c/em\u003e overgrowth. A culture-based study conducted on the healthy skin of 38 HIV-infected and 40 HIV-uninfected persons had reported a high density of \u003cem\u003eMalassezia\u003c/em\u003e in the HIV patients (Pech\u0026egrave;re et al., \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e1995\u003c/span\u003e). However, a recent study reported a non-statistically significant difference of 69% and 79% of \u003cem\u003eMalassezia\u003c/em\u003e yeast isolation from the healthy skin of 46 HIV-infected patients and 46 healthy controls, respectively, with (Krzyściak et al., \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). In addition, the authors found that HIV-infected patients with high CD\u003csub\u003e4\u003c/sub\u003e T cells had a higher \u003cem\u003eMalassezia\u003c/em\u003e colonization. However, the authors of this study did not provide data on the abundance of \u003cem\u003eMalassezia\u003c/em\u003e yeasts isolated from the two groups. Also, the fungal and bacterial skin microbiome was not explored, which may provide a better understanding of the skin microbiome associated with HIV infection (Krzyściak et al., \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2020\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eOn the other hand, the distribution of species varies in epidemiological studies for several reasons such as geographical location, culture media used, sampling and identification methods (Prohic et al., \u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e2016\u003c/span\u003e; Saunte, Gaitanis and Hay, \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). It is considered, for example, that \u003cem\u003eM. sympodialis\u003c/em\u003e is the dominant species in Europe where the culture method is more widely used, whereas \u003cem\u003eM. restricta\u003c/em\u003e and \u003cem\u003eM. globosa\u003c/em\u003e are more dominant in Asia where molecular methods are more widely used (Saunte, Gaitanis and Hay, \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). Furthermore, it is important to note that most of the studies investigating the cutaneous distribution of \u003cem\u003eMalassezia\u003c/em\u003e species have been performed by sampling a single period in time. The question of the dynamics and stability of \u003cem\u003eMalassezia\u003c/em\u003e yeasts is rarely addressed on the skin. If \u003cem\u003eMalassezia\u003c/em\u003e abundance varies over time or if certain \u003cem\u003eMalassezia\u003c/em\u003e species dominate the skin at all times is a question to be answered. The objectives of this study were: 1) to quantify \u003cem\u003eMalassezia\u003c/em\u003e yeasts in healthy skin of HIV-infected patients compared to healthy controls, 2) to evaluate the stability of \u003cem\u003eMalassezia\u003c/em\u003e species on the skin, and 3) to investigate the fungal and bacterial skin microbiome associated with HIV infection.\u003c/p\u003e"},{"header":"Patients and Methods","content":"\u003cp\u003e\u003cb\u003eInclusion.\u003c/b\u003e Participants of this study were recruited at the Infectious Diseases outpatient ward at the \u0026ldquo;Institut Hospitalo-Universitaire M\u0026eacute;diterran\u0026eacute;e Infection\u0026rdquo; (IHU-MI), La Timone University Hospital of Marseille, France. A total of 33 volunteers were included, comprising 23 HIV-infected patients (HIV+) and 10 healthy (non-HIV infected) controls. Inclusion criteria were: age at least 18 years; no history of systemic or local antifungal treatment within the last 30 days. All participants gave informed consent and completed a form with age, sex, and whether they had taken local or systemic antifungal treatment in the previous 30 days.\u003c/p\u003e \u003cp\u003e\u003cb\u003eEthical clearance\u003c/b\u003e. This study protocol was conducted in accordance with the Helsinki Declaration and was approved by the ethics committee \u0026ldquo;Comit\u0026eacute; de Protection des Personnes Ile de France II\u0026rdquo; (N19.05.29.69947 RIPH3, dated 21 October 2019).\u003c/p\u003e \u003cp\u003e \u003cb\u003eSamples collection.\u003c/b\u003e A longitudinal cohort study was conducted from November 2019 to June 2021. At each visit of the 5 visits, samples were collected from 4 body sites, including the chest, scalp, face, and left nasolabial fold, by rubbing for 5\u0026ndash;10 s, as previously (Abdillah et al., \u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e2020\u003c/span\u003e), a sterile gauze (non-woven sterile swabs 10 cm x 10 cm, SYLAMED, Paris, France) for \u003cem\u003eMalassezia\u003c/em\u003e species isolation. Dry swab samples were also collected from each body site at 1 or 2 visits and stored in liquid transport medium at -20\u0026deg;C for DNA extraction and further ITS and 16S metabarcoding.\u003c/p\u003e \u003cp\u003e \u003cb\u003eCulture medium.\u003c/b\u003e The MalaSelect medium (4.3% Sch\u0026aelig;dler agar, 2% peptone, 1% glucose, 1% malt extract, 0.5% ox-bile, 0.5% Tween 60, 0.2% oleic acid and 0.25% glycerol [pH6], each from Sigma-Aldrich, Saint-Quentin Fallavier, France) containing 0.5 g/L cycloheximide (CliniSciences, Nanterre, France) and 4 mg/L rapamycin (CliniSciences, Nanterre, France) was prepared as previously (Abdillah and Ranque, \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2021\u003c/span\u003e), supplemented with 0.5 g/L chloramphenicol (Sigma-Aldrich). After cooling to approximately 56\u0026deg;C, 0.03 g/L colistin (Sigma-Aldrich) and 4 mg/L rapamycin were supplemented before dispensing the medium into Petri dishes.\u003c/p\u003e \u003cp\u003e \u003cb\u003eMalassezia\u003c/b\u003e \u003cb\u003eisolation and identification.\u003c/b\u003e Sterile gauze specimens were directly inoculated onto the MalaSelect medium plates within one hour after collection at the IHU-MI mycology laboratory. Unused sterile gauze were also plated on MalaSelect medium as negative control. All plates were sealed into plastic bags, incubated aerobically at 30\u0026deg;C for 3 to 10 days, and examined daily for the growth of \u003cem\u003eMalassezia\u003c/em\u003e species. \u003cem\u003eMalassezia\u003c/em\u003e colony forming units (CFU) were counted and identified via MALDI-TOF Mass Spectrometry (MALDI Biotyper, Bruker Daltonics GmbH, Bremen, Germany) with a reference spectra library supplemented with in house (including \u003cem\u003eMalassezia\u003c/em\u003e spp.) reference spectra, as previously described (Cassagne et al., \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e2016\u003c/span\u003e; Diongue et al., \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). The identification procedure was systematically carried out on 1 to 5 CFU per plate. \u003cem\u003eMalassezia\u003c/em\u003e CFU abundance was categorized as follows: negative (0 CFU), low (\u0026le;\u0026thinsp;20 CFU), intermediate (20\u0026thinsp;\u0026lt;\u0026thinsp;CFU\u0026thinsp;\u0026le;\u0026thinsp;100) and high (\u0026gt;\u0026thinsp;100 CFU).\u003c/p\u003e \u003cp\u003e \u003cb\u003eITS and 16S Metabarcoding.\u003c/b\u003e The total DNA from the swab samples was extracted with the EZ1 DNA tissue kit (Qiagen GmbH, Hilden, Germany) following an automated extraction protocol of EZ1 Advanced XL (QIAGEN Instruments Hombrechtikon, Switzerland) with the DNA card bacteria V 1.066069118 QIAGEN. Briefly, 200 \u0026micro;L of samples and 200 \u0026micro;L of G2 lysis buffer were mixed in a 2 mL Eppendorf tube. Glass powders (Sigma-Aldrich, ref. G4649-500g) were added and mechanical lysis was performed with the FastPrep-24\u003csup\u003eTM\u003c/sup\u003e5G V. 6005.1 (M.P Biomedicals, LLC Santa Ana CA, USA) at 6 m/s for 40 s, and then incubated at 100\u0026deg;C for 10 min. After centrifugation at 10,000 g for 1 min, 200 \u0026micro;L of the supernatant was recovered, and 10 \u0026micro;L of proteinase K was added, followed by 2h incubation at 56\u0026deg;C. DNA was then extracted according to the manufacturer's instructions, and eluted in 200 \u0026micro;L. For the fungi, the ITS1 and ITS2 region were amplified in triplicate with hybridization temperatures of either 52\u0026deg;C or 55\u0026deg;C, using a previously described procedure (Hamad et al., \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2017\u003c/span\u003e). The 25 \u0026micro;l amplification reaction mix consisted of 12.5 \u0026micro;l AmpliTaq Gold master mix, 0.75 \u0026micro;l of each primer (Eurogentec, Seraing, Belgium), 6 \u0026micro;l distilled water, and 5 \u0026micro;l DNA template. PCR cycling conditions were: 95\u0026deg;C for 10 min, 40 cycles of 95\u0026deg;C for 30 s, (55\u0026deg;C or 52\u0026deg;C) for 30 s, and 72\u0026deg;C for 1 min, followed by a 5 min final extension step at 72\u0026deg;C. For each sample, the amplicons of each ITS1 and ITS2 PCR replicates at the two temperatures were then pooled. For bacteria, the 16S \u0026ldquo;V3-V4\u0026rdquo; regions were amplified using the primers with overhang adapters described herein (Kodio et al., \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). The amplification reaction mix consisted of 12.5 \u0026micro;l de Kapa HiFi HotStart ReadyMix 2x (Kapa Biosystems Inc, Wilmington, MA U.S.A), 0.5 \u0026micro;l of each primer (Eurogentec, Seraing, Belgium), 1.5 \u0026micro;l distilled water and 10 \u0026micro;l DNA template for 25 \u0026micro;l volume. PCR cycling conditions were as follows: 95\u0026deg;C for 3 min, 45 cycles of 95\u0026deg;C for 30 s, 55\u0026deg;C for 30 s, and 72\u0026deg;C for 30 s, followed by a 5 min final extension step at 72\u0026deg;C.\u003c/p\u003e \u003cp\u003ePCR products were then purified on AMPure beads (Beckman Coulter Inc, Fullerton, CA, USA), quantified using High sensitivity Qubit technology (Beckman Coulter Inc, Fullerton, CA,USA), pooled and barcoded before sequencing for ITS and 16S rRNA on a MiSeq system (Illumina, Inc, San Diego CA 92121, USA) with paired end strategy as previously described (Kodio et al., \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e2019\u003c/span\u003e, \u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e2021\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003cb\u003eBioinformatics and statistical analysis.\u003c/b\u003e The bioinformatics analyses of the ITS reads were performed using the PIPITS automated pipeline that was developed for the analysis of ITS sequences from Illumina sequencing (Gweon et al., \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). The obtained OTU table was completed by manually analysing the sequences obtained of the operational taxonomic units (OTU) from the ITS1 and ITS2 regions via the standard Basic Local Alignment nucleotide Search Tool (BLASTN) search as previously described (Kodio et al., \u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). The criteria for taxonomic assignment of fungal OTUs were established as follows: PID (percentage of identity)\u0026thinsp;\u0026gt;\u0026thinsp;97% assignment to species level; PID between 95 and 97%: assignment to genus; PID between 90 and 95%: assignment to the family; PID below 90%: assignment to the kingdom. Sequences that were well assigned taxonomically to the family or genus level and not to the species level, for example, were named unclassified to the species level. For 16S sequences, the reads were analysed by the MetaGX and VSEARCH tools as previously described (Kodio et al., \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). The SILVA database as well as the Culturomics and Diagnostics in-house databases were used for the taxonomic assignments of bacterial OTUs. The criteria for taxonomic assignment of bacterial OTUs were established as follows: 1) presence of one or more BLAST hits associated with a reference sequence (100% coverage; identity\u0026thinsp;\u0026gt;\u0026thinsp;97% corresponds to the assignment of OTUs to the species associated with the best BLAST hit); 2) presence of less relevant BLAST hits (identity between 95 and 97%: assignment to genus level; between 90 and 95%: assignment to the family; below 90%: assignment to the kingdom) with, in each case, the creation of a putative species; 3) no BLAST hits (creation of putative new bacterial species).\u003c/p\u003e \u003cp\u003eWe used R software (Version 4.2.1) to computer the alpha and beta diversity. Alpha diversity was estimated by the observed OTU richness and Shannon diversity. The Wilcoxon test was used to test whether there was a difference between HIV-infected patients and healthy controls. Beta diversity was computed using the Bray-Curtis dissimilarity calculated using the vegdist function from R package \u003cem\u003evegan\u003c/em\u003e. Community composition was visualized using non-metric-multidimensional scaling (NMDS). To test whether HIV status explained community composition, Permutational Multivariate Analysis of Variance (PERMANOVA) test was performed using the anosim function from R package \u003cem\u003evegan\u003c/em\u003e. Boxplots were made using the \u003cem\u003eggplot2\u003c/em\u003e R package. The relative abundance of bacterial and fungal taxa was assessed between the two groups, by combining together OTUs designating the same phylum, genus or species. Because the ITS does not allow precise identification for some fungi, sectional grouping was performed for \u003cem\u003eAspergillus\u003c/em\u003e and \u003cem\u003ePenicillium\u003c/em\u003e. The linear discriminant analysis (LDA) effect size (LEfSe) was performed to identify the bacterial and fungal taxa differentially represented between groups at the species level (Segata et al., \u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e2011\u003c/span\u003e). Correlation analyses between fungal and bacterial genera were performed using the \u003cem\u003ecorrplot\u003c/em\u003e R package. All statistical tests with a \u003cem\u003ep\u003c/em\u003e-value under 0.05 was considered statistically significant.\u003c/p\u003e"},{"header":"Results","content":"\u003cp\u003e \u003cb\u003eStudy participants\u0026rsquo; baseline characteristics.\u003c/b\u003e Of the 33 volunteers included in this study, 10 were healthy controls and 23 were HIV-infected. Of the 23 HIV-infected patients, 10 patients were immunocompromised, as defined by a CD\u003csub\u003e4\u003c/sub\u003e T-cell count below 200, with 105.9 (\u0026plusmn;\u0026thinsp;48.8 SD) mean CD\u003csub\u003e4\u003c/sub\u003e T-cell count, and 13 non-immunocompromised patients (as defined by a CD\u003csub\u003e4\u003c/sub\u003e T-cell count above 500), with 701.7 (\u0026plusmn;\u0026thinsp;228.6 SD) mean CD\u003csub\u003e4\u003c/sub\u003e T-cell count. The 10 immunocompromised patients had a mean age of 47.5 (\u0026plusmn;\u0026thinsp;8.6 SD); 8 were males (2 females); and their HIV load was undetectable in 50%. The 13 non-immunocompromised HIV infected patients had a mean age of 54 (\u0026plusmn;\u0026thinsp;9.5 SD); 9 were males (4 females); and their HIV load was undetectable in 46%. All HIV-infected patients were on highly active antiretroviral therapy and none of them had skin lesions on the sampling sites. In the healthy controls, the mean age was 34.6\u0026thinsp;\u0026plusmn;\u0026thinsp;14.3 years with 8 males and 2 females. None of them complained of disease-related symptoms.\u003c/p\u003e \u003cp\u003e \u003cb\u003eFollow-up study\u003c/b\u003e. All 10 healthy controls participated in all visits. Because many HIV-infected patients, had an incomplete follow-up (most were lost to follow-up and 2 of the immunocompromised patients died) due to the SARS-CoV-2 pandemic-related crisis, all HIV-infected patients were grouped, irrespective of their CD4 levels, in the follow-up analyses.\u003c/p\u003e \u003cp\u003e \u003cb\u003eMalassezia\u003c/b\u003e \u003cb\u003ecultivation and abundance.\u003c/b\u003e All subjects in this study had at least one culture positive for \u003cem\u003eMalassezia\u003c/em\u003e species within visit1. The prevalence of positive cultures varied according to body site and HIV status (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). The prevalence of positive cultures on chest samples was high in both immunocompromised patients (100%) and healthy volunteers (80%) while it was high on the nasolabial fold in non-immunocompromised patients (92.3%). Depending on the HIV immune status, the rate of positive culture appeared to have no apparent difference. Considering all HIV-infected patients, the chest and the nasolabial fold were the two most colonized sites with a positive culture prevalence of 91.3% compared to healthy controls (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003ePrevalence of \u003cem\u003eMalassezia\u003c/em\u003e-positive cultures at visit1 according to body site.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"5\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\" morerows=\"2\" rowspan=\"3\"\u003e \u003cp\u003ePositive cultures\u003c/p\u003e \u003cp\u003ebody sites\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eControls\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAll HIV+\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003eHIV+\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u0026gt;\u0026thinsp;500 CD\u003csub\u003e4\u003c/sub\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u0026lt;\u0026thinsp;200 CD\u003csub\u003e4\u003c/sub\u003e\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003e(n\u0026thinsp;=\u0026thinsp;10)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003e(n\u0026thinsp;=\u0026thinsp;23)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003e(n\u0026thinsp;=\u0026thinsp;13)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003e(n\u0026thinsp;=\u0026thinsp;10)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eChest \u0026ndash; no. (%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e8 (80%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003e21 (91.3%)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e11 (84.6%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e10 (100%)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eScalp \u0026ndash; no. (%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e6 (60%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e18 (78.2%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e11 (84.6%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e7 (70%)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eForhead \u0026ndash; no. (%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e4 (40%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e19 (82.6%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e11 (84.6%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e8 (80%)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNasolabial fold \u0026ndash; no. (%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e6 (60%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003e21 (91.3%)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e12 (92.3%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e9 (90%)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eWhen analysing the level of \u003cem\u003eMalassezia\u003c/em\u003e abundance, colonization was slightly higher in non-immunocompromised patients with CFU\u0026thinsp;\u0026gt;\u0026thinsp;100 on the chest (15.4% \u003cem\u003evs\u003c/em\u003e 10%), scalp (7.7% \u003cem\u003evs\u003c/em\u003e 0%) and nasolabial fold (15.4% \u003cem\u003evs\u003c/em\u003e 10%) when compared to immunocompromised patients (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eA, \u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB and \u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eD). However, immunocompromised patients were more abundantly colonized on the forehead compared to non-immunocompromised patients (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eC). On the scalp, 70% of immunocompromised patients had low colonization with \u0026le;\u0026thinsp;20 CFU compared to 46.1% in non-immunocompromised patients (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB). Analysis of 4 sampled body sites showed that 52.2% of all HIV-infected patients had CFU\u0026thinsp;\u0026gt;\u0026thinsp;100 while 70% of healthy controls had CFU\u0026thinsp;\u0026le;\u0026thinsp;20, suggesting a high colonization of \u003cem\u003eMalassezia\u003c/em\u003e species in HIV-infected patients.\u003c/p\u003e \u003cp\u003eWithin visit1, 4 \u003cem\u003eMalassezia\u003c/em\u003e species were isolated including \u003cem\u003eM. sympodialis\u003c/em\u003e (41%), \u003cem\u003eM. globosa\u003c/em\u003e (24.7%), \u003cem\u003eM. restricta\u003c/em\u003e (21.7%) and \u003cem\u003eM. furfur\u003c/em\u003e (12.6%). The frequency of isolation of \u003cem\u003eM. sympodialis\u003c/em\u003e, \u003cem\u003eM. globosa\u003c/em\u003e and \u003cem\u003eM. restricta\u003c/em\u003e was 39.1% \u003cem\u003evs\u003c/em\u003e 30%, 86.9% \u003cem\u003evs\u003c/em\u003e 90% and 78.2% \u003cem\u003evs\u003c/em\u003e 40% in HIV-infected patients and healthy controls, respectively. \u003cem\u003eM. furfur\u003c/em\u003e was isolated only in HIV-infected patients (13%) with high colonization on the chest (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eE). The distribution of isolated species varied according to site and group (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eE-\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eH). \u003cem\u003eM. sympodialis\u003c/em\u003e was most abundant on the forehead (84.6%), nasolabial fold (58%) and chest (55.7%) while \u003cem\u003eM. globosa\u003c/em\u003e was most abundant on the scalp (69.2%) in healthy controls (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eE-\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eH). In contrast, \u003cem\u003eM. sympodialis\u003c/em\u003e was most abundant on the scalp (67.5%) and nasolabial fold (51.5%) while \u003cem\u003eM. globosa\u003c/em\u003e and \u003cem\u003eM. restricta\u003c/em\u003e were most abundant on the chest (42.7%) and forehead (63.2%) in HIV-infected patients. The analysis of all sampled body sites showed 39.9% \u003cem\u003evs\u003c/em\u003e 53.4%, 23.3% \u003cem\u003evs\u003c/em\u003e 42.7%, 23.1% \u003cem\u003evs\u003c/em\u003e 3.8% and 13.6% \u003cem\u003evs\u003c/em\u003e 0.0% abundance for \u003cem\u003eM. sympodialis\u003c/em\u003e, \u003cem\u003eM. globosa\u003c/em\u003e, \u003cem\u003eM. restricta\u003c/em\u003e, and \u003cem\u003eM. furfur\u003c/em\u003e in HIV-infected patients and healthy controls, respectively.\u003c/p\u003e \u003cp\u003eDepending on the HIV immune status, the frequency of isolation of \u003cem\u003eM. sympodialis\u003c/em\u003e, \u003cem\u003eM. globosa\u003c/em\u003e, \u003cem\u003eM. restricta\u003c/em\u003e, and \u003cem\u003eM. furfur\u003c/em\u003e was 50% \u003cem\u003evs\u003c/em\u003e 30.8%, 90% \u003cem\u003evs\u003c/em\u003e 84.6%, 70% \u003cem\u003evs\u003c/em\u003e 84.6% and 20% \u003cem\u003evs\u003c/em\u003e 7.7% in immunocompromised patients and non-immunocompromised patients, respectively. \u003cem\u003eM. restricta\u003c/em\u003e appeared to be more abundant in immunocompromised patients on the scalp, face and nasolabial fold compared to non-immunocompromised patients (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eF, \u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eG and \u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eH).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003cb\u003eStability of\u003c/b\u003e \u003cb\u003eMalassezia\u003c/b\u003e \u003cb\u003eskin colonization over time.\u003c/b\u003e We sought to determine the stability of \u003cem\u003eMalassezia\u003c/em\u003e species in body sites sampled depending on HIV status. All subjects sampled within 5 visits had at least one positive culture for \u003cem\u003eMalassezia\u003c/em\u003e species. During the 5 visits, the prevalence of positive cultures varied according to body site and HIV status (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). The chest was the site with the highest prevalence of positive cultures on all visits, particularly in HIV-infected patients (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003ePrevalence of \u003cem\u003eMalassezia\u003c/em\u003e-positive cultures in 5 visits according to body site.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"6\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c2\" namest=\"c1\"\u003e \u003cp\u003ePositive cultures/body sites\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eChest \u0026ndash; no. (%)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eScalp \u0026ndash; no. (%)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eForehead \u0026ndash; no. (%)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eNasolabial fold \u0026ndash; no. (%)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eVisit1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHealthy (n\u0026thinsp;=\u0026thinsp;10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e8 (80)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e6 (60)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e4 (40)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e6 (60)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHIV+ (n\u0026thinsp;=\u0026thinsp;23)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e21 (91.3)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e18 (78.2)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e19 (82.6)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e21 (91.3)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eVisit2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHealthy (n\u0026thinsp;=\u0026thinsp;10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e10 (100)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e8 (80)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e7 (70)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e7 (70)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHIV+ (n\u0026thinsp;=\u0026thinsp;11)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e11 (100)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e10 (90.9)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e11 (100)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e10 (90.9)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eVisit3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHealthy (n\u0026thinsp;=\u0026thinsp;10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e10 (100)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e9 (90)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e8 (80)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e6 (60)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHIV+ (n\u0026thinsp;=\u0026thinsp;8)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e8 (100)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e8 (100)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e8 (100)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e8 (100)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eVisit4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHealthy (n\u0026thinsp;=\u0026thinsp;10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e10 (100)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e10 (100)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e8 (80)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e9 (90)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHIV+ (n\u0026thinsp;=\u0026thinsp;8)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e8 (100)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7 (87.5)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e7 (87.5)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e8 (100)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eVisit5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHealthy (n\u0026thinsp;=\u0026thinsp;10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e9 (90)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e9 (90)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e6 (60)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e8 (80)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHIV+ (n\u0026thinsp;=\u0026thinsp;7)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e7 (100)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e6 (87.5)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e7 (100)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e7 (100)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eAnalysis of \u003cem\u003eMalassezia\u003c/em\u003e CFU abundance level showed that HIV-infected patients were highly colonized, and this was stable over time compared to healthy controls (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eA). Considering all sites together, the mean percentage of HIV-infected patients with CFU\u0026thinsp;\u0026gt;\u0026thinsp;100 was 64.6% compared to 38% in healthy controls on all visits. Over the 5 visits, the mean percentage of HIV-infected patients with CFU\u0026thinsp;\u0026gt;\u0026thinsp;100 was 35.9%, 7.7%, 4.5%, and 18.8% compared with 16%, 4%, 0%, and 0% in healthy controls on the chest, scalp, forehead, and nasolabial fold, respectively. The high colonization levels remained relatively stable on the chest and nasolabial fold of HIV-infected patients (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eA).\u003c/p\u003e \u003cp\u003eAt the species level, the \u003cem\u003eMalassezia\u003c/em\u003e community structure was highly heterogeneous according to the sampling site and time (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). \u003cem\u003eM. sympodialis\u003c/em\u003e, \u003cem\u003eM. globosa\u003c/em\u003e, \u003cem\u003eM. restricta\u003c/em\u003e, and \u003cem\u003eM. furfur\u003c/em\u003e were isolated at each visit, while \u003cem\u003eM. dermatis\u003c/em\u003e was only isolated at visits 3, 4 and 5. In HIV-infected patients and healthy controls, the mean abundance of \u003cem\u003eM. sympodialis\u003c/em\u003e, \u003cem\u003eM. globosa\u003c/em\u003e, \u003cem\u003eM. restricta\u003c/em\u003e and \u003cem\u003eM. furfur\u003c/em\u003e was 39.8% \u003cem\u003evs\u003c/em\u003e 55.7%, 21.3% \u003cem\u003evs\u003c/em\u003e 32.7%, 18.5% \u003cem\u003evs\u003c/em\u003e 8.6% and 16.5% \u003cem\u003evs\u003c/em\u003e 2.8%, respectively. \u003cem\u003eM. dermatis\u003c/em\u003e was isolated with 15.6%, 0.05% and 3.3% abundance in HIV-infected patients at visits 3, 4 and 5, respectively. While in healthy controls, \u003cem\u003eM. dermatis\u003c/em\u003e was isolated at visit 4 only with 0.5% abundance (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eB). \u003cem\u003eM. sympodialis\u003c/em\u003e colonization was stable independently of the sampling sites and the HIV status. In HIV-infected patients, \u003cem\u003eM. furfur\u003c/em\u003e colonization remained stable at each sampling site, and was particularly abundant on the chest, whereas \u003cem\u003eM. restricta\u003c/em\u003e remained stable and relatively more abundant on the forehead and nasolabial fold (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eB). In healthy controls, species diversity was low on the chest, a sampling site where \u003cem\u003eM. sympodialis\u003c/em\u003e and \u003cem\u003eM. globosa\u003c/em\u003e were dominant over time (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eB).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003cb\u003eITS and 16S Metagenomic sequencing.\u003c/b\u003e A total of 10 healthy controls and 13 HIV-infected patients were sampled for metagenomic analysis at all 4 body sites, for a total of 92 samples. One sample from the nasolabial fold of an HIV-infected patient failed ITS bioinformatics analysis. ITS metabarcoding yielded 2,702,739 reads and 1135 single OTUs including 1,423,691 reads and 735 single OTUs from ITS1 and 1,279,048 reads and 400 single OTUs from ITS2, respectively. Although 1002 fungal OTUs (651 in ITS1 and 351 in ITS2) were classified at the genus level, 133 OTUs (84 in ITS1 and 49 in ITS2) were classified as \"Unknown\" due to missing precise information in the databases. Most OTUs belonged to the phyla of Ascomycota (56.7% in ITS1 and 52.2% in ITS2) and Basidiomycota (38.2% in ITS1 and 42.7% in ITS2). For 16S, 3,124,342 reads and 1639 OTUs were yielded including 720 bacterial OTUs, 6 Candidate phyla radiation (CPR) OTUs and 913 unassigned OTUs.\u003c/p\u003e \u003cp\u003eThe fungal and bacterial alpha diversity indices, as measured by observed OTUs and Shannon diversity, are summarized in Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e4\u003c/span\u003e. There were no significant differences between HIV-infected patients and healthy controls for either observed OTUs (Wilcox test; \u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;1 in ITS1, \u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.877 in ITS2 and \u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.1 in 16S) or Shannon diversity (Wilcox test; \u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.483 in ITS1, \u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.131 in ITS2 and \u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.738 in 16S) (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eA and \u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eB). However, Venn diagrams of detected OTUs showed that fungal and bacterial microbial diversity was increased in HIV-infected patients compared to healthy controls (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eC-\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eE). Community composition analysis showed no clustering between HIV-infected patients or healthy controls in either ITS1 (PERMANOVA; \u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.9968), ITS2 (PERMANOVA; \u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.3435) or 16S (PERMANOVA; \u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.7945) (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003eA-\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003eC).\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab3\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 4\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eAlpha diversity of fungal and bacterial communities.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"7\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e\u0026nbsp;\u003c/th\u003e \u003cth align=\"left\" colspan=\"3\" nameend=\"c4\" namest=\"c2\"\u003e \u003cp\u003eObserved OTUs\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"3\" nameend=\"c7\" namest=\"c5\"\u003e \u003cp\u003eShannon diversity\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eITS1\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eITS2\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003e16S\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eITS1\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eITS2\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003e16S\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMean: HIV\u0026thinsp;+\u0026thinsp;\u003cem\u003evs\u003c/em\u003e HC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e175.3 \u003cem\u003evs\u003c/em\u003e 173.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e97.8 \u003cem\u003evs\u003c/em\u003e 96.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e208.8 \u003cem\u003evs\u003c/em\u003e 178.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e3.9 \u003cem\u003evs\u003c/em\u003e 3.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2.7 \u003cem\u003evs\u003c/em\u003e 2.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e4.5 \u003cem\u003evs\u003c/em\u003e 4.3\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMedian: HIV\u0026thinsp;+\u0026thinsp;\u003cem\u003evs\u003c/em\u003e HC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e163 \u003cem\u003evs\u003c/em\u003e 188\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e102 \u003cem\u003evs\u003c/em\u003e 92.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e189 \u003cem\u003evs\u003c/em\u003e 168.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e3.9 \u003cem\u003evs\u003c/em\u003e 3.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2.9 \u003cem\u003evs\u003c/em\u003e 2.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e4.5 \u003cem\u003evs\u003c/em\u003e 4.5\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMinimum: HIV\u0026thinsp;+\u0026thinsp;\u003cem\u003evs\u003c/em\u003e HC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e90 \u003cem\u003evs\u003c/em\u003e 82\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e44 \u003cem\u003evs\u003c/em\u003e 79\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e161 \u003cem\u003evs\u003c/em\u003e 121\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e3.0 \u003cem\u003evs\u003c/em\u003e 2.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1.6 \u003cem\u003evs\u003c/em\u003e 1.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e3.4 \u003cem\u003evs\u003c/em\u003e 3.0\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMaximum: HIV\u0026thinsp;+\u0026thinsp;\u003cem\u003evs\u003c/em\u003e HC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e263 \u003cem\u003evs\u003c/em\u003e 240\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e146 \u003cem\u003evs\u003c/em\u003e 119\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e272 \u003cem\u003evs\u003c/em\u003e 293\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e5.1 \u003cem\u003evs\u003c/em\u003e 4.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e3.4 \u003cem\u003evs\u003c/em\u003e 3.0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e5.5 \u003cem\u003evs\u003c/em\u003e 5.3\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eThe relative abundance of Basidiomycota was very high in ITS2 compared to ITS1 but with almost equal proportions between HIV-infected patients and healthy controls (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eA). While for 16, the abundance of unassigned reads (71.32%) was very high followed by bacterial phyla (28.67%) and CPR (0.01%). Bacterial phyla were dominated by Actinobacteria, Firmicutes and Proteobacteria with an abundance of 14.0% \u003cem\u003evs\u003c/em\u003e 17.8%, 8.1% \u003cem\u003evs\u003c/em\u003e 6.7% and 4.4% \u003cem\u003evs\u003c/em\u003e 3.3% in HIV-infected patients and healthy controls, respectively (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eB). Fungal genera with abundance\u0026thinsp;\u0026gt;\u0026thinsp;0.1% were dominated by \u003cem\u003eMalassezia\u003c/em\u003e, followed by \u003cem\u003eNeocamarosporium\u003c/em\u003e and \u003cem\u003eCandida\u003c/em\u003e in ITS1 and \u003cem\u003eDebaryomyces\u003c/em\u003e and \u003cem\u003ePenicillium\u003c/em\u003e in ITS2 (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eC and \u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eD). The abundance of \u003cem\u003eMalassezia\u003c/em\u003e was slightly increased in HIV-infected patients compared to healthy controls in ITS1 (39.4% \u003cem\u003evs\u003c/em\u003e 32.3%) while in ITS2 (91.1% \u003cem\u003evs\u003c/em\u003e 93.4%) the abundance was relatively equal (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eC). Remarkably, the abundance of the genus \u003cem\u003ePichia\u003c/em\u003e was high while that of the genus \u003cem\u003eRhodotorula\u003c/em\u003e was low in HIV-infected patients compared to healthy controls in both ITS1 and ITS2 (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eC and \u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eD). At the 16S level, the genera \u003cem\u003eCutibacterium/Propionibacterium\u003c/em\u003e, \u003cem\u003eStaphylococcus\u003c/em\u003e and \u003cem\u003eCorynebacterium\u003c/em\u003e dominated with an abundance of 31.3% \u003cem\u003evs\u003c/em\u003e 40.2%, 21.5% \u003cem\u003evs\u003c/em\u003e 19.2% and 7.1% \u003cem\u003evs\u003c/em\u003e 8.4% in HIV-infected patients and healthy controls, respectively (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eE). The abundance of \u003cem\u003eStreptococcus\u003c/em\u003e, a common skin genus, was increased in HIV-infected patients (1.8%) compared to healthy controls (0.6%) (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eE).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eBy analysing fungal species with an abundance\u0026thinsp;\u0026gt;\u0026thinsp;0.1%, we found in ITS1 that species such as \u003cem\u003eM. globosa\u003c/em\u003e (7.5% \u003cem\u003evs\u003c/em\u003e 2.5%), \u003cem\u003eM. dermatis\u003c/em\u003e (0.9% \u003cem\u003evs\u003c/em\u003e 0.01%) and \u003cem\u003eErythrobasidium yunnanense\u003c/em\u003e (0.3% \u003cem\u003evs\u003c/em\u003e 0.0%) had a slightly increased abundance in HIV-infected patients compared to healthy controls, respectively (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003eA). The abundance of \u003cem\u003eM. restricta\u003c/em\u003e in ITS1, the most frequently detected \u003cem\u003eMalassezia\u003c/em\u003e species in metagenomics, was 26.3% \u003cem\u003evs\u003c/em\u003e 28.9% in HIV-infected patients and healthy controls, respectively (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003eA). Other \u003cem\u003eMalassezia\u003c/em\u003e species were also detected with low abundance. \u003cem\u003eM. sympodialis\u003c/em\u003e and \u003cem\u003eM. furfur\u003c/em\u003e were detected with an abundance of 0.3% \u003cem\u003evs\u003c/em\u003e 0.5% and 0.04% \u003cem\u003evs\u003c/em\u003e 0.006% in HIV-infected patients and healthy controls, respectively. \u003cem\u003eM. obtusa\u003c/em\u003e (1 read only in a healthy control) and \u003cem\u003eM. slooffiae\u003c/em\u003e (19 reads only in an HIV-infected patient) were detected with very low abundance. While in ITS2, \u003cem\u003eM. restricta\u003c/em\u003e (36.1% \u003cem\u003evs\u003c/em\u003e 16.5%), \u003cem\u003eM. globosa\u003c/em\u003e (15.3% \u003cem\u003evs\u003c/em\u003e 9.7%), \u003cem\u003eM. dermatis\u003c/em\u003e (2.0% \u003cem\u003evs\u003c/em\u003e 0.03%) and \u003cem\u003ePichia kluyveri\u003c/em\u003e (0.2% \u003cem\u003evs\u003c/em\u003e 0.0%) had a slightly increased abundance in HIV-infected patients compared to healthy controls, respectively (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003eB). \u003cem\u003eM. arunalokei\u003c/em\u003e was detected in ITS2 with a relatively evenness between HIV-infected patients (4.7%) and healthy controls (3.7%). The linear discriminant analysis (LDA) effect size (LEfSe) of fungal and bacterial species that displayed a significantly heterogeneous distribution between HIV-infected patients and healthy controls is presented in Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e. In ITS1, \u003cem\u003eCladosporium halotolerans\u003c/em\u003e and \u003cem\u003eErythrobasidium yunnanense\u003c/em\u003e were significantly more abundant in HIV-infected patients while \u003cem\u003eAllophoma cylindrispora\u003c/em\u003e was more significantly abundant in healthy controls (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003eC). In ITS2, \u003cem\u003eAspergillus sydowii\u003c/em\u003e was significantly more abundant in HIV-infected patients while \u003cem\u003eUnclassified_Malassezia\u003c/em\u003e, \u003cem\u003eCladosporium oxysporium/tenuissimum/colocasiae\u003c/em\u003e and \u003cem\u003eBuckleyzyma aurantiaca\u003c/em\u003e were significantly more abundant in healthy controls (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003eD). In level of bacterial species, \u003cem\u003eNeisseria cinerea\u003c/em\u003e, \u003cem\u003eShingomonas spp\u003c/em\u003e., \u003cem\u003eCorynebacterium aurimucosum\u003c/em\u003e and \u003cem\u003eStreptococcus spp\u003c/em\u003e. were significantly more abundant in HIV-infected patients while \u003cem\u003eIHU_PS_89_Bacteria_70108\u003c/em\u003e was more significantly abundant in healthy controls (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003eE).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eWe sought to investigate the correlations between fungal and bacterial genera by analysing ITS and 16S data from the same samples. In general, the negative correlations found between fungal and bacterial genera tended to be stronger (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e). While some genera such as \u003cem\u003eAcinetobacter\u003c/em\u003e were strongly negatively correlated to \u003cem\u003eMalassezia\u003c/em\u003e, positive correlations were found between \u003cem\u003eMalassezia\u003c/em\u003e and the genera \u003cem\u003eCutibacterium\u003c/em\u003e/\u003cem\u003ePropionibacterium\u003c/em\u003e, \u003cem\u003eLawsonella\u003c/em\u003e and \u003cem\u003eNeoactinobaculum\u003c/em\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003eA).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eWe then sought to determine the stability of the skin mycobiome of HIV-infected patients and healthy controls. We performed a second consecutive time sampling (S2) in 9 HIV-infected patients and 10 healthy controls. We determined the prevalence of fungal species in all volunteers, and the fungal species that had a prevalence\u0026thinsp;\u0026ge;\u0026thinsp;50% are shown in Tables\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e5\u003c/span\u003e and \u003cspan refid=\"Tab5\" class=\"InternalRef\"\u003e6\u003c/span\u003e. Some \u003cem\u003eMalassezia\u003c/em\u003e species such as \u003cem\u003eM. globosa\u003c/em\u003e and \u003cem\u003eM. restricta\u003c/em\u003e were present with a prevalence of 100% on the two successive samples while other species such as \u003cem\u003eM. sympodialis\u003c/em\u003e and \u003cem\u003eM. dermatis\u003c/em\u003e had a low prevalence (Tables\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e5\u003c/span\u003e and \u003cspan refid=\"Tab5\" class=\"InternalRef\"\u003e6\u003c/span\u003e). At S2 in ITS1, the abundance of \u003cem\u003eM. restricta\u003c/em\u003e, \u003cem\u003eM. globosa\u003c/em\u003e and \u003cem\u003eM. dermatis\u003c/em\u003e were 24.5% \u003cem\u003evs\u003c/em\u003e 22.2%, 6.2% \u003cem\u003evs\u003c/em\u003e 2.0% and 0.2% \u003cem\u003evs\u003c/em\u003e 0.3% in HIV-infected patients and healthy controls, respectively. While in ITS2, the abundance of \u003cem\u003eM. restricta\u003c/em\u003e, \u003cem\u003eM. globosa\u003c/em\u003e and \u003cem\u003eM. dermatis\u003c/em\u003e was 23.1% \u003cem\u003evs\u003c/em\u003e 13.7%, 12.3% \u003cem\u003evs\u003c/em\u003e 8.8% and 2.2% \u003cem\u003evs\u003c/em\u003e 0.3% in HIV-infected patients and healthy controls, respectively. The other more prevalent non-\u003cem\u003eMalassezia\u003c/em\u003e fungal species were mainly filamentous fungi such as \u003cem\u003eAspergillus\u003c/em\u003e, \u003cem\u003ePenicillium\u003c/em\u003e, \u003cem\u003eFusarium\u003c/em\u003e and \u003cem\u003eCladosporium\u003c/em\u003e (Tables\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e5\u003c/span\u003e and \u003cspan refid=\"Tab5\" class=\"InternalRef\"\u003e6\u003c/span\u003e). Interestingly, the prevalence of \u003cem\u003eCladosporium halotolerans\u003c/em\u003e was higher on both samples in HIV-infected patients compared to healthy controls (Table\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e5\u003c/span\u003e). The bacterial genera \u003cem\u003eCutibacterium/Propionibacterium\u003c/em\u003e (37.5% \u003cem\u003evs\u003c/em\u003e 42.1%), \u003cem\u003eStaphylococcus\u003c/em\u003e (17.0% \u003cem\u003evs\u003c/em\u003e 17.3%), and \u003cem\u003eCorynebacterium\u003c/em\u003e (4.6% \u003cem\u003evs\u003c/em\u003e 9.7%) were most abundant in HIV-infected patients and healthy controls, respectively. The genus \u003cem\u003eStreptococcus\u003c/em\u003e (1.6% \u003cem\u003evs\u003c/em\u003e 0.6%) was also abundant at S2 in HIV-infected patients compared to healthy controls, suggesting an association with HIV infection.\u003c/p\u003e \u003cp\u003eAn analysis of the variability of the fungal and bacterial skin microbiota was performed for the two successive time samples by calculating the Bray-Curtis dissimilarity. A comparison was then performed between HIV-infected patients and within HIV-infected patients as well as between healthy controls and within healthy controls. A significant difference in variability was found in ITS2 between HIV-infected patients and within HIV-infected patients (Wilcox test; \u003cem\u003ep\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.041) (Fig.\u0026nbsp;\u003cspan refid=\"Fig8\" class=\"InternalRef\"\u003e8\u003c/span\u003eA). However, no significant difference was found for the other cases in ITS1 and 16S (Fig.\u0026nbsp;\u003cspan refid=\"Fig8\" class=\"InternalRef\"\u003e8\u003c/span\u003eA et 8B).\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab4\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 5\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eFungal species present in \u0026ge;\u0026thinsp;50% of all volunteers in sample 1 (S1).\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"7\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colspan=\"4\" nameend=\"c4\" namest=\"c1\"\u003e \u003cp\u003eSample 1 (S1)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"3\" nameend=\"c7\" namest=\"c5\"\u003e \u003cp\u003eSample 2 (2)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eFungal species from ITS1\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003e% of Healthy with species (n\u0026thinsp;=\u0026thinsp;10)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003e% of HIV\u0026thinsp;+\u0026thinsp;with species (n\u0026thinsp;=\u0026thinsp;13)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003e% of All volunteers with species (n\u0026thinsp;=\u0026thinsp;23)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003e% of Healthy with species (n\u0026thinsp;=\u0026thinsp;10)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003e% of HIV\u0026thinsp;+\u0026thinsp;with species (n\u0026thinsp;=\u0026thinsp;9)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003e% of All volunteers with species (n\u0026thinsp;=\u0026thinsp;19)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCladosporium_sp.\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eMalassezia_globosa\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eMalassezia_restricta\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAlternaria_sp.\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e90\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e95.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAspergillus_sect_Fumigati\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e90\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e92.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e91.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCandida_albicans\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e80\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e91.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eNeocamarosporium_betae\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e80\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e91.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAspergillus_sect_Nigri\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e80\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e92.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e86.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003ePenicillium_sect_Fasciculata\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e90\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e84.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e86.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003ePlectosphaerella_sp.\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e86.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eFusarium_sp.\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e80\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e84.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e82.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eDebaryomyces_sp.\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e84.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e78.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eFusarium_equiseti\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e80\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e69.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e73.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eSaccharomyces_cerevisiae\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e90\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e61.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e73.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eFusarium_delphinoides\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e61.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e65.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAureobasidium_leucospermi\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e61.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e65.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003ePenicillium_sect_Brevicompacta\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e60\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e61.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e60.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCandida_parapsilosis\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e50\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e69.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e60.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCandida_sp.\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e53.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e60.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eEremothecium_sinecaudum\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e50\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e69.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e60.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAspergillus_fumigatus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e60\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e53.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e56.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003ePenicillium_sect_Cinnamopurpurea\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e60\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e53.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e56.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAureobasidium_melanogenum/pullulans\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e60\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e53.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e56.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCladosporium_sphaerospermum\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e46.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e56.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCladosporium_langeronii\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e50\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e61.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e56.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eMalassezia_sympodialis\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e46.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e56.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAspergillus_sp.\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e50\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e53.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e52.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eFusarium_longifundum\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e50\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e53.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e52.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003ePenicillium_digitatum\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e40\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e61.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e52.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCladosporium_spp.\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e60\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e46.15\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e52.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eFilobasidium_magnum\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e38.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e52.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eFusarium_wereldwijsianum\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e60\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e46.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e52.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eMalassezia_dermatis\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e50\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e53.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e52.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003ePlectosphaerella_niemeijerarum\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e60\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e46.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e52.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab5\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 6\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eFungal species present in \u0026ge;\u0026thinsp;50% of all volunteers in sample 1 (S1).\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"7\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colspan=\"4\" nameend=\"c4\" namest=\"c1\"\u003e \u003cp\u003eSample 1 (S1)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"3\" nameend=\"c7\" namest=\"c5\"\u003e \u003cp\u003eSample 2 (S2)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eFungal species from ITS2\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003e% of Healthy with species (n\u0026thinsp;=\u0026thinsp;10)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003e% of HIV\u0026thinsp;+\u0026thinsp;with species (n\u0026thinsp;=\u0026thinsp;13)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003e% of All volunteers with species (n\u0026thinsp;=\u0026thinsp;23)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003e% of Healthy with species (n\u0026thinsp;=\u0026thinsp;10)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003e% of HIV\u0026thinsp;+\u0026thinsp;with species (n\u0026thinsp;=\u0026thinsp;9)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003e% of All volunteers with species (n\u0026thinsp;=\u0026thinsp;19)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eDebaryomyces_prosopidis/vindobonensis/fabryi\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eMalassezia_arunalokei\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eMalassezia_globosa\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eMalassezia_restricta\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003ePenicillium_Sect_Fasciculata\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eSaccharomyces_cerevisiae\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003ePenicillium_Sect_Chrysogena\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e90\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e95.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e90\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e94.7\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCladosporium_sp.\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e84.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e91.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e60\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e77.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e68.4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAspergillus_Sect_Fumigati\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e90\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e84.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e86.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCladosporium_austrohemisphaericum/langeronii\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e100\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e76.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e86.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e60\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e77.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e68.4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eMalassezia_sympodialis\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e90\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e61.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e73.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e80\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e77.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e78.9\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003ePenicillium_Sect_Roquefortorum\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e69.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e69.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e60\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e66.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e63.1\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAureobasidium_lini\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e53.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e60.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e40\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e66.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e52.6\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCladosporium_halotolerans\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e30\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e76.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e56.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e40\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e66.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e52.6\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eMalassezia_dermatis\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e60\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e53.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e56.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e55.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e63.1\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003ePenicillium_Sect_Brevicompacta\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e60\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e53.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e56.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e30\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e33.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e31.5\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAlternaria_doliconidium/destruens\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e50\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e53.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e52.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e50\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e33.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e42.1\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003e \u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003eThe culture data from our study showed a prevalence of 100% positive culture for \u003cem\u003eMalassezia\u003c/em\u003e yeast in healthy controls and HIV-infected patients at visit1. However, the level of \u003cem\u003eMalassezia\u003c/em\u003e CFU abundance was higher in HIV-infected patients, regardless of immune status, compared to healthy controls (Figs.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e and \u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). The high abundance was observed during all visits in our study, showing a high colonization of \u003cem\u003eMalassezia\u003c/em\u003e yeasts on the skin of HIV-infected patients. Wikler \u003cem\u003eet al\u003c/em\u003e., quantified \u003cem\u003eMalassezia\u003c/em\u003e by culture in 21 HIV-infected and 10 non-HIV-infected patients without SD and found similar prevalence of positive cultures. In addition, a recent study analysing 46 HIV-infected patients and 46 healthy controls found no difference in the frequency of isolation of \u003cem\u003eMalassezia\u003c/em\u003e yeasts (Krzyściak et al., \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). Our data and those of other studies show that the rate of positive culture cannot be a criterion for comparing the skin colonization of \u003cem\u003eMalassezia\u003c/em\u003e yeasts in HIV-infected patients and healthy controls. However, the \u003cem\u003eMalassezia\u003c/em\u003e CFU abundance could be used as a more discriminant criterion for \u003cem\u003eMalassezia\u003c/em\u003e skin colonization evaluation. By categorizing the CFU counts, we have shown that HIV-infected patients are highly colonized by \u0026gt;\u0026thinsp;100 CFU \u003cem\u003eMalassezia\u003c/em\u003e yeast. Our results are in agree with those of Peche et al. (1995), who quantified by culture the density of \u003cem\u003eMalassezia\u003c/em\u003e yeasts on healthy forehead skin in 38 HIV-infected and 40 non-HIV-infected persons. In addition, a culture study conducted by Bergbrant et al (1996), found similar results on the healthy skin of the chest of 21 healthy controls and 41 HIV-infected patients.\u003c/p\u003e \u003cp\u003eIn this study, 4 \u003cem\u003eMalassezia\u003c/em\u003e species were isolated from all groups at the visit1 including \u003cem\u003eM. sympodialis\u003c/em\u003e (41%), \u003cem\u003eM. globosa\u003c/em\u003e (24.7%), \u003cem\u003eM. restricta\u003c/em\u003e (21.7%) and \u003cem\u003eM. furfur\u003c/em\u003e (12.6%). The predominance of \u003cem\u003eM. sympodialis\u003c/em\u003e and \u003cem\u003eM. globosa\u003c/em\u003e is in agree with the results of Krzyściak \u003cem\u003eet al\u003c/em\u003e. (Krzyściak et al., \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). In line with our observation, these authors found that \u003cem\u003eM. sympodialis\u003c/em\u003e was the dominant species in particular in healthy controls, whereas \u003cem\u003eM. furfur\u003c/em\u003e was dominant in HIV-infected patients. Geographically, our results are comparable to those of other European countries where \u003cem\u003eM. sympodialis\u003c/em\u003e and \u003cem\u003eM. globosa\u003c/em\u003e are found to be the most frequent species in the population (Prohic et al., \u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e2016\u003c/span\u003e). Noteworthy, the follow-up study showed a trend in HIV-infected patients to have a higher \u003cem\u003eMalassezia\u003c/em\u003e species diversity in culture and, notably, \u003cem\u003eM. dermatis\u003c/em\u003e and \u003cem\u003eM. furfur\u003c/em\u003e were more frequently isolated compared to healthy controls. A similar trend in \u003cem\u003eMalassezia\u003c/em\u003e species diversity was observed by other authors (Krzyściak et al., \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). Whether the HIV infection and/or its treatment, alters the skin surface lipids composition and subsequently influences \u003cem\u003eMalassezia\u003c/em\u003e species diversity remains to be elucidated. As a high abundance of yeast can be found on healthy skin, it has been hypothesized that the pathogenicity of \u003cem\u003eMalassezia\u003c/em\u003e in SD is probably determined by the type of strain colonizing the skin rather than the high abundance of yeast (Pech\u0026egrave;re and Saurat, \u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e1997\u003c/span\u003e). Although most species were isolated on all visits, some species were dominant on some sites. \u003cem\u003eM. sympodialis\u003c/em\u003e colonization was stable at all sites and regardless of HIV status. In HIV-infected patients, \u003cem\u003eM. furfur\u003c/em\u003e colonization was stable at all sampling sites with a high abundance on the chest, whereas \u003cem\u003eM. restricta\u003c/em\u003e was stable on the forehead and nasolabial fold (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eB). In healthy controls, \u003cem\u003eM. sympodialis\u003c/em\u003e and \u003cem\u003eM. globosa\u003c/em\u003e dominated on each visit on the chest (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eB).\u003c/p\u003e \u003cp\u003eMetagenomic sequencing data from our study showed that there was no significant difference in alpha diversity, and no community composition was observed between HIV-infected patients and healthy controls (Figs.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e and \u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e). However, the number of fungal and bacterial OTUs detected in HIV-infected patients was high compared to healthy controls, suggesting a high microbial diversity on the skin of HIV-infected patients. ITS metabarcoding showed a slightly increased relative abundance of fungal species, including \u003cem\u003eM. restricta\u003c/em\u003e, \u003cem\u003eM. globosa\u003c/em\u003e, \u003cem\u003eM. dermatis\u003c/em\u003e, \u003cem\u003eE. yunnanense\u003c/em\u003e, \u003cem\u003eC. halotolerans\u003c/em\u003e and \u003cem\u003eP. kluyveri\u003c/em\u003e on the skin of HIV-infected patients compared to healthy controls. \u003cem\u003eE. yunnanense\u003c/em\u003e, \u003cem\u003eP. kluyveri\u003c/em\u003e and \u003cem\u003eC. halotolerans\u003c/em\u003e are opportunistic fungal species and are not associated with the skin microbiota. Their presence is probably due to the hazard although \u003cem\u003eC. halotolerans\u003c/em\u003e was abundant in HIV-infected patients on both time samples. However, \u003cem\u003eMalassezia\u003c/em\u003e species are known to be commensal to the skin. When analysing the second S2 time point sampling, the abundance of \u003cem\u003eM. restricta\u003c/em\u003e, \u003cem\u003eM. globosa\u003c/em\u003e and \u003cem\u003eM. dermatis\u003c/em\u003e was also found to be slightly increased in HIV-infected patients compared to healthy controls, showing an effect of HIV status on the density of skin colonization of \u003cem\u003eMalassezia\u003c/em\u003e species. Although \u003cem\u003eMalassezia\u003c/em\u003e is commensal to the skin, this fungal genus is often designated as a biomarker for SD (Lin et al., \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). Our culture and metagenomic findings have shown high colonization of \u003cem\u003eMalassezia\u003c/em\u003e on the skin of HIV-infected patients. As SD can be a common dermatological condition in both HIV-infected and HIV-uninfected patients, it is possible that the overgrowth of \u003cem\u003eMalassezia\u003c/em\u003e in HIV-infected patients promotes more SD in these patient categories. The increased abundance of \u003cem\u003eMalassezia\u003c/em\u003e in other body sites has been reported in HIV-infected patients, including the gut (Hamad et al., \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e2018\u003c/span\u003e) and oral cavity (Chang et al., \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). As suggested in the introduction, it is possible that HIV infection is a risk factor for \u003cem\u003eMalassezia\u003c/em\u003e overgrowth although the physiological conditions are not well known. To explain the prevalence of SD, several hypotheses were suggested regarding the involvement of \u003cem\u003eMalassezia\u003c/em\u003e. One hypothesis is the immune deficiency associated with HIV infection. However, the studies are conflicting on this subject (Panjaitan, Pudjiati and Siswati, \u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e2014\u003c/span\u003e; Forrestel et al., \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2016\u003c/span\u003e; Krzyściak et al., \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). In our study, we did not observe a trend between CD\u003csub\u003e4\u003c/sub\u003e T cell count and \u003cem\u003eMalassezia\u003c/em\u003e CFU count on the skin of HIV-infected patients. This is in agreement with other studies that have reported that there is no significant relationship between the CD\u003csub\u003e4\u003c/sub\u003e T cell count and the number of \u003cem\u003eMalassezia\u003c/em\u003e CFU in HIV-infected patients (Panjaitan, Pudjiati and Siswati, \u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e2014\u003c/span\u003e). While other authors demonstrated that there was a trend between numbers of \u003cem\u003eMalassezia\u003c/em\u003e yeasts present on lesional skin, severity of seborrheic dermatitis and CD\u003csub\u003e4\u003c/sub\u003e T cell counts in HIV-positive patients (Schechtman, Hay and Midgley, \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e1995\u003c/span\u003e). Another possible hypothesis, which is little studied, is the investigation of the composition of skin surface lipids. Two studies have reported an association between abnormal skin surface lipid composition and HIV infection but also an association between abnormal skin surface lipid composition and SD (Vidal et al., \u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e1990\u003c/span\u003e; Ostlere et al., \u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e1996\u003c/span\u003e). At the level of bacteria, the abundance of genera \u003cem\u003eCutibacterium/Propionibacterium\u003c/em\u003e and \u003cem\u003eCorynebacterium\u003c/em\u003e were decreased while \u003cem\u003eStreptococcus\u003c/em\u003e was increased in HIV-infected patients, showing a cutaneous bacterial dysbiosis. \u003cem\u003eStreptococcus\u003c/em\u003e is a genus usually found on the skin and its high abundance on both time samplings in HIV-infected patients deserves further investigation. Because many bacterial OTUs were not accurately classified, it is difficult to identify skin-associated bacterial species in HIV-infected patients. In this study, negative correlations between \u003cem\u003eMalassezia\u003c/em\u003e and some bacterial genera including \u003cem\u003eAcinetobacter\u003c/em\u003e and \u003cem\u003eStreptococcus\u003c/em\u003e were found (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e). However, the biological significance of these fungal-bacterial interactions on healthy skin of HIV-infected and HIV-uninfected patients is not known. Our data may provide an opportunity for research to understand the role of skin microbiota interactions in the occurrence of SD in HIV-infected patients.\u003c/p\u003e \u003cp\u003eStudies of fungal and bacterial microbiota on healthy skin of HIV-infected patients are infrequent. Our knowledge is limited on the fungal and bacterial skin microbiota associated with HIV infection. Most studies of the cutaneous microbiota have focused on diseased skin of patients with common dermatological conditions such as SD. In this study, by combining culture, ITS1, ITS2 and 16S metabarcoding, our study provided some insights into the dynamics of cutaneous \u003cem\u003eMalassezia\u003c/em\u003e as well as the fungal and bacterial skin microbiome in HIV infected patients. Our study showed the advantage of combining several methodical approaches. We detected by metagenomics \u003cem\u003eMalassezia\u003c/em\u003e species not isolated in culture such as \u003cem\u003eM. slooffiae\u003c/em\u003e, \u003cem\u003eM. obtusa\u003c/em\u003e and \u003cem\u003eM. arunalokei\u003c/em\u003e. In addition, by targeting both ITS1 and ITS2, we detected many fungal species that would not have been detected with ITS1 or ITS2 only. Targeting both ITS1 and ITS2 might seem fastidious for the analyses but it is important since there is an amplification bias between ITS1 and ITS2 (Hamad et al., \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2017\u003c/span\u003e; Mbareche et al., \u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e2020\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThis study had interesting strengths as it studied the dynamics of the cutaneous \u003cem\u003eMalassezia\u003c/em\u003e yeast community over time, which is rarely investigated. In addition, we studied by metagenomics the fungal and bacterial skin microbiota associated with HIV infection. However, our study had some limitations. First, a metagenomic analysis was not performed to test the immune status between HIV-infected patients. Second, the sample collection period and follow-up were not the same for all participants, and many HIV-infected patients were lost to follow-up, due to the pandemic crisis of coronavirus disease 2019 (COVID-19). Third, the size of the participant cohort was not large, due to recruitment difficulties. Fourth, the absence of HIV-infected patients with seborrheic dermatitis, which would have allowed us to compare the evolution of the abundance of \u003cem\u003eMalassezia\u003c/em\u003e yeasts over time. Fifth, many of the fungal and bacterial sequences were not well classified, due to incomplete databases.\u003c/p\u003e \u003cp\u003eIn conclusion, the HIV-infected patients studied here showed an increased colonization of \u003cem\u003eMalassezia\u003c/em\u003e on the skin. A fungal and bacterial skin dysbiosis was observed in the HIV-infected patients, characterized by an increase of \u003cem\u003eC. halotolerans\u003c/em\u003e and \u003cem\u003eStreptococcus\u003c/em\u003e. Future studies, with a large size of the participant cohort and long follow-up time, are needed to understand if there is any relationship between skin surface lipid composition, \u003cem\u003eMalassezia\u003c/em\u003e abundance and the type of strain colonizing the skin of HIV-infected patients. This will help to better understand the occurrence of SD in these patients and thus improve their management.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAuthor Contributions:\u003c/strong\u003e A.A.: Conceptualization; Data curation; Investigation; Formal analysis; Methodology; Visualization; Writing the original draft. I.R.: Methodology; Investigation. S.M.: Methodology; Investigation. S.R.: Conceptualization; Methodology; Investigation; Formal analysis; Resources; Supervision; Writing - Review \u0026amp; Editing.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData are available at\u003c/strong\u003e: DOI: 10.13140/RG.2.2.17697.21607.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding:\u003c/strong\u003e This research was funded by the Institut Hospitalo-Universitaire (IHU) M\u0026eacute;diterran\u0026eacute;e Infection, the French Government under the program \u0026ldquo;Investissements d\u0026rsquo;avenir\u0026rdquo; managed by National Agency for Research, reference ANR-10-IAHU-03, the R\u0026eacute;gion Provence Alpes C\u0026ocirc;te d\u0026rsquo;Azur and European funding FEDER PRIMI.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConflicts of Interest:\u003c/strong\u003e The authors declare no conflict of interests.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eAbdillah, A. \u003cem\u003eet al.\u003c/em\u003e (2020) \u0026lsquo;Comparison of three skin sampling methods and two media for culturing malassezia yeast\u0026rsquo;, \u003cem\u003eJournal of Fungi\u003c/em\u003e, 6(4), pp. 1\u0026ndash;7. doi: 10.3390/jof6040350.\u003c/li\u003e\n\u003cli\u003eAbdillah, A. and Ranque, S. 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Fungi\u003c/em\u003e, 7(10), p. 824. doi: 10.3390/jof7100824.\u003c/li\u003e\n\u003cli\u003eBaroni, A. \u003cem\u003eet al.\u003c/em\u003e (2004) \u0026lsquo;Possible role of Malassezia furfur in psoriasis: Modulation of TGF-??1, integrin, and HSP70 expression in human keratinocytes and in the skin of psoriasis-affected patients\u0026rsquo;, \u003cem\u003eJournal of Cutaneous Pathology\u003c/em\u003e, 31(1), pp. 35\u0026ndash;42. doi: 10.1046/j.0303-6987.2004.0135.x.\u003c/li\u003e\n\u003cli\u003eCassagne, C. \u003cem\u003eet al.\u003c/em\u003e (2016) \u0026lsquo;Routine identification and mixed species detection in 6,192 clinical yeast isolates\u0026rsquo;, \u003cem\u003eMedical Mycology\u003c/em\u003e, 54(3), pp. 256\u0026ndash;265. doi: 10.1093/mmy/myv095.\u003c/li\u003e\n\u003cli\u003eChang, S. \u003cem\u003eet al.\u003c/em\u003e (2021) \u0026lsquo;Comparative Analysis of Salivary Mycobiome Diversity in Human Immunode fi ciency Virus- Infected Patients\u0026rsquo;, \u003cem\u003eFront Cell Infect Microbiol\u003c/em\u003e, 11(December), pp. 1\u0026ndash;9. doi: 10.3389/fcimb.2021.781246.\u003c/li\u003e\n\u003cli\u003eDiongue, K. \u003cem\u003eet al.\u003c/em\u003e (2018) \u0026lsquo;MALDI-TOF MS identification of Malassezia species isolated from patients with pityriasis versicolor at the seafarers\u0026rsquo; medical service in Dakar, Senegal\u0026rsquo;, \u003cem\u003eJournal de Mycologie Medicale\u003c/em\u003e, 28(4), pp. 590\u0026ndash;593. doi: 10.1016/j.mycmed.2018.09.007.\u003c/li\u003e\n\u003cli\u003eForrestel, A. 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(1997) \u0026lsquo;Malassezia yeast density in HIV-positive individuals.\u0026rsquo;, \u003cem\u003eThe British journal of dermatology\u003c/em\u003e, 136(1), pp. 138\u0026ndash;9. doi: 10.1111/j.1365-2133.1997.tb08770.x.\u003c/li\u003e\n\u003cli\u003eProhic, A. \u003cem\u003eet al.\u003c/em\u003e (2016) \u0026lsquo;Malassezia species in healthy skin and in dermatological conditions\u0026rsquo;, \u003cem\u003eInternational Journal of Dermatology\u003c/em\u003e, 55(5), pp. 494\u0026ndash;504. doi: 10.1111/ijd.13116.\u003c/li\u003e\n\u003cli\u003eRhimi, W. \u003cem\u003eet al.\u003c/em\u003e (2020) \u0026lsquo;Malassezia spp. Yeasts of Emerging Concern in Fungemia\u0026rsquo;, \u003cem\u003eFrontiers in Cellular and Infection Microbiology\u003c/em\u003e, 10(July). doi: 10.3389/fcimb.2020.00370.\u003c/li\u003e\n\u003cli\u003eSaunte, D. M. L., Gaitanis, G. and Hay, R. J. (2020) \u0026lsquo;Malassezia-Associated Skin Diseases, the Use of Diagnostics and Treatment\u0026rsquo;, \u003cem\u003eFrontiers in Cellular and Infection Microbiology\u003c/em\u003e, 10(March), pp. 1\u0026ndash;11. doi: 10.3389/fcimb.2020.00112.\u003c/li\u003e\n\u003cli\u003eSchechtman, R. ., Hay, R. J. and Midgley, G. (1995) \u0026lsquo;HIV disease and Malassezia yeasts : a quantitative study of patients presenting with seborrhoeic dermatitis\u0026rsquo;, \u003cem\u003eBr J Dermatol\u003c/em\u003e, pp. 694\u0026ndash;698.\u003c/li\u003e\n\u003cli\u003eSegata, N. \u003cem\u003eet al.\u003c/em\u003e (2011) \u0026lsquo;Metagenomic biomarker discovery and explanation\u0026rsquo;, \u003cem\u003eGenome Biology\u003c/em\u003e. BioMed Central Ltd, 12(6), p. R60. doi: 10.1186/gb-2011-12-6-r60.\u003c/li\u003e\n\u003cli\u003eTragiannidis, A. \u003cem\u003eet al.\u003c/em\u003e (2010) \u0026lsquo;Minireview : Malassezia infections in immunocompromised patients\u0026rsquo;, \u003cem\u003emycoses\u003c/em\u003e, pp. 187\u0026ndash;195. doi: 10.1111/j.1439-0507.2009.01814.x.\u003c/li\u003e\n\u003cli\u003eVidal, C. \u003cem\u003eet al.\u003c/em\u003e (1990) . \u0026lsquo;Seborrheic dermatitis and HIV infection\u0026rsquo;, \u003cem\u003eJournal of the American Academy of Dermatology\u003c/em\u003e. American Academy of Dermatology, Inc., 23(6), pp. 1106\u0026ndash;1110. doi: 10.1016/0190-9622(90)70341-E.\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Malassezia, skin, HIV infection, colonization, fungal and bacterial microbiome, mycobiome, dysbiosis","lastPublishedDoi":"10.21203/rs.3.rs-4139174/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4139174/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e \u003cem\u003eMalassezia\u003c/em\u003e species are lipid-dependent yeasts of the normal skin mycobiota in humans and some animals, which can cause skin infections. Yet, both the dynamic of \u003cem\u003eMalassezia\u003c/em\u003e skin colonization and the associated fungal and bacterial skin microbiome remain unknown in HIV-infected patients. The purpose of this study was to compare \u003cem\u003eMalassezia\u003c/em\u003e yeast community structure and associated microbiome on the healthy skin of HIV-infected patients and healthy controls.\u003c/p\u003e \u003cp\u003eA total of 23 HIV-infected patients and 10 healthy controls were included and followed-up for a maximum of 5 visits over 10 to 17 months. At each visit, chest, face, nasolabial fold, and scalp skin samples were subjected to both culture and MALDI-TOF MS identification, and ITS/16S metabarcoding. The participants were categorized according to their \u003cem\u003eMalassezia\u003c/em\u003e colony forming unit (CFU) abundance.\u003c/p\u003e \u003cp\u003e \u003cem\u003eMalassezia\u003c/em\u003e were cultured from each participant at each visit. HIV-infected patients were highly colonized on all visits with CFU\u0026thinsp;\u0026gt;\u0026thinsp;100. \u003cem\u003eM. sympodialis\u003c/em\u003e and \u003cem\u003eM. globosa\u003c/em\u003e were the most dominant species overall. \u003cem\u003eM. furfur\u003c/em\u003e and \u003cem\u003eM. dermatis\u003c/em\u003e were more prevalent in HIV-infected than in healthy participants. \u003cem\u003eM. sympodialis\u003c/em\u003e prevalence was stable at each sampling sites over time. \u003cem\u003eM. furfur\u003c/em\u003e prevalence was stable and more abundant over time on HIV-infected patients\u0026rsquo; chest. Although not statistically significant, the metagenomic analysis showed a higher fungal and bacterial diversity and an increased abundance of \u003cem\u003eCladosporium halotolerans\u003c/em\u003e and \u003cem\u003eStreptococcus\u003c/em\u003e in HIV-infected patients than in controls.\u003c/p\u003e \u003cp\u003eOur data showed a high skin colonization of \u003cem\u003eMalassezia\u003c/em\u003e yeasts as well as a dysbiosis of both fungal and bacterial communities in HIV-infected patients.\u003c/p\u003e","manuscriptTitle":"Population dynamics of Malassezia species on the skin of HIV-infected patients","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-04-02 19:13:18","doi":"10.21203/rs.3.rs-4139174/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"a493d70c-1c73-46cc-8492-8e2fa05de056","owner":[],"postedDate":"April 2nd, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2024-05-23T21:08:41+00:00","versionOfRecord":[],"versionCreatedAt":"2024-04-02 19:13:18","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-4139174","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4139174","identity":"rs-4139174","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}