Insights into the relationship between nasal bacterial composition and susceptibility to early-life respiratory disease: a pilot observational study

Background Early-life susceptibility to viral respiratory infections is associated with long-term respiratory morbidity in children. Currently, no reliable tools exist to predict susceptibility to these infections. Because the endogenous microbiota can influence pathogen virulence and airway inflammation, it represents a potential target for prevention. In this pilot study, we hypothesised that distinct nasal microbial communities are associated with susceptibility to viral respiratory infections and wheezing outcomes during the first year of life.

We analyzed 90 nasal swabs from 55 infants enrolled in the AERIAL study, representing asymptomatic samples collected at scheduled visits (∼4 months) and symptomatic samples. Bacterial profiling was done blind to clinical data using full-length 16S rRNA sequencing, and bacterial load was quantified using a pan-bacterial TaqMan® assay.

Bacterial diversity was similar between asymptomatic and symptomatic swabs, with community composition differences largely driven by inter-individual variation. In paired samples, symptomatic swabs showed reduced diversity but no change in bacterial load. Virus-bacteria interactions were observed in rhinovirus-positive swabs, but not SARS-CoV-2-positive swabs. Two nasal endotypes were identified, dominated by Moraxella or Streptococcus and differing in alpha diversity. Endotypes were associated with age at wheeze onset, and their relationship with wheezing episode rates showed a suggestive sex-dependent pattern that warrants further investigation.

Our pilot data suggest that the nasal microbiota might shape early wheezing outcomes in a sex-dependent manner, and highlight the value of longitudinal studies for clarifying how host-bacteria-virus interactions in early life. What is tested Whether distinct nasal microbiota endotypes in infancy are associated with later respiratory phenotypes, particularly wheeze. What the study showed Two endotypes were identified. Moraxella-dominated and Streptococcus-dominated, with differences in alpha diversity and associations with age at wheeze onset and wheezing rates. The significance and clinical impact of the research outcomes Nasal microbiota endotypes may help identify infants at risk of wheeze and support early risk stratification, pending validation in larger cohorts. Competing Interest Statement AB is a co-founder, equity holder, and director of the startup company Respiradigm Pty Ltd that is related to this work. AB is the founder of the startup company INSiGENe Pty Ltd that is unrelated to this work. No other authors have conflict of interest to disclose. Funding Statement S.M.S. received funding from the National Health and Medical Research Council (project grant number NHMRC115648) to support the AERIAL study and is also recipient of a NHMRC Investigator grant (NHMRC 2007725). A.K. is a Rothwell Family Fellow. T.I. is supported by a Stan Perron Charitable Foundation People Fellowship. S.P.A.-R. received funding from the Branchi family. A.B. is supported by the NIH (R21 AI176305-01A1, R01AI099108-11A1). Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics committee/IRB of Ramsey Health Care HREC WA-SA gave ethical approval for this work (reference number 1908). Informed consent was obtained from the parents or caregivers of all children participating in the study. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Footnotes During revision, we conducted an additional audit of symptom status annotations and participant metadata linkage. This identified one infant whose metadata had been omitted and one infant whose clinical metadata had been incorrectly linked to a sibling rather than the correct participant. These issues were corrected in the revised dataset and are reflected in the updated supplementary tables. We re-ran the analyses using the corrected annotations. The direction and overall interpretation of the results were unchanged, although there were small changes in effect estimates. In the revised analysis, the comparison of age at first wheeze between endotypes now reaches statistical significance (Figure 3D), with endotype 2 associated with later onset of wheeze. The manuscript text, figures, and supplementary materials have been updated accordingly. We have also updated the Data Availability Statement to include a link to the Mendeley Data repository. In addition, we have revised the manuscript throughout to address the reviewers comments and improve clarity. Our primary conclusions remain unchanged. Data Availability The R code is available in the accompanying GitHub repository: https://github.com/jacapmar/MicrobiomeAERIAL. De-identified taxonomy count tables for participants who provided consent for data sharing are available in the Mendeley Data repository (Caparros-Martin, JA, Kicic-Starcevich E, Agudelo-Romero P, Hancock D, Iosifidis T, Karpievitch Y et al. AERIAL Nasal Microbiome Taxonomy Table. Mendeley Data, V1. doi: 10.17632/vtr3m7tvzc.1). Raw sequencing files cannot be made publicly available due to ethical and privacy restrictions related to participant confidentiality and the conditions of the study consent.