Fecal microbiota transplantation improves Sansui duck growth performance by balancing the cecum microbiome

Fecal microbiota transplantation improves Sansui duck growth performance by balancing the cecum microbiome | 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 Article Fecal microbiota transplantation improves Sansui duck growth performance by balancing the cecum microbiome Yong Yue, Bingnong Yao, Fuyou Liao, Zhiqiang He, Papungkorn Sangsawad, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5863134/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 01 Jul, 2025 Read the published version in Scientific Reports → Version 1 posted 6 You are reading this latest preprint version Abstract Improving growth performance is vital in poultry production. Although several studies have established associations between gut microbiota and growth, the direct impacts remain unclear. A total of 120 1-day-old Sansui ducks were randomly assigned to FMT and control (CON) groups. From the 1st day, ducks in the FMT group were orally administrated with 0.5 mL fecal microbiota suspension for three consecutive days, while sterile PBS solution was used as a substitute in the CON group. The results revealed that FMT substantially improved average daily gain (ADG) and body weight (BW) (P < 0.001), with a tendency for a better feed conversion rate (FCR). LEfSe analysis determined that markedly increased the abundance of the genera Lactobacillus (P < 0.001), Bifidobacterium (P = 0.006), Megamonas (P = 0.008), and Subdoligranulum (P = 0.005) in FMT group. Similarly, the phyla Firmicutes/Bacteroidetes ratio was higher in the FMT group. Additionally, the ACE, Chao, Shannon, and Simpson indexes were also significantly higher in the FMT group (P < 0.001). To sum up, FMT enhanced growth performance, which could be associated with reducing proinflammatory pathogen colonization in the duck cecum. This modulating effect likely results from increased microbial diversity and the enrichment of beneficial bacteria. Biological sciences/Microbiology Biological sciences/Zoology Fecal microbiota transplantation Cecum microbiota Growth performance Sansui ducks Figures Figure 1 Figure 2 Figure 3 Figure 4 Introduction In recent years, the gut microbiome, frequently called a "microbial organ," has garnered significant research attention due to its symbiotic relationship with host health and critical roles in nutrient digestion and absorption, immune system development, and protection against pathogens 1 – 3 . Maintaining a balanced intestinal microbiota benefits the host by inhibiting pathogen colonization, enhancing intestinal barrier integrity, supporting normal nutrient metabolism, and fostering the proliferation of commensal microbes 4 . Moreover, the gut microbiota plays a crucial role in breaking down various food components and nutrients and synthesizing a range of metabolites that interact with the host 5 , 6 . The gut microbiota is a diverse and complex community of microorganisms that colonizes ducks' gastrointestinal (GI) tract, with the cecum exhibiting the highest microbial diversity and dynamic population 7 , 8 . Research on the duck cecum has consistently emphasized the role of gut microbiota in enhancing feed digestion, nutrient absorption, host defense, and immune function 3 , 7 – 9 . A stable gut microbiota supports the host by preventing colonization, facilitating pathogen clearance, and enhancing growth performance 10 . Notably, over the past decade, fecal microbiota transplantation (FMT) and probiotic supplementation have emerged as promising therapeutic and preventive approaches for reestablishing intestinal microbiota, mitigating inflammatory responses, and promoting growth and development 11 , 12 . For instance, transferring fecal microbiota from healthy chickens could influence the early establishment of gut microbiota in recipient chicks, potentially leading to long-term effects on host-microbe interactions and development 13 . It is reassuring that FMT has shown potential in enhancing weight gain and pathogen resistance in broilers 14 . Glendinning et al. 15 demonstrated that transplanting cecal microbiota from Roslin broilers to different chicken breeds during the first week of life increased the richness and diversity of microbiota in the recipients. Furthermore, FMT has enhanced intestinal morphology in broilers by increasing the thickness of serous membranes and muscle layers 16 . Manipulating gut microbiota through FMT or probiotics has been demonstrated to influence chicken growth and development. For instance, transferring fecal microbiota from 30-day-old chickens with high feed efficiency to newly hatched chicks has increased feed intake and body weight in female chickens 17 . Similarly, administering fecal microbiota from chickens with high feed conversion ratios affects early gut microbiota colonization, intestinal permeability, gut morphology, and innate immune responses in recipients 18 . Probiotic supplementation, comprising strains such as Lactobacillus reuteri , Bacillus subtilis , and Saccharomyces cerevisiae , has improved plasma immunoglobulin levels and enhanced growth performance in chickens 19 . Moreover, gut microbes produce diverse metabolites derived from dietary components or endogenous substrates, which mediate host-microbiota communication, particularly at the microbiota-mucosal interface 20 . Alterations in gut microbiota composition are often accompanied by changes in microbial metabolites and their interactions with gut epithelial cells. For example, dietary fiber supports the growth of short-chain fatty acid (SCFA) producing bacteria, and the SCFAs, especially butyrate, serve as an energy source for gut epithelial cells, promoting their growth and function 21 . This study investigates the effects of fecal microbiota on the growth performance of Sansui ducks using 16S rRNA gene amplicon sequencing. We aimed to integrate FMT into the management of duck production, presenting a novel approach to improving duck growth performance. Materials and Methods Experimental Conditions A total of 120 1-day-old Sansui ducks were selected as recipients and randomly divided into two groups: a control (CON) group (n = 60) and a fecal microbiota transplantation (FMT) group (n = 60); each group comprised four replicates. The ducks were distributed into ten cages (0.65 m H × 0.8 m W × 1.2 m D), and the experiment lasted 42 days. The initial temperature was maintained at 37 ± 1 ℃, with a systematic weekly reduction of 2 ℃ until ambient room temperature was achieved. Humidity levels were sustained between 65–70%, and a light-dark cycle of 23:1 was implemented. The duck house was cleaned each morning and disinfected daily with a 5% sodium hypochlorite solution. From the 1st day, ducks in the FMT group orally received fecal suspension with 0.5 mL every afternoon for 3 days. Ducks in the CON group orally received PBS with 0.5 mL, and the ducks had free access to feed and water during the experiment. The ingredients and nutrient composition of the experimental diets are shown in Table 1 . Table 1 Ingredients and chemical composition of the experimental diets. Ingredients,% Content,% Corn 63.85 Soybean meal 27.83 Wheat bran 1.50 RaPeseed cake 4.00 CaHPO 4 1.50 Limestone 0.85 NaCl 0.25 Premix a 0.22 Total 100.00 Nutrient levels b Crude protein 18.92 Metabo lizable energy, MJ/kg 11.78 Calcium 0.81 Total phosphorus 0.42 Lysine 0.95 Methionine 0.292 a The premix provided the following per kg of diets: Vitamin A 4 000 IU; Vitamin 20 mg; Vitamin K32 mg; Vitamin B1 3. 5 mg; Vitamin B12 0.01 mg; Folic acid 1.0 mg; Copper 10 mg; Iron 80 mg; Manganese 60 mg; Zinc 60 mg; Deng 0.4 mg; Selenium 0.2 mg; Niacin 50 mg; Biotin 0.1 mg; Calcium pantothenate 10 mg; Pyridoxine 2.5 mg. 10 mg; pyridoxine 2.5 mg. b Crude protein was measured values; while the others were calculated values. Table 1 Preparation of fecal microbiota suspension Six healthy female Sansui ducks with the same genetic background (42-day-old) were selected as fecal donors. Once the donor ducks defecated in the morning, the excreta's white part was removed immediately because it mainly comprised of uric acid. Feces (15g) were collected daily in a sterile tube (50 mL). Based on ELISA, E. coli-phage and Salmonella- phage ELISA kits (48T) were purchased from Zhejiang of China Zhiyi Biotechnology Co., Ltd. Escherichia coli and Salmonella were rapidly detected by ELISA, and 15g of feces without Escherichia coli and Salmonella were selected and homogenized in 150 mL of sterile PBS and centrifuged for 5min at 2000 r.p.m., 4°C. The mixture was kept on ice until precipitates were fully settled, and the supernatant was collected and filtered with sterile gauze to get fecal suspension. The microbial suspensions were stored at -80°C until used for FMT. Sample collection and growth performance The rearing cycle of ducks was 42 days, and ducks were weighed in duplicates at 1, 14, and 28 days. Feed consumption was monitored throughout the study period for each group, and the average daily feed intake (ADFI), body weight (BW), average daily gain (ADG), and feed conversation rate (FCR) for each replicate were then computed. At 42 days into the feeding study, we randomly selected two birds from each replicate, which were euthanized through cervical dislocation following a 12 h feed deprivation, and their cecal contents samples were collected, frozen in liquid nitrogen, and stored at -80°C for subsequent analysis. Microbial genomic DNA extraction and 16S rRNA gene sequencing The cecal contents were used from 200 mg samples using the QIAamp DNA Stool Mini Kit (QIAGEN, Hilden, Germany) following the manufacturer's instructions. A total of 16 samples were used for 16S rDNA sequencing, eight samples per group. The hypervariable regions V3-V4 of the bacterial 16S rRNA gene were amplified with the forward primer 357F (5'-ACTCCTACGGRAGGCAGCAG-3') and reverse primer 806R (5'-GGACTACHVGGGTWTCTAAT-3'). DNA sequencing was performed on a Novaseq sequencer (Illumina) with services from TinyGene Bio-Tech. The PCR reaction was set up in a 50 µL mixture containing 1–2 µL of DNA, 200 µM dNTPs, 0.2 µM primers, 10 µL of 5X buffer, and 1 U Phusion DNA Polymerase. The amplification program included an initial denaturation at 94°C for 2 minutes, followed by 25 cycles (94°C for 30, 56°C for 30, 72°C for 30), and a final extension at 72°C for 5 minutes. After PCR, barcoded products were purified using a DNA gel extraction kit (Axygen) and quantified with an FTC-3000 PCR system. For the second PCR, dual barcodes were added, and amplification conditions were as follows: denaturation at 94°C for 3 minutes, followed by eight cycles (94°C for 30s, 56°C for 30s, 72°C for 30s), and final extension at 72°C for 5 minutes. The library was purified and sequenced with paired-end reads on the Novaseq platform. Sequencing data analysis The raw 16S rRNA gene sequencing reads were demultiplexed according to their barcodes. All paired-end (PE) reads were processed with Trimmomatic (version 0.35) to eliminate low-quality bases, applying the parameters (SLIDING WINDOW: 50:20, MINLEN: 50). Subsequently, the trimmed reads were merged using the FLASH program (version 1.2.11) with default settings. Low-quality contigs were discarded via the screen.seqs command, using the following criteria: maxambig = 0, minlength = 200, maxlength = 485, and maxhomop = 8. For 16S sequence analysis, a combination of software tools was employed: Mothur (version 1.33.3), UPARSE (search version v8.1.1756, http://drive5.com/uparse ), and R (version 3.6.3). The demultiplexed reads were clustered into operational taxonomic units (OTUs) at 97% sequence identity, and singleton OTUs were removed using the UPARSE pipeline ( http://drive5.com/usearch/manual/uparse_cmds.html ). With the classification, the taxonomic assignment of OTU representative sequences was performed against the Silva 128 database, using a confidence threshold of ≥ 0.6. Seqs command in Mothur. OTU taxonomies, ranging from phylum to species, were determined based on the NCBI database. For the analysis of alpha diversity, indices including Shannon, Simpson, Chao1, ACE, and rarefaction curves were calculated using Mothur and visualized with R. Beta diversity was assessed by calculating the weighted and unweighted UniFrac distance matrices using Mothur, with visualization performed through Principal Coordinate Analysis (PCoA) using the ape package in R, Non-metric multidimensional scaling (NMDS) was performed using the vegan package in R and hierarchical clustering using the end extend package in R. The Bray-Curtis and Jaccard metrics were calculated with the vegan package in R and visualized similarly to the UniFrac analysis. R and hierarchical clustering via the end extend package in R. Additionally, Bray-Curtis and Jaccard metrics were calculated with the vegan package in R and visualized in the same manner as the UniFrac analysis. Statistical analysis Data were collected and tabulated separately for each treatment. First, a normality test was performed to assess the distribution of the data. Statistical analysis was conducted using SPSS software for Windows (Version 19.0; SPSS Inc., Armonk, NY, USA). One-way ANOVA was applied to compare more than two groups, followed by Tukey's post-hoc multiple comparison test. An unpaired two-tailed t-test was used to compare the two groups. Data are expressed as the mean ± standard error (SE). Statistical significance was set at P < 0.05. Results FMT improves growth performance in Sansui ducks The growth performance of ducks was significantly enhanced following FMT treatment compared to the control (CON) group, as evidenced by improvements in average daily gain (ADG), body weight (BW), and feed conversion rate (FCR). During the first 1–14 days, the FMT group achieved a significantly higher ADG (P < 0.001) compared to the CON group (Fig. 1 a,b), and this improvement continued during the 15–28 day period, with a similarly significant increase (P < 0.001). Moreover, BW in the FMT group was markedly greater (P 0.05), there was a linear increasing trend in which the FMT group exhibited a lower FCR over the entire 1–28 day period (Fig. 1 e). Figure 1 FMT changes the community composition of cecum microbiota To investigate the effects of FMT on the community composition of cecum microbiota in ducks, we utilized 16S rRNA sequencing and comprehensive microbiome analysis. Microbiome analysis revealed profound changes in the composition of the phylum and genus in the cecum (Fig. 2 ). Specifically, at the phylum level (Fig. 2 a), Firmicutes and Bacteroides were the two phyla that accounted for the immense proportions, Actinobacteria was an enriched bacteria in the FMT group (P = 0.039). In contrast, the average abundance of Proteobacteria was lower than the CON group (P > 0.05). Remarkably, the phyla Firmicutes / Bacteroidetes ratio in the FMT group was higher than in the CON group (P > 0.05). At the genus level (Fig. 2 b), the top 3 abundance bacteria in the FMT group were Bacteroides (25.71%), Fusobacterium (7.42%), and Alistipes (3.18%). In comparison, the CON group was Bacteroides (30.20%), Fusobacterium (5.48%), and Alistipes (4.74%). Additionally, as demonstrated through principal component analysis (PCA) and the heatmap of beta diversity analyses, they showed distinct clustering between FMT and CON groups, signifying substantial differences in microbial community composition (Fig. 2 c,d). Figure 2 FMT alters the alpha diversity of the cecum microbiota and enriches specific bacterial populations As illustrated in Fig. 3 a, FMT significantly enriched the alpha diversity of the cecum microbiota, as evidenced by significantly higher values in the FMT group of the ACE (P < 0.001), Chao (P < 0.001), Shannon (P < 0.001), and Simpson (P < 0.001) indices compared to the CON group. Notably, FMT significantly enriched core bacterial genera (Fig. 3 b), including Lactobacillus (P < 0.001), Bifidobacterium (P = 0.006), Megamonas (P = 0.008), and Subdoligranulum (P = 0.005). Likewise, evident from the taxonomic cladogram obtained by linear discriminant analysis effect size (LEfSe) (Fig. 3 c,d), LEfSe identified signature genera associated with FMT treatment, which includes Peptococcus , Faecalitalea , Streptococcus , and Turicibacter . In addition, FMT markedly increased the abundance of the class Coriobacteriia. Particularly, the orders of Lactobacillales, Bifidobacteriales, Selenomonadales, and Coriobacteriales were spotlighted, with a pronounced increase in the families Bifidobacteriaceae , Peptococcaceae , Coriobacteriaceae , and Enterococcaceae . Similarly, at the species level, FMT significantly augmented the abundance of Lactobacillus influviei , Ruminococcaceae bacterium , Enterococcus cecorum , Faecalococcus pleomorphus , and Veillonella magna . Conversely, FMT led to a significant decrease in the abundance of the genera Rikenella , Epsilonproteobacteria , Sutterella , Collinsella tanakaei , Helicobacteraceae , Mucispirillum , and Deferribacterales . These differences were evident in the core microbiota compositions in the FMT and CON groups. Figure 3 Correlations between cecum microbiota and growth performance To explore the correlation between the abunance of the genus in the cecum and duck growth performance, a Spearman correlation analysis was performed to evaluate the potential link between alterations in gut microbiota composition and growth performance in ducks (Fig. 4 ). The genera Megamonas (r = 0.633; P = 0.009), Subdoligranulum (r = 0.668; P = 0.005), and Lactobacillus (r = 0.553; P = 0.026) were positively correlated with growth performance, but genera Oscillospira (r = − 0.505; P = 0.046), Mucispirillum (r = − 0.638; P = 0.008), Sutterella (r = − 0.548; P = 0.028), and Anaerobiospirillum (r = − 0.581; P = 0.018) were negatively correlated with growth performance. Figure 4 Discussion Fecal microbiota transplantation (FMT) is an emergent technique that reshapes the gut microbiome of the recipient in birds. 22 . Several studies demonstrated that the intestinal microbiome is closely associated with duck growth performance 1 , 3 , 4 , 7 . Nevertheless, the available data regarding the effects of FMT on the cecal microbiota of ducks remain relatively limited. The intestinal microbiota is rapidly established and evolves continuously after hatching due to environmental exposure in poultry by approximately 42 days of age. The intestinal microbial community achieves a stable state characterized by increased structural diversity 23 . Further investigations were carried out to analyze the cecal microbiota of ducks in the FMT and CON groups to elucidate the beneficial effects of fecal microbiota transplantation (FMT). The diversity of gut microbiota is a reliable indicator of host health, and higher microbial diversity is generally associated with improved host health outcomes. 24 . Notably, in this study, FMT might have distinctly altered the microbial community diversity and abundance, as seen by the elevated Ace, Chao1, Shannon, and Simpson indices. Additionally, the cecum microbiota in the FMT and CON groups showed evident differences in beta diversity. Also, it was reported that various Firmicutes and Bacteroidetes phyla members contribute positively to host health and growth performance 25 , 26 . For example, an elevation in Firmicutes has been associated with enhanced nutrient absorption and increased body weight (BW) gain 27 , 28 . It is worth mentioning that the Firmicutes/Bacteroidetes ratio is a crucial indicator of microbiota functionality, with a higher ratio favoring the reduction of pathogenic organisms 29 . Our findings showed that FMT raised the Firmicutes/Bacteroidetes ratio, which aligns with results from a previous study 30 . Given the observed increase in the Firmicutes/Bacteroidetes ratio alongside improved average daily gain (ADG), we postulated that the alterations in the Firmicutes/Bacteroidetes ratios induced by FMT treatment might contribute to the enhanced growth performance observed in ducks. Several studies have indicated that FMT could modulate the gut microbiome of birds by reconstituting their intestinal microecology. This process alters host phenotypic traits by regulating nutrient metabolism and increasing feed intake and body weight, positively impacting bird growth performance. 31 , 32 . Differential analysis data from the taxonomic cladogram obtained by LEfSe revealed that FMT treatment increased the abundance of several beneficial bacteria, such as Lactobacillus , Bifidobacterium , Subdoligranulum , and Lactobacillus influviei , which contributes to the maintenance of the overall microbiota structure. These findings are partially consistent with the results reported in previous studies 22 , 33 . Subdoligranulum is known as a butyrate-producing bacteria 34 . Microbially derived butyrate has been revealed to improve intestinal epithelial barrier function in poultry 35 . Correspondingly, the Subdoligranulum benefits necrotizing enterocolitis (NEC) by modulating the bacterial phage population and enhancing butyrate production, which is crucial for maintaining gut health and reducing inflammation 36 . In our study, the relative abundances of the Subdoligranulum were positively correlated with average daily gain (ADG). In addition, SCFAs produced by gut microbiota play a vital role in enhancing ducks' antioxidant and anti-inflammatory capacities 37 . Lactobacillus ingluviei , a novel strain of probiotic lactic acid bacteria, has demonstrated several beneficial effects on birds, such as anti- Salmonella activity and growth promotion 38 . Studies also revealed that L. ingluviei is associated with significant weight gain in ducks 39 . Recent studies have shown that a decrease in Lactobacillus abundance caused a reduction in bird growth performance because optimal levels of stable Lactobacillus indicate balanced gut microbiome-mediated higher growth and vice versa 40 – 42 . Other studies also reported that increased Lactobacillus abundance in the intestine significantly improves bird growth performance. Conversely, decreased Lactobacillus levels allow harmful bacteria to proliferate, negatively impacting growth performance 43 , 44 . How the increased abundance of Lactobacillus in the cecum enhances duck growth performance is highly intriguing. Remarkably, the gastrointestinal (GI) tract of newly hatched birds is almost entirely non-colonized by microorganisms, and a diverse range of bacteria begins to colonize it as the bird develops 45 . We hypothesized that increased Lactobacillus could be suppressed via multiple mechanisms, including competitive exclusion and pathogen antagonism. The pathogenesis and colonization of harmful bacteria begin when they bind to the host's gut epithelium, triggering immune responses, disrupting the epithelial barrier, and enabling bacterial proliferation, leading to infection and inflammation 46 – 47 . However, owing to their competitive advantages over other bacteria, if Lactobacilli successfully colonized the duck gut, they could prevent the colonization of pathogenic bacteria by avoiding their binding to the adhesion sites of the gut epithelium 46 . In agreement with these reports, our study demonstrated a significantly higher abundance of Lactobacillus in the FMT group than in the CON group. Thus, combined with the improvement in body weight gain of ducks, we can further speculate that FMT treatment could stimulate intestinal development and improve cecum health in ducks by facilitating the relative abundance of Subdoligranulum , Lactobacillus and L. ingluviei . Nonetheless, the specific Lactobacillus strains that play a crucial role in enhancing duck growth performance remain to be further investigated. Currently, the role of Megamonas in animal health is unclear. Interestingly, a cluster dominated by Megamonas , resembling an enterotype-like structure, is significantly associated with human obesity 48 . Growing evidence suggests that Alistipes are often viewed as harmful bacteria, with their increased abundance closely associated with inflammatory responses 49 . In the present study, FMT reduced the abundance of Alistipes and decreased the overall abundance of the phylum Proteobacteria, which is known to contain potential pathogenic bacteria. It should be noted that Anaerobiospirillum , Mucispirillum , and Sutterella , which are negatively associated with duck growth performance, could be potential pathogens. FMT showed an exciting prospect in improving the gut health of birds. Regrettably, our study has certain limitations that should be acknowledged. Firstly, identifying the composition of core microorganisms in fecal suspensions through 16S rRNA or metagenomic sequencing methods is crucial before FMT treatment. Secondly, conducting in vitro experiments simulating gastrointestinal digestion before FMT would be necessary, although in vitro experiments cannot ultimately reveal the complex interaction mechanism between the gastrointestinal microbiome and host in vivo 50 , 51 . Overall, these results indicated that the improved growth performance through FMT could be associated with reducing proinflammatory pathogen colonization in the duck cecum. This protective effect likely results from increased microbial diversity and enhanced cecal health. Conclusions Taken together, this study highlights the potential of fecal microbiota transplantation (FMT) as an emerging technique to reshape the recipient gut microbiome substantially in ducks. An early FMT could persistently improve duck growth performance by maintaining beneficial bacteria abundance at a higher level in the cecum, such as Lactobacillus , Bifidobacterium , and Subdoligranulum , which could keep the cecum healthy. These results contribute to an understanding that facilitating the bacterial diversity in the cecum by early microbiota transplantation is an effective way to improve duck growth performance. Future research should focus on optimizing FMT protocols for duck production by utilizing a more defined and precise microbiota consortium rather than relying on crude fecal microbes and exploring the long-term impacts on immune and metabolic functions. Declarations Acknowledgments We sincerely thank Guizhou University for offering the facilities and equipment essential for experimenting. We also extend our heartfelt gratitude to Professor S.L.Y for their invaluable guidance and support in preparing this article. Author Contributions Y.Y, B.L.Y, F.Y.L, and Z.Q.H made data curation; B.L.Y, F.Y.L, Z.Q.H, and P.S are involved in the Methodology; Y.Y and B.L.Y conducted the statistical analysis; Y.Y and S.L.Y wrote the original draft preparation; Y.Y and S.L.Y wrote and revised the manuscript. All authors have read and agreed to the published version of the manuscript. Funding This work was supported by the National Nature Science Foundation of China (No. 31960682), the Chinese Government Grant for Supporting the Development of Local Science and Technology (No. (2019)4021), the Agricultural Major Special Project of Guizhou Province (No. (2019)5203), the Special Research Projects of Guizhou Province (No. (2020)1Y041), and the Guizhou University College Students SRT Plan Project (No. GD SRT 20), respectively. Approval for animal experiments This experiment was approved by the Animal Ethics Committee of Guizhou University (No. EAE-GZU-2020-E012). We confirm that all methods were performed under relevant guidelines and regulations. Additionally, we confirm that we have fully complied with the latest version of the ARRIVE guidelines in this study 67 . Data Availability Raw data have been deposited to the National Center for Biotechnology Information (NCBI) under the BioProject number PRJNA1210849 (https://dataview.ncbi.nlm.nih.gov/object/PRJNA1210849?reviewer=5lkj28jecn65hcbsk758lqfe4k). All other data are available upon request to the corresponding author. Conflict of interest We certify no conflict of interest with any financial organization regarding the material discussed in the manuscript. References Liu, Y. et al. Temporal variation in production performance, biochemical and oxidative stress markers, and gut microbiota in Pekin ducks during the late growth stage. Poult. Sci. 103 , 103894. https://doi.org/10.1016/j.psj.2024.103894 (2024). Wu, D. et al. 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Microbiol. 55 , 939–945. https://doi.org/10.1007/s12275-017-7202-0 (2017). Ge, C. et al. Plant essential oils improve growth performance by increasing antioxidative capacity, enhancing intestinal barrier function, and modulating gut microbiota in Muscovy ducks. Poult. Sci. 102, 102813. https://doi.10.1016/j.psj.102813 (2023). (2023). Yang, J. et al. Ameliorative effect of buckwheat polysaccharides on colitis via regulation of the gut microbiota. Int. J. Biol. Macromol. 227, 872883. https://doi.10.1016/j.ijbiomac.12.155 (2023). (2022). Fu, Y. et al. Effects of early-life cecal microbiota transplantation from divergently selected inbred chicken lines on growth, gut serotonin, and immune parameters in recipient chickens. Poult. Sci. 101 , 101925. https://doi.org/10.1016/j.psj.2022.101925 (2022). Song, J. et al. Early fecal microbiota transplantation from high abdominal fat chickens affects recipient cecal microbiome and metabolism. Front. Microbiol. 14, 1332230. https://doi.10.3389/fmicb.1332230 (2024). (2023). Zhang, S. et al. Dietary supplementation of bilberry anthocyanin on growth performance, intestinal mucosal barrier and cecal microbes of chickens challenged with Salmonella Typhimurium. J. Anim. Sci. Biotechnol. 14, 15. https://doi.10.1186/s40104-022-00799-9 (2023). Radjabzadeh, D. et al. Gut microbiome-wide association study of depressive symptoms. Nat. Commun. 13, 7128. https://doi.10.1038/s41467-022-34502-3 (2022). Onrust, L. et al. Steering Endogenous Butyrate Production in the Intestinal Tract of Broilers as a Tool to Improve Gut Health. Front. Vet. Sci. 2 , 75. https://doi.org/10.3389/fvets.2015.00075 (2015). Lin, H. et al. Multiomics Study Reveals Enterococcus and Subdoligranulum Are Beneficial to Necrotizing Enterocolitis. Front. Microbiol. 12, 752102. https://doi.10.3389/fmicb.752102 (2021). (2021). Fu, Y. et al. Pleurotus eryngii polysaccharides alleviate aflatoxin B1-induced liver inflammation in ducks involving in remodeling gut microbiota and regulating SCFAs transport via the gut-liver axis. Int. J. Biol. Macromol. 271 , 132371. https://doi.org/10.1016/j.ijbiomac.2024.132371 (2024). Thomas, J. V. et al. Effect of Turkey-Derived Beneficial Bacteria Lactobacillus salivarius and Lactobacillus ingluviei on a Multidrug-Resistant Salmonella Heidelberg Strain in Turkey Poults. J Food Prot. 82, 435440. https://doi.10.4315/0362-028X.JFP-18-286 (2019). Angelakis, E. & Didier, R. The increase of Lactobacillus species in the gut flora of newborn broiler chicks and ducks is associated with weight gain. PloS one . 5 , e10463. https://doi.org/10.1371/journal.pone.0010463 (2010). Xi, Y. et al. Characteristics of the intestinal flora of specific pathogen free chickens with age. Microb. Pathog . 132 , 32534. https://doi.org/10.1016/j.micpath.2019.05.014 (2019). An, K. et al. Dietary Lactobacillus plantarum improves the growth performance and intestinal health of Pekin ducks. Poult. Sci. 101 , 101844. https://doi.org/10.1016/j.psj.2022.101844 (2022). Abdel-Moneim, A. E., Elbaz, A. M., Khidr, R. E. & Badri, F. B. Effect of in Ovo Inoculation of Bifidobacterium spp. on Growth Performance, Thyroid Activity, Ileum Histomorphometry, and Microbial Enumeration of Broilers. Probiotics Antimicrob. Proteins. 12, 873882. https://doi.10.1007/s12602-019-09613-x (2020). Forte, C. et al. Dietary Lactobacillus acidophilus positively influences growth performance, gut morphology, and gut microbiology in rurally reared chickens. Poult. Sci. 97 , 930936. https://doi.org/10.3382/ps/pex396 (2018). Shokryazdan, P. et al. Effects of a Lactobacillus salivarius mixture on performance, intestinal health and serum lipids of broiler chickens. PloS one . 12 , e0175959. https://doi.org/10.1371/journal.pone.0175959 (2017). Varmuzova, K. et al. Composition of Gut Microbiota Influences Resistance of Newly Hatched Chickens to Salmonella Enteritidis Infection. Front. Microbiol. 7 , 957. https://doi.org/10.3389/fmicb.2016.00957 (2016). Huang, R. et al. Lactobacillus and intestinal diseases: Mechanisms of action and clinical applications. Microbiol. Res. 260 , 127019. https://doi.org/10.1016/j.micres.2022.127019 (2022). Zeise, K. D. et al. Interplay between Candida albicans and Lactic Acid Bacteria in the Gastrointestinal Tract: Impact on Colonization Resistance, Microbial Carriage, Opportunistic Infection, and Host Immunity. Clin. Microbiol. Rev. 34 , e0032320. https://doi.org/10.1128/CMR.00323-20 (2021). Wu, C. et al. Obesity-enriched gut microbe degrades myo-inositol and promotes lipid absorption. Cell Host Microbe. 32, 13011314. https://doi.10.1016/j.chom.06.012 (2024). (2024). Cobo, F. et al. First description of abdominal infection due to Alistipes onderdonkii. Anaerobe 66 , 102283. https://doi.org/10.1016/j.anaerobe.2020.102283 (2020). Zhang, T. et al. Washed microbiota transplantation vs. manual fecal microbiota transplantation: clinical findings, animal studies and in vitro screening. Protein Cell. 11 , 251–266. https://doi.org/10.1007/s13238-019-00684-8 (2020). Ma, Z. et al. Fecal microbiota transplantation improves chicken growth performance by balancing jejunal Th17/Treg cells. Microbiome 11, 137. (2023). https://doi.org/10.1186/s40168-023-01569-z Additional Declarations No competing interests reported. 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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-5863134","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":434757874,"identity":"380fbd79-ed67-4be3-b7b8-92c739d077aa","order_by":0,"name":"Yong Yue","email":"","orcid":"","institution":"Guizhou University","correspondingAuthor":false,"prefix":"","firstName":"Yong","middleName":"","lastName":"Yue","suffix":""},{"id":434757875,"identity":"d363db1a-2a5e-41e6-9691-3306c7ffb454","order_by":1,"name":"Bingnong Yao","email":"","orcid":"","institution":"Guizhou University","correspondingAuthor":false,"prefix":"","firstName":"Bingnong","middleName":"","lastName":"Yao","suffix":""},{"id":434757876,"identity":"9ca6eec9-0509-4200-b63d-cc53082bbfe0","order_by":2,"name":"Fuyou Liao","email":"","orcid":"","institution":"Guizhou University","correspondingAuthor":false,"prefix":"","firstName":"Fuyou","middleName":"","lastName":"Liao","suffix":""},{"id":434757877,"identity":"69a3389d-9a2e-4e1a-8098-0ab924db984c","order_by":3,"name":"Zhiqiang He","email":"","orcid":"","institution":"Guizhou University","correspondingAuthor":false,"prefix":"","firstName":"Zhiqiang","middleName":"","lastName":"He","suffix":""},{"id":434757878,"identity":"42091721-1948-4499-8fb9-2b3dce65fbd0","order_by":4,"name":"Papungkorn Sangsawad","email":"","orcid":"","institution":"Suranaree University of Technology","correspondingAuthor":false,"prefix":"","firstName":"Papungkorn","middleName":"","lastName":"Sangsawad","suffix":""},{"id":434757879,"identity":"cf574415-adf7-4c16-9169-475f6fbb2ff8","order_by":5,"name":"Shenglin Yang","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA7UlEQVRIiWNgGAWjYBAC+RlAgrFBgsHgAJDxwcBGjqAWgxtIWhhnFKQZE9YiAdbCwCAJxMw8Hw4nEtYi3Xzs4dcGizx+9rOHX9sYMCcwsB8+ugGvX+YcSzeWbZAoZuPJS7POMWDLY+BJS7uB15obOWbSkg0SiW0MOWbGOQY8xQwSPGYEtOR/g2jhf2NmbGEgkdhAWEsOm+RHkBaJHOPHDAYGhLUY3Egzk2YEa3ljxthjkGDMRsgv8jOSn0n+/FMHdFiO8Ycff/7L8bMfPobfYQyg6IDQbBJgkpByEGD8AdX6gRjVo2AUjIJRMPIAAD+PSRMokqhnAAAAAElFTkSuQmCC","orcid":"","institution":"Guizhou University","correspondingAuthor":true,"prefix":"","firstName":"Shenglin","middleName":"","lastName":"Yang","suffix":""}],"badges":[],"createdAt":"2025-01-20 06:38:17","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5863134/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5863134/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41598-025-04942-0","type":"published","date":"2025-07-01T15:58:52+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":79423362,"identity":"ee25bb29-32c3-4a43-b8f9-4eced4651eb6","added_by":"auto","created_at":"2025-03-28 09:00:45","extension":"jpeg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":78965,"visible":true,"origin":"","legend":"\u003cp\u003eEffects of FMT on the growth performance of ducks.\u003cstrong\u003e \u003c/strong\u003e(\u003cstrong\u003ea\u003c/strong\u003e) Average daily gain from 1 to 14 days, (\u003cstrong\u003eb\u003c/strong\u003e) Average daily gain from 15 to 28 days, (\u003cstrong\u003ec\u003c/strong\u003e) Body weight from 1 to 14 days (\u003cstrong\u003ed\u003c/strong\u003e) Body weight from 15 to 28 days, (\u003cstrong\u003ee\u003c/strong\u003e) Feed conversion rate from 1 to 28 days. *P \u0026lt; 0.05, **P \u0026lt; 0.01, ***P \u0026lt; 0.001.\u003c/p\u003e","description":"","filename":"floatimage1.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-5863134/v1/3b4017b1c06e09a608f6d238.jpeg"},{"id":79423364,"identity":"9c50c232-d4e3-4456-b23a-7fe0dfc38caf","added_by":"auto","created_at":"2025-03-28 09:00:45","extension":"jpeg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":219562,"visible":true,"origin":"","legend":"\u003cp\u003eFMT changes the community composition of cecum microbiota. (\u003cstrong\u003ea\u003c/strong\u003e)\u003cstrong\u003e \u003c/strong\u003eThe phyla are in the top 5 abundance and average abundance, (\u003cstrong\u003eb\u003c/strong\u003e) Relative abundance of genus (\u003cstrong\u003ec\u003c/strong\u003e) Principal component analysis in FMT and CON groups, (\u003cstrong\u003ed\u003c/strong\u003e) The genus of beta diversity heatmap. *P \u0026lt; 0.05, **P \u0026lt; 0.01, ***P \u0026lt; 0.001.\u003c/p\u003e","description":"","filename":"floatimage2.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-5863134/v1/96216d849e06ee010becd9cf.jpeg"},{"id":79423363,"identity":"7785411d-ab06-4400-b58e-1e7d3e70d7c1","added_by":"auto","created_at":"2025-03-28 09:00:45","extension":"jpeg","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":230556,"visible":true,"origin":"","legend":"\u003cp\u003eFMT alters the alpha diversity of the cecum microbiota and enriches specific bacterial populations. (\u003cstrong\u003ea\u003c/strong\u003e) Alpha diversity analysis of cecal microbiota, including ACE, Chao, Shannon, and Simpson indexes, (\u003cstrong\u003eb\u003c/strong\u003e) Differential analysis of core microbial genera in cucum, (\u003cstrong\u003ec,d\u003c/strong\u003e) The taxonomic cladogram obtained by linear discriminant analysis effect size (LEfSe). *P \u0026lt; 0.05, **P \u0026lt; 0.01, ***P \u0026lt; 0.001.\u003c/p\u003e","description":"","filename":"floatimage3.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-5863134/v1/07948b0b7595f6ba57239383.jpeg"},{"id":79422874,"identity":"2554caa0-0e39-4c44-90ec-d0a13d7c79c6","added_by":"auto","created_at":"2025-03-28 08:52:45","extension":"jpeg","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":167861,"visible":true,"origin":"","legend":"\u003cp\u003eCorrelations between cecum microbiota and average daily gain in ducks.. *P \u0026lt; 0.05, **P \u0026lt; 0.01, ***P \u0026lt; 0.001.\u003c/p\u003e","description":"","filename":"floatimage4.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-5863134/v1/80dfe6017bcf52e6e5d18dd7.jpeg"},{"id":86179704,"identity":"2840bb61-b868-4308-bdd1-5efe745b52ac","added_by":"auto","created_at":"2025-07-07 16:18:35","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1567763,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5863134/v1/7580eb2d-56d2-4f5c-a68e-8cc27d42eabc.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Fecal microbiota transplantation improves Sansui duck growth performance by balancing the cecum microbiome","fulltext":[{"header":"Introduction","content":"\u003cp\u003eIn recent years, the gut microbiome, frequently called a \"microbial organ,\" has garnered significant research attention due to its symbiotic relationship with host health and critical roles in nutrient digestion and absorption, immune system development, and protection against pathogens\u003csup\u003e\u003cspan additionalcitationids=\"CR2\" citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e\u003c/sup\u003e. Maintaining a balanced intestinal microbiota benefits the host by inhibiting pathogen colonization, enhancing intestinal barrier integrity, supporting normal nutrient metabolism, and fostering the proliferation of commensal microbes\u003csup\u003e\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e\u003c/sup\u003e. Moreover, the gut microbiota plays a crucial role in breaking down various food components and nutrients and synthesizing a range of metabolites that interact with the host\u003csup\u003e\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e,\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e\u003c/sup\u003e. The gut microbiota is a diverse and complex community of microorganisms that colonizes ducks' gastrointestinal (GI) tract, with the cecum exhibiting the highest microbial diversity and dynamic population\u003csup\u003e\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e,\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e\u003c/sup\u003e. Research on the duck cecum has consistently emphasized the role of gut microbiota in enhancing feed digestion, nutrient absorption, host defense, and immune function\u003csup\u003e\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e,\u003cspan additionalcitationids=\"CR8\" citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e\u003c/sup\u003e. A stable gut microbiota supports the host by preventing colonization, facilitating pathogen clearance, and enhancing growth performance\u003csup\u003e\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eNotably, over the past decade, fecal microbiota transplantation (FMT) and probiotic supplementation have emerged as promising therapeutic and preventive approaches for reestablishing intestinal microbiota, mitigating inflammatory responses, and promoting growth and development\u003csup\u003e\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e,\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e\u003c/sup\u003e. For instance, transferring fecal microbiota from healthy chickens could influence the early establishment of gut microbiota in recipient chicks, potentially leading to long-term effects on host-microbe interactions and development\u003csup\u003e\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e\u003c/sup\u003e. It is reassuring that FMT has shown potential in enhancing weight gain and pathogen resistance in broilers\u003csup\u003e\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e\u003c/sup\u003e. Glendinning et al.\u003csup\u003e\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e\u003c/sup\u003e demonstrated that transplanting cecal microbiota from Roslin broilers to different chicken breeds during the first week of life increased the richness and diversity of microbiota in the recipients. Furthermore, FMT has enhanced intestinal morphology in broilers by increasing the thickness of serous membranes and muscle layers\u003csup\u003e\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eManipulating gut microbiota through FMT or probiotics has been demonstrated to influence chicken growth and development. For instance, transferring fecal microbiota from 30-day-old chickens with high feed efficiency to newly hatched chicks has increased feed intake and body weight in female chickens\u003csup\u003e\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e\u003c/sup\u003e. Similarly, administering fecal microbiota from chickens with high feed conversion ratios affects early gut microbiota colonization, intestinal permeability, gut morphology, and innate immune responses in recipients\u003csup\u003e\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e\u003c/sup\u003e. Probiotic supplementation, comprising strains such as \u003cem\u003eLactobacillus reuteri\u003c/em\u003e, \u003cem\u003eBacillus subtilis\u003c/em\u003e, and \u003cem\u003eSaccharomyces cerevisiae\u003c/em\u003e, has improved plasma immunoglobulin levels and enhanced growth performance in chickens\u003csup\u003e\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eMoreover, gut microbes produce diverse metabolites derived from dietary components or endogenous substrates, which mediate host-microbiota communication, particularly at the microbiota-mucosal interface\u003csup\u003e\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e\u003c/sup\u003e. Alterations in gut microbiota composition are often accompanied by changes in microbial metabolites and their interactions with gut epithelial cells. For example, dietary fiber supports the growth of short-chain fatty acid (SCFA) producing bacteria, and the SCFAs, especially butyrate, serve as an energy source for gut epithelial cells, promoting their growth and function\u003csup\u003e\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e\u003c/sup\u003e. This study investigates the effects of fecal microbiota on the growth performance of Sansui ducks using 16S rRNA gene amplicon sequencing. We aimed to integrate FMT into the management of duck production, presenting a novel approach to improving duck growth performance.\u003c/p\u003e"},{"header":"Materials and Methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eExperimental Conditions\u003c/h2\u003e \u003cp\u003eA total of 120 1-day-old Sansui ducks were selected as recipients and randomly divided into two groups: a control (CON) group (n\u0026thinsp;=\u0026thinsp;60) and a fecal microbiota transplantation (FMT) group (n\u0026thinsp;=\u0026thinsp;60); each group comprised four replicates. The ducks were distributed into ten cages (0.65 m H \u0026times; 0.8 m W \u0026times; 1.2 m D), and the experiment lasted 42 days. The initial temperature was maintained at 37\u0026thinsp;\u0026plusmn;\u0026thinsp;1 ℃, with a systematic weekly reduction of 2 ℃ until ambient room temperature was achieved. Humidity levels were sustained between 65\u0026ndash;70%, and a light-dark cycle of 23:1 was implemented. The duck house was cleaned each morning and disinfected daily with a 5% sodium hypochlorite solution. From the 1st day, ducks in the FMT group orally received fecal suspension with 0.5 mL every afternoon for 3 days. Ducks in the CON group orally received PBS with 0.5 mL, and the ducks had free access to feed and water during the experiment. The ingredients and nutrient composition of the experimental diets are shown in 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\u003eIngredients and chemical composition of the experimental diets.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"2\"\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 \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eIngredients,%\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eContent,%\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCorn\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e63.85\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSoybean meal\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e27.83\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eWheat bran\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e1.50\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eRaPeseed cake\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e4.00\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCaHPO\u003csub\u003e4\u003c/sub\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e1.50\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eLimestone\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0.85\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNaCl\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0.25\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePremix\u003csup\u003ea\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0.22\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTotal\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e100.00\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c2\" namest=\"c1\"\u003e \u003cp\u003eNutrient levels\u003csup\u003eb\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCrude protein\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e18.92\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMetabo lizable energy, MJ/kg\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e11.78\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCalcium\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0.81\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTotal phosphorus\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0.42\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eLysine\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0.95\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMethionine\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0.292\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003ctfoot\u003e \u003ctr\u003e\u003ctd colspan=\"2\"\u003e\u003csup\u003ea\u003c/sup\u003eThe premix provided the following per kg of diets: Vitamin A 4 000 IU; Vitamin 20 mg; Vitamin K32 mg; Vitamin B1 3. 5 mg; Vitamin B12 0.01 mg; Folic acid 1.0 mg; Copper 10 mg; Iron 80 mg; Manganese 60 mg; Zinc 60 mg; Deng 0.4 mg; Selenium 0.2 mg; Niacin 50 mg; Biotin 0.1 mg; Calcium pantothenate 10 mg; Pyridoxine 2.5 mg. 10 mg; pyridoxine 2.5 mg. \u003csup\u003eb\u003c/sup\u003eCrude protein was measured values; while the others were calculated values.\u003c/td\u003e\u003c/tr\u003e \u003c/tfoot\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eTable\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003ePreparation of fecal microbiota suspension\u003c/h3\u003e\n\u003cp\u003eSix healthy female Sansui ducks with the same genetic background (42-day-old) were selected as fecal donors. Once the donor ducks defecated in the morning, the excreta's white part was removed immediately because it mainly comprised of uric acid. Feces (15g) were collected daily in a sterile tube (50 mL). Based on ELISA, \u003cem\u003eE. coli-phage\u003c/em\u003e and \u003cem\u003eSalmonella-\u003c/em\u003ephage ELISA kits (48T) were purchased from Zhejiang of China Zhiyi Biotechnology Co., Ltd. \u003cem\u003eEscherichia coli\u003c/em\u003e and \u003cem\u003eSalmonella\u003c/em\u003e were rapidly detected by ELISA, and 15g of feces without \u003cem\u003eEscherichia coli\u003c/em\u003e and \u003cem\u003eSalmonella\u003c/em\u003e were selected and homogenized in 150 mL of sterile PBS and centrifuged for 5min at 2000 r.p.m., 4\u0026deg;C. The mixture was kept on ice until precipitates were fully settled, and the supernatant was collected and filtered with sterile gauze to get fecal suspension. The microbial suspensions were stored at -80\u0026deg;C until used for FMT.\u003c/p\u003e\n\u003ch3\u003eSample collection and growth performance\u003c/h3\u003e\n\u003cp\u003eThe rearing cycle of ducks was 42 days, and ducks were weighed in duplicates at 1, 14, and 28 days. Feed consumption was monitored throughout the study period for each group, and the average daily feed intake (ADFI), body weight (BW), average daily gain (ADG), and feed conversation rate (FCR) for each replicate were then computed. At 42 days into the feeding study, we randomly selected two birds from each replicate, which were euthanized through cervical dislocation following a 12 h feed deprivation, and their cecal contents samples were collected, frozen in liquid nitrogen, and stored at -80\u0026deg;C for subsequent analysis.\u003c/p\u003e\n\u003ch3\u003eMicrobial genomic DNA extraction and 16S rRNA gene sequencing\u003c/h3\u003e\n\u003cp\u003eThe cecal contents were used from 200 mg samples using the QIAamp DNA Stool Mini Kit (QIAGEN, Hilden, Germany) following the manufacturer's instructions. A total of 16 samples were used for 16S rDNA sequencing, eight samples per group. The hypervariable regions V3-V4 of the bacterial 16S rRNA gene were amplified with the forward primer 357F (5'-ACTCCTACGGRAGGCAGCAG-3') and reverse primer 806R (5'-GGACTACHVGGGTWTCTAAT-3'). DNA sequencing was performed on a Novaseq sequencer (Illumina) with services from TinyGene Bio-Tech.\u003c/p\u003e \u003cp\u003eThe PCR reaction was set up in a 50 \u0026micro;L mixture containing 1\u0026ndash;2 \u0026micro;L of DNA, 200 \u0026micro;M dNTPs, 0.2 \u0026micro;M primers, 10 \u0026micro;L of 5X buffer, and 1 U Phusion DNA Polymerase. The amplification program included an initial denaturation at 94\u0026deg;C for 2 minutes, followed by 25 cycles (94\u0026deg;C for 30, 56\u0026deg;C for 30, 72\u0026deg;C for 30), and a final extension at 72\u0026deg;C for 5 minutes. After PCR, barcoded products were purified using a DNA gel extraction kit (Axygen) and quantified with an FTC-3000 PCR system. For the second PCR, dual barcodes were added, and amplification conditions were as follows: denaturation at 94\u0026deg;C for 3 minutes, followed by eight cycles (94\u0026deg;C for 30s, 56\u0026deg;C for 30s, 72\u0026deg;C for 30s), and final extension at 72\u0026deg;C for 5 minutes. The library was purified and sequenced with paired-end reads on the Novaseq platform.\u003c/p\u003e\n\u003ch3\u003eSequencing data analysis\u003c/h3\u003e\n\u003cp\u003eThe raw 16S rRNA gene sequencing reads were demultiplexed according to their barcodes. All paired-end (PE) reads were processed with Trimmomatic (version 0.35) to eliminate low-quality bases, applying the parameters (SLIDING WINDOW: 50:20, MINLEN: 50). Subsequently, the trimmed reads were merged using the FLASH program (version 1.2.11) with default settings. Low-quality contigs were discarded via the screen.seqs command, using the following criteria: maxambig\u0026thinsp;=\u0026thinsp;0, minlength\u0026thinsp;=\u0026thinsp;200, maxlength\u0026thinsp;=\u0026thinsp;485, and maxhomop\u0026thinsp;=\u0026thinsp;8.\u003c/p\u003e \u003cp\u003eFor 16S sequence analysis, a combination of software tools was employed: Mothur (version 1.33.3), UPARSE (search version v8.1.1756, \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://drive5.com/uparse\u003c/span\u003e\u003cspan address=\"http://drive5.com/uparse\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e), and R (version 3.6.3). The demultiplexed reads were clustered into operational taxonomic units (OTUs) at 97% sequence identity, and singleton OTUs were removed using the UPARSE pipeline (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://drive5.com/usearch/manual/uparse_cmds.html\u003c/span\u003e\u003cspan address=\"http://drive5.com/usearch/manual/uparse_cmds.html\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e). With the classification, the taxonomic assignment of OTU representative sequences was performed against the Silva 128 database, using a confidence threshold of \u0026ge;\u0026thinsp;0.6. Seqs command in Mothur. OTU taxonomies, ranging from phylum to species, were determined based on the NCBI database. For the analysis of alpha diversity, indices including Shannon, Simpson, Chao1, ACE, and rarefaction curves were calculated using Mothur and visualized with R. Beta diversity was assessed by calculating the weighted and unweighted UniFrac distance matrices using Mothur, with visualization performed through Principal Coordinate Analysis (PCoA) using the ape package in R, Non-metric multidimensional scaling (NMDS) was performed using the vegan package in R and hierarchical clustering using the end extend package in R. The Bray-Curtis and Jaccard metrics were calculated with the vegan package in R and visualized similarly to the UniFrac analysis. R and hierarchical clustering via the end extend package in R. Additionally, Bray-Curtis and Jaccard metrics were calculated with the vegan package in R and visualized in the same manner as the UniFrac analysis.\u003c/p\u003e \u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003eStatistical analysis\u003c/h2\u003e \u003cp\u003eData were collected and tabulated separately for each treatment. First, a normality test was performed to assess the distribution of the data. Statistical analysis was conducted using SPSS software for Windows (Version 19.0; SPSS Inc., Armonk, NY, USA). One-way ANOVA was applied to compare more than two groups, followed by Tukey's post-hoc multiple comparison test. An unpaired two-tailed t-test was used to compare the two groups. Data are expressed as the mean\u0026thinsp;\u0026plusmn;\u0026thinsp;standard error (SE). Statistical significance was set at P\u0026thinsp;\u0026lt;\u0026thinsp;0.05.\u003c/p\u003e \u003c/div\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec10\" class=\"Section2\"\u003e \u003ch2\u003eFMT improves growth performance in Sansui ducks\u003c/h2\u003e \u003cp\u003eThe growth performance of ducks was significantly enhanced following FMT treatment compared to the control (CON) group, as evidenced by improvements in average daily gain (ADG), body weight (BW), and feed conversion rate (FCR). During the first 1\u0026ndash;14 days, the FMT group achieved a significantly higher ADG (P\u0026thinsp;\u0026lt;\u0026thinsp;0.001) compared to the CON group (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ea,b), and this improvement continued during the 15\u0026ndash;28 day period, with a similarly significant increase (P\u0026thinsp;\u0026lt;\u0026thinsp;0.001). Moreover, BW in the FMT group was markedly greater (P\u0026thinsp;\u0026lt;\u0026thinsp;0.001) than that of the CON group during both the 1\u0026ndash;14 and 15\u0026ndash;28 day intervals (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ec,d). Although the feed conversion rate was insignificant (P\u0026thinsp;\u0026gt;\u0026thinsp;0.05), there was a linear increasing trend in which the FMT group exhibited a lower FCR over the entire 1\u0026ndash;28 day period (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ee).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eFigure \u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec11\" class=\"Section2\"\u003e \u003ch2\u003eFMT changes the community composition of cecum microbiota\u003c/h2\u003e \u003cp\u003eTo investigate the effects of FMT on the community composition of cecum microbiota in ducks, we utilized 16S rRNA sequencing and comprehensive microbiome analysis. Microbiome analysis revealed profound changes in the composition of the phylum and genus in the cecum (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). Specifically, at the phylum level (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003ea), Firmicutes and Bacteroides were the two phyla that accounted for the immense proportions, Actinobacteria was an enriched bacteria in the FMT group (P\u0026thinsp;=\u0026thinsp;0.039). In contrast, the average abundance of Proteobacteria was lower than the CON group (P\u0026thinsp;\u0026gt;\u0026thinsp;0.05). Remarkably, the phyla Firmicutes / Bacteroidetes ratio in the FMT group was higher than in the CON group (P\u0026thinsp;\u0026gt;\u0026thinsp;0.05). At the genus level (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eb), the top 3 abundance bacteria in the FMT group were \u003cem\u003eBacteroides\u003c/em\u003e (25.71%), \u003cem\u003eFusobacterium\u003c/em\u003e (7.42%), and \u003cem\u003eAlistipes\u003c/em\u003e (3.18%). In comparison, the CON group was \u003cem\u003eBacteroides\u003c/em\u003e (30.20%), \u003cem\u003eFusobacterium\u003c/em\u003e (5.48%), and \u003cem\u003eAlistipes\u003c/em\u003e (4.74%). Additionally, as demonstrated through principal component analysis (PCA) and the heatmap of beta diversity analyses, they showed distinct clustering between FMT and CON groups, signifying substantial differences in microbial community composition (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003ec,d).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eFigure \u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec12\" class=\"Section2\"\u003e \u003ch2\u003eFMT alters the alpha diversity of the cecum microbiota and enriches specific bacterial populations\u003c/h2\u003e \u003cp\u003eAs illustrated in Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003ea, FMT significantly enriched the alpha diversity of the cecum microbiota, as evidenced by significantly higher values in the FMT group of the ACE (P\u0026thinsp;\u0026lt;\u0026thinsp;0.001), Chao (P\u0026thinsp;\u0026lt;\u0026thinsp;0.001), Shannon (P\u0026thinsp;\u0026lt;\u0026thinsp;0.001), and Simpson (P\u0026thinsp;\u0026lt;\u0026thinsp;0.001) indices compared to the CON group. Notably, FMT significantly enriched core bacterial genera (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eb), including \u003cem\u003eLactobacillus\u003c/em\u003e (P\u0026thinsp;\u0026lt;\u0026thinsp;0.001), \u003cem\u003eBifidobacterium\u003c/em\u003e (P\u0026thinsp;=\u0026thinsp;0.006), \u003cem\u003eMegamonas\u003c/em\u003e (P\u0026thinsp;=\u0026thinsp;0.008), and \u003cem\u003eSubdoligranulum\u003c/em\u003e (P\u0026thinsp;=\u0026thinsp;0.005). Likewise, evident from the taxonomic cladogram obtained by linear discriminant analysis effect size (LEfSe) (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003ec,d), LEfSe identified signature genera associated with FMT treatment, which includes \u003cem\u003ePeptococcus\u003c/em\u003e, \u003cem\u003eFaecalitalea\u003c/em\u003e, \u003cem\u003eStreptococcus\u003c/em\u003e, and \u003cem\u003eTuricibacter\u003c/em\u003e. In addition, FMT markedly increased the abundance of the class Coriobacteriia. Particularly, the orders of Lactobacillales, Bifidobacteriales, Selenomonadales, and Coriobacteriales were spotlighted, with a pronounced increase in the families \u003cem\u003eBifidobacteriaceae\u003c/em\u003e, \u003cem\u003ePeptococcaceae\u003c/em\u003e, \u003cem\u003eCoriobacteriaceae\u003c/em\u003e, and \u003cem\u003eEnterococcaceae\u003c/em\u003e. Similarly, at the species level, FMT significantly augmented the abundance of \u003cem\u003eLactobacillus influviei\u003c/em\u003e, \u003cem\u003eRuminococcaceae bacterium\u003c/em\u003e, \u003cem\u003eEnterococcus cecorum\u003c/em\u003e, \u003cem\u003eFaecalococcus pleomorphus\u003c/em\u003e, and \u003cem\u003eVeillonella magna\u003c/em\u003e. Conversely, FMT led to a significant decrease in the abundance of the genera \u003cem\u003eRikenella\u003c/em\u003e, \u003cem\u003eEpsilonproteobacteria\u003c/em\u003e, \u003cem\u003eSutterella\u003c/em\u003e, \u003cem\u003eCollinsella tanakaei\u003c/em\u003e, \u003cem\u003eHelicobacteraceae\u003c/em\u003e, \u003cem\u003eMucispirillum\u003c/em\u003e, and \u003cem\u003eDeferribacterales\u003c/em\u003e. These differences were evident in the core microbiota compositions in the FMT and CON groups.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eFigure \u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec13\" class=\"Section2\"\u003e \u003ch2\u003eCorrelations between cecum microbiota and growth performance\u003c/h2\u003e \u003cp\u003eTo explore the correlation between the abunance of the genus in the cecum and duck growth performance, a Spearman correlation analysis was performed to evaluate the potential link between alterations in gut microbiota composition and growth performance in ducks (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e). The genera \u003cem\u003eMegamonas\u003c/em\u003e (r\u0026thinsp;=\u0026thinsp;0.633; P\u0026thinsp;=\u0026thinsp;0.009), \u003cem\u003eSubdoligranulum\u003c/em\u003e (r\u0026thinsp;=\u0026thinsp;0.668; P\u0026thinsp;=\u0026thinsp;0.005), and \u003cem\u003eLactobacillus\u003c/em\u003e (r\u0026thinsp;=\u0026thinsp;0.553; P\u0026thinsp;=\u0026thinsp;0.026) were positively correlated with growth performance, but genera \u003cem\u003eOscillospira\u003c/em\u003e (r\u0026thinsp;=\u0026thinsp;\u0026minus;\u0026thinsp;0.505; P\u0026thinsp;=\u0026thinsp;0.046), \u003cem\u003eMucispirillum\u003c/em\u003e (r\u0026thinsp;=\u0026thinsp;\u0026minus;\u0026thinsp;0.638; P\u0026thinsp;=\u0026thinsp;0.008), \u003cem\u003eSutterella\u003c/em\u003e (r\u0026thinsp;=\u0026thinsp;\u0026minus;\u0026thinsp;0.548; P\u0026thinsp;=\u0026thinsp;0.028), and \u003cem\u003eAnaerobiospirillum\u003c/em\u003e (r\u0026thinsp;=\u0026thinsp;\u0026minus;\u0026thinsp;0.581; P\u0026thinsp;=\u0026thinsp;0.018) were negatively correlated with growth performance.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eFigure \u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e\u003c/p\u003e \u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003eFecal microbiota transplantation (FMT) is an emergent technique that reshapes the gut microbiome of the recipient in birds.\u003csup\u003e\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e\u003c/sup\u003e. Several studies demonstrated that the intestinal microbiome is closely associated with duck growth performance\u003csup\u003e\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e,\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e,\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e,\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e\u003c/sup\u003e. Nevertheless, the available data regarding the effects of FMT on the cecal microbiota of ducks remain relatively limited. The intestinal microbiota is rapidly established and evolves continuously after hatching due to environmental exposure in poultry by approximately 42 days of age. The intestinal microbial community achieves a stable state characterized by increased structural diversity\u003csup\u003e\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e\u003c/sup\u003e. Further investigations were carried out to analyze the cecal microbiota of ducks in the FMT and CON groups to elucidate the beneficial effects of fecal microbiota transplantation (FMT). The diversity of gut microbiota is a reliable indicator of host health, and higher microbial diversity is generally associated with improved host health outcomes.\u003csup\u003e\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e\u003c/sup\u003e. Notably, in this study, FMT might have distinctly altered the microbial community diversity and abundance, as seen by the elevated Ace, Chao1, Shannon, and Simpson indices. Additionally, the cecum microbiota in the FMT and CON groups showed evident differences in beta diversity.\u003c/p\u003e \u003cp\u003eAlso, it was reported that various Firmicutes and Bacteroidetes phyla members contribute positively to host health and growth performance\u003csup\u003e\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e,\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e\u003c/sup\u003e. For example, an elevation in Firmicutes has been associated with enhanced nutrient absorption and increased body weight (BW) gain\u003csup\u003e\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e,\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e\u003c/sup\u003e. It is worth mentioning that the Firmicutes/Bacteroidetes ratio is a crucial indicator of microbiota functionality, with a higher ratio favoring the reduction of pathogenic organisms\u003csup\u003e\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e\u003c/sup\u003e. Our findings showed that FMT raised the Firmicutes/Bacteroidetes ratio, which aligns with results from a previous study\u003csup\u003e\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e\u003c/sup\u003e. Given the observed increase in the Firmicutes/Bacteroidetes ratio alongside improved average daily gain (ADG), we postulated that the alterations in the Firmicutes/Bacteroidetes ratios induced by FMT treatment might contribute to the enhanced growth performance observed in ducks.\u003c/p\u003e \u003cp\u003eSeveral studies have indicated that FMT could modulate the gut microbiome of birds by reconstituting their intestinal microecology. This process alters host phenotypic traits by regulating nutrient metabolism and increasing feed intake and body weight, positively impacting bird growth performance.\u003csup\u003e\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e,\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e\u003c/sup\u003e. Differential analysis data from the taxonomic cladogram obtained by LEfSe revealed that FMT treatment increased the abundance of several beneficial bacteria, such as \u003cem\u003eLactobacillus\u003c/em\u003e, \u003cem\u003eBifidobacterium\u003c/em\u003e, \u003cem\u003eSubdoligranulum\u003c/em\u003e, and \u003cem\u003eLactobacillus influviei\u003c/em\u003e, which contributes to the maintenance of the overall microbiota structure. These findings are partially consistent with the results reported in previous studies\u003csup\u003e\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e,\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e\u003c/sup\u003e. \u003cem\u003eSubdoligranulum\u003c/em\u003e is known as a butyrate-producing bacteria\u003csup\u003e\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e\u003c/sup\u003e. Microbially derived butyrate has been revealed to improve intestinal epithelial barrier function in poultry\u003csup\u003e\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e\u003c/sup\u003e. Correspondingly, the \u003cem\u003eSubdoligranulum\u003c/em\u003e benefits necrotizing enterocolitis (NEC) by modulating the bacterial phage population and enhancing butyrate production, which is crucial for maintaining gut health and reducing inflammation\u003csup\u003e\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e\u003c/sup\u003e. In our study, the relative abundances of the \u003cem\u003eSubdoligranulum\u003c/em\u003e were positively correlated with average daily gain (ADG).\u003c/p\u003e \u003cp\u003eIn addition, SCFAs produced by gut microbiota play a vital role in enhancing ducks' antioxidant and anti-inflammatory capacities\u003csup\u003e\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e\u003c/sup\u003e. \u003cem\u003eLactobacillus ingluviei\u003c/em\u003e, a novel strain of probiotic lactic acid bacteria, has demonstrated several beneficial effects on birds, such as anti-\u003cem\u003eSalmonella\u003c/em\u003e activity and growth promotion\u003csup\u003e\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e\u003c/sup\u003e. Studies also revealed that \u003cem\u003eL. ingluviei\u003c/em\u003e is associated with significant weight gain in ducks\u003csup\u003e\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e\u003c/sup\u003e. Recent studies have shown that a decrease in \u003cem\u003eLactobacillus\u003c/em\u003e abundance caused a reduction in bird growth performance because optimal levels of stable \u003cem\u003eLactobacillus\u003c/em\u003e indicate balanced gut microbiome-mediated higher growth and vice versa\u003csup\u003e\u003cspan additionalcitationids=\"CR41\" citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e\u003c/sup\u003e. Other studies also reported that increased \u003cem\u003eLactobacillus\u003c/em\u003e abundance in the intestine significantly improves bird growth performance. Conversely, decreased \u003cem\u003eLactobacillus\u003c/em\u003e levels allow harmful bacteria to proliferate, negatively impacting growth performance\u003csup\u003e\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e,\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eHow the increased abundance of \u003cem\u003eLactobacillus\u003c/em\u003e in the cecum enhances duck growth performance is highly intriguing. Remarkably, the gastrointestinal (GI) tract of newly hatched birds is almost entirely non-colonized by microorganisms, and a diverse range of bacteria begins to colonize it as the bird develops\u003csup\u003e\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e\u003c/sup\u003e. We hypothesized that increased \u003cem\u003eLactobacillus\u003c/em\u003e could be suppressed via multiple mechanisms, including competitive exclusion and pathogen antagonism. The pathogenesis and colonization of harmful bacteria begin when they bind to the host's gut epithelium, triggering immune responses, disrupting the epithelial barrier, and enabling bacterial proliferation, leading to infection and inflammation\u003csup\u003e\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e\u003c/sup\u003e. However, owing to their competitive advantages over other bacteria, if \u003cem\u003eLactobacilli\u003c/em\u003e successfully colonized the duck gut, they could prevent the colonization of pathogenic bacteria by avoiding their binding to the adhesion sites of the gut epithelium\u003csup\u003e\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e\u003c/sup\u003e. In agreement with these reports, our study demonstrated a significantly higher abundance of \u003cem\u003eLactobacillus\u003c/em\u003e in the FMT group than in the CON group. Thus, combined with the improvement in body weight gain of ducks, we can further speculate that FMT treatment could stimulate intestinal development and improve cecum health in ducks by facilitating the relative abundance of \u003cem\u003eSubdoligranulum\u003c/em\u003e, \u003cem\u003eLactobacillus\u003c/em\u003e and \u003cem\u003eL. ingluviei\u003c/em\u003e. Nonetheless, the specific \u003cem\u003eLactobacillus\u003c/em\u003e strains that play a crucial role in enhancing duck growth performance remain to be further investigated.\u003c/p\u003e \u003cp\u003eCurrently, the role of \u003cem\u003eMegamonas\u003c/em\u003e in animal health is unclear. Interestingly, a cluster dominated by \u003cem\u003eMegamonas\u003c/em\u003e, resembling an enterotype-like structure, is significantly associated with human obesity\u003csup\u003e\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e\u003c/sup\u003e. Growing evidence suggests that \u003cem\u003eAlistipes\u003c/em\u003e are often viewed as harmful bacteria, with their increased abundance closely associated with inflammatory responses\u003csup\u003e\u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e\u003c/sup\u003e. In the present study, FMT reduced the abundance of \u003cem\u003eAlistipes\u003c/em\u003e and decreased the overall abundance of the phylum Proteobacteria, which is known to contain potential pathogenic bacteria. It should be noted that \u003cem\u003eAnaerobiospirillum\u003c/em\u003e, \u003cem\u003eMucispirillum\u003c/em\u003e, and \u003cem\u003eSutterella\u003c/em\u003e, which are negatively associated with duck growth performance, could be potential pathogens.\u003c/p\u003e \u003cp\u003eFMT showed an exciting prospect in improving the gut health of birds. Regrettably, our study has certain limitations that should be acknowledged. Firstly, identifying the composition of core microorganisms in fecal suspensions through 16S rRNA or metagenomic sequencing methods is crucial before FMT treatment. Secondly, conducting in vitro experiments simulating gastrointestinal digestion before FMT would be necessary, although in \u003cem\u003evitro\u003c/em\u003e experiments cannot ultimately reveal the complex interaction mechanism between the gastrointestinal microbiome and host in \u003cem\u003evivo\u003c/em\u003e\u003csup\u003e\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e,\u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e51\u003c/span\u003e\u003c/sup\u003e. Overall, these results indicated that the improved growth performance through FMT could be associated with reducing proinflammatory pathogen colonization in the duck cecum. This protective effect likely results from increased microbial diversity and enhanced cecal health.\u003c/p\u003e"},{"header":"Conclusions","content":"\u003cp\u003eTaken together, this study highlights the potential of fecal microbiota transplantation (FMT) as an emerging technique to reshape the recipient gut microbiome substantially in ducks. An early FMT could persistently improve duck growth performance by maintaining beneficial bacteria abundance at a higher level in the cecum, such as \u003cem\u003eLactobacillus\u003c/em\u003e, \u003cem\u003eBifidobacterium\u003c/em\u003e, \u003cem\u003eand Subdoligranulum\u003c/em\u003e, which could keep the cecum healthy. These results contribute to an understanding that facilitating the bacterial diversity in the cecum by early microbiota transplantation is an effective way to improve duck growth performance. Future research should focus on optimizing FMT protocols for duck production by utilizing a more defined and precise microbiota consortium rather than relying on crude fecal microbes and exploring the long-term impacts on immune and metabolic functions.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgments\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe sincerely thank Guizhou University for offering the facilities and equipment essential for experimenting. We also extend our heartfelt gratitude to Professor S.L.Y for their invaluable guidance and support in preparing this article.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor Contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eY.Y, B.L.Y, F.Y.L, and Z.Q.H made data curation; B.L.Y, F.Y.L, Z.Q.H, and P.S are involved in the Methodology; Y.Y and B.L.Y conducted the statistical analysis; Y.Y and S.L.Y wrote the original draft preparation; Y.Y and S.L.Y wrote and revised the manuscript. All authors have read and agreed to the published version of the manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis work was supported by the National Nature Science Foundation of China (No. 31960682), the Chinese Government Grant for Supporting the Development of Local Science and Technology (No. (2019)4021), the Agricultural Major Special Project of Guizhou Province (No. (2019)5203), the Special Research Projects of Guizhou Province (No. (2020)1Y041), and the Guizhou University College Students SRT Plan Project (No. GD SRT 20), respectively.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eApproval for animal experiments\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis experiment was approved by the Animal Ethics Committee of Guizhou University (No. EAE-GZU-2020-E012). We confirm that all methods were performed under relevant guidelines and regulations. Additionally, we confirm that we have fully complied with the latest version of the ARRIVE guidelines in this study\u003csup\u003e67\u003c/sup\u003e.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData Availability\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eRaw data have been deposited to the National Center for Biotechnology Information (NCBI) under the BioProject number PRJNA1210849 (https://dataview.ncbi.nlm.nih.gov/object/PRJNA1210849?reviewer=5lkj28jecn65hcbsk758lqfe4k). All other data are available upon request to the corresponding author.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConflict of interest\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe certify no conflict of interest with any financial organization regarding the material discussed in the manuscript.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eLiu, Y. et al. 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(2023). \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1186/s40168-023-01569-z\u003c/span\u003e\u003cspan address=\"10.1186/s40168-023-01569-z\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific Reports","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Fecal microbiota transplantation, Cecum microbiota, Growth performance, Sansui ducks","lastPublishedDoi":"10.21203/rs.3.rs-5863134/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5863134/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eImproving growth performance is vital in poultry production. Although several studies have established associations between gut microbiota and growth, the direct impacts remain unclear. A total of 120 1-day-old Sansui ducks were randomly assigned to FMT and control (CON) groups. From the 1st day, ducks in the FMT group were orally administrated with 0.5 mL fecal microbiota suspension for three consecutive days, while sterile PBS solution was used as a substitute in the CON group. The results revealed that FMT substantially improved average daily gain (ADG) and body weight (BW) (P\u0026thinsp;\u0026lt;\u0026thinsp;0.001), with a tendency for a better feed conversion rate (FCR). LEfSe analysis determined that markedly increased the abundance of the genera \u003cem\u003eLactobacillus\u003c/em\u003e (P\u0026thinsp;\u0026lt;\u0026thinsp;0.001), \u003cem\u003eBifidobacterium\u003c/em\u003e (P\u0026thinsp;=\u0026thinsp;0.006), \u003cem\u003eMegamonas\u003c/em\u003e (P\u0026thinsp;=\u0026thinsp;0.008), and \u003cem\u003eSubdoligranulum\u003c/em\u003e (P\u0026thinsp;=\u0026thinsp;0.005) in FMT group. Similarly, the phyla Firmicutes/Bacteroidetes ratio was higher in the FMT group. Additionally, the ACE, Chao, Shannon, and Simpson indexes were also significantly higher in the FMT group (P\u0026thinsp;\u0026lt;\u0026thinsp;0.001). To sum up, FMT enhanced growth performance, which could be associated with reducing proinflammatory pathogen colonization in the duck cecum. This modulating effect likely results from increased microbial diversity and the enrichment of beneficial bacteria.\u003c/p\u003e","manuscriptTitle":"Fecal microbiota transplantation improves Sansui duck growth performance by balancing the cecum microbiome","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-03-28 08:52:40","doi":"10.21203/rs.3.rs-5863134/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-04-02T06:02:38+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-04-01T17:20:13+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"303287497644052373248333476421322483689","date":"2025-03-30T15:07:08+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-03-27T10:07:58+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-03-25T11:56:08+00:00","index":"","fulltext":""},{"type":"submitted","content":"Scientific Reports","date":"2025-03-19T17:45:36+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific Reports","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"71c31ad9-ab18-4ea0-87a6-e7e56de3b4e4","owner":[],"postedDate":"March 28th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":46292266,"name":"Biological sciences/Microbiology"},{"id":46292267,"name":"Biological sciences/Zoology"}],"tags":[],"updatedAt":"2025-07-07T16:09:59+00:00","versionOfRecord":{"articleIdentity":"rs-5863134","link":"https://doi.org/10.1038/s41598-025-04942-0","journal":{"identity":"scientific-reports","isVorOnly":false,"title":"Scientific Reports"},"publishedOn":"2025-07-01 15:58:52","publishedOnDateReadable":"July 1st, 2025"},"versionCreatedAt":"2025-03-28 08:52:40","video":"","vorDoi":"10.1038/s41598-025-04942-0","vorDoiUrl":"https://doi.org/10.1038/s41598-025-04942-0","workflowStages":[]},"version":"v1","identity":"rs-5863134","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5863134","identity":"rs-5863134","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}