ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Microbial Symbioses
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1602641
This article is part of the Research TopicNew Insights into the Avian Gut MicrobiomesView all 5 articles
Breed-Specific Gut Microbiota and Enterotype Divergence in Chinese Indigenous Ducks
Provisionally accepted
Hao Chen*
Yongfei Wu
Jing OuyangLuping WangJingyan Hu
Hongbo TangSumei ZhengYanpeng XiongYuren GaoYan WuRui XiongYuxuan HuangRui XuanYanhua Chen- Jiangxi Science and Technology Normal University, Nanchang, China
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The gut microbiota of domestic ducks plays an important role in digestion and absorption, immune regulation, and overall health. However, our knowledge about the gut microbial composition in ducks of various phylogeny is insufficient, especially if raised in the same farm environment. In this study, 260 fecal samples from 15 Chinese indigenous duck breeds living in a uniformed farm were collected and 16S rRNA gene sequencing was performed.In addition, 202 blood samples from these ducks were used for whole-genome sequencing (WGS). The WGS results showed that the these domestic duck breeds exhibit breed-specific genetic characteristics. The gut microbiota of different native duck breeds exhibited great similarity at the phylum level with the most dominant phyla being Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes, while harboring distinct gut microbial communities at finer taxonomic levels. The host genetic-specific are associated with the microbial of these duck breeds. The prediction of metagenomic functions showed that the metabolism and function of the gut microbiomes among different duck breeds were more similar than that of their species composition. In addition, Principal coordinates analysis (PCoA) revealed that the gut microbiota of the 15 duck breeds could be divided into two distinct enterotype clusters based on Jensen-Shannon distance (JSD) dissimilarities, with representative breeds corresponding to layer ducks and dual-purpose ducks, respectively. There was no difference in richness index of the gut microbial composition and function between the two enterotypes, but the Shannon index values was significantly different. This study investigated the gut microbial structure and diversity among domestic duck populations with different genetic backgrounds, providing new insights into the relationship between host genetic variation and gut microbiota.
Keywords: host species, Domestic duck, Gut Microbiota, 16S rRNA gene, Microbial Diversity
Received: 31 Mar 2025; Accepted: 20 Jun 2025.
Copyright: © 2025 Chen, Wu, Ouyang, Wang, Hu, Tang, Zheng, Xiong, Gao, Wu, Xiong, Huang, Xuan and Chen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Hao Chen, Jiangxi Science and Technology Normal University, Nanchang, China
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