Data Sheet 2_Breed-specific gut microbiota and enterotype divergence in Chinese indigenous ducks.pdf

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 16 S 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.

家鸭肠道微生物群在消化吸收、免疫调节及机体整体健康中发挥关键作用。然而，当前学界对不同系统发育背景家鸭的肠道微生物组成认知仍较为有限，尤其是在同一养殖环境下饲养的鸭群。本研究收集了饲养于统一标准化养殖场的15个中国地方鸭品种的260份粪便样本，并对其开展16S rRNA基因测序。此外，采集了这些鸭只的202份血液样本用于全基因组测序（WGS，whole-genome sequencing）。全基因组测序结果显示，这些家鸭品种具有品种特异性的遗传特征。不同地方鸭品种的肠道微生物群在门水平上表现出较高的相似性，优势菌门依次为厚壁菌门（Firmicutes）、变形菌门（Proteobacteria）、放线菌门（Actinobacteria）以及拟杆菌门（Bacteroidetes）；但在更精细的分类学水平上，其肠道微生物群落结构则存在显著差异。宿主遗传特异性与这些鸭品种的肠道微生物群密切相关。宏基因组功能预测结果表明，相较于物种组成，不同鸭品种的肠道微生物组的代谢功能更为相似。此外，主坐标分析（PCoA，Principal coordinates analysis）显示，基于Jensen-Shannon距离（JSD）的群落差异性，15个鸭品种的肠道微生物群可划分为两个不同的肠型簇，其代表性品种分别为蛋用鸭和兼用鸭。两种肠型的肠道微生物组成及功能的丰富度指数并无显著差异，但香农指数（Shannon index）值存在显著差异。本研究解析了不同遗传背景家鸭种群的肠道微生物结构与多样性，为宿主遗传变异与肠道微生物群之间的关联研究提供了全新视角。