Table 7_Combined analysis of 16S rRNA gene sequencing data reveals core vaginal bacteria across livestock species.xlsx

Investigating the livestock vaginal microbiota is of increasing interest due to its relationship with animal reproductive performance. Recent publications have uncovered a high degree of variability of the livestock vaginal microbiota, making it difficult to focus functional research on individual microorganisms. To address this variability, we conducted a combined analysis of publicly available 16S rRNA gene amplicon sequencing datasets to reveal the core vaginal microbiota in cattle, sheep, and pigs. The goal of this combined analysis was to identify bacterial genera that were shared despite a diverse overall sample population. A total of 2,911 vaginal samples (715 cattle, 964 sheep, and 1,232 pigs) from 29 different datasets were used in this combined analysis. Beta diversity analysis revealed structural differences of the vaginal microbiota between different animal species. Compositionally, the most abundant phyla were Bacillota, Pseudomonadota, and Bacteroidota. At the genus level, an unclassified Pasteurellaceae genus, Ureaplasma, and Streptococcus were the most abundant. Across the vaginal microbiota of individual livestock species, compositional differences were observed. The cattle and sheep vaginal microbiota contained a higher abundance of Ureaplasma and Histophilus whereas the pig vaginal microbiota contained more Fusobacterium and Parvimonas than that of the other livestock samples. Among the cattle, 120 OTUs and 82 genera were present in 70% of the vaginal samples. At the same threshold, pig samples had 40 core OTUs and 63 core genera, while the sheep samples had 22 core OTUs and 50 core genera. There were 19 overlapping core vaginal genera across the three animal species. The core vaginal OTUs were largely species-specific, although there were eight overlapping OTUs. These included Streptococcus (OTU 21), Clostridium sensu stricto 1 (OTU 18), and Corynebacterium (OTU 6), which were also some of the most abundant members of the livestock core vaginal microbiota. A better understanding of the livestock vaginal microbiota is required for future studies aimed at elucidation of the functional significance of individual microbes with respect to livestock reproductive efficiency. The core vaginal genera identified in this analysis will help guide research on mechanisms/pathways through which individual organisms enhance or impede animal reproductive efficiency.

鉴于畜禽阴道微生物组（vaginal microbiota）与动物繁殖性能的密切关联，对其开展研究的关注度与日俱增。近期研究表明，畜禽阴道微生物组存在高度异质性，这使得针对单一微生物开展功能研究的难度大幅提升。为解决这一异质性问题，本研究整合分析了公开可用的16S rRNA基因扩增子测序数据集，以解析牛、绵羊和猪的核心阴道微生物组。本次整合分析的目标是，在整体样本群体具有多样性的前提下，识别出共享的细菌菌属。本次分析共纳入来自29项不同数据集的2911份阴道样本，其中牛样本715份、绵羊样本964份、猪样本1232份。β多样性分析结果显示，不同动物物种的阴道微生物组结构存在显著差异。从群落组成来看，丰度最高的菌门依次为厚壁菌门（Bacillota）、变形菌门（Pseudomonadota）和拟杆菌门（Bacteroidota）。在菌属水平上，未分类的巴斯德菌科（Pasteurellaceae）菌属、脲原体属（Ureaplasma）和链球菌属（Streptococcus）为丰度最高的菌属。不同畜禽物种的阴道微生物组组成亦存在特异性差异：牛和绵羊的阴道微生物组中脲原体属和嗜血杆菌属（Histophilus）的丰度更高，而猪样本中梭杆菌属（Fusobacterium）和小杆菌属（Parvimonas）的丰度则显著高于另外两类畜禽。在牛的阴道微生物组中，有120个操作分类单元（OTU，Operational Taxonomic Unit）和82个菌属在70%以上的样本中被检出。在相同的阈值下，猪样本包含40个核心OTU和63个核心菌属，绵羊样本则包含22个核心OTU和50个核心菌属。三类畜禽共有的核心阴道菌属共有19个。核心阴道OTU大多具有物种特异性，但其中存在8个共享OTU。这些共享OTU包括链球菌属（Streptococcus，OTU 21）、严格梭菌簇1（Clostridium sensu stricto 1，OTU 18）和棒状杆菌属（Corynebacterium，OTU 6），它们同时也是畜禽核心阴道微生物组中丰度较高的成员之一。未来若要阐明单一微生物对畜禽繁殖效率的功能意义，需先对畜禽阴道微生物组形成更为深入的认知。本次分析所鉴定出的核心阴道菌属，将为探究单一微生物调控或阻碍动物繁殖效率的作用机制与通路提供研究指引。