Table 1_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.

鉴于家畜阴道微生物群与动物繁殖性能的密切关联，相关研究的关注度与日俱增。近期已有研究证实，家畜阴道微生物群具有高度的变异性，这使得针对单一微生物开展功能研究的难度显著增加。为解决这一变异性问题，本研究对公开可得的16S rRNA基因扩增子测序数据集进行整合分析，以阐明牛、绵羊和猪的核心阴道微生物群。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，筛选出共享的细菌属。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群结构存在显著差异。在群落组成上，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）。在属水平上，丰度最高的菌属分别为未分类的巴斯德菌科菌属、脲原体属（Ureaplasma）和链球菌属（Streptococcus）。针对单一家畜物种的阴道微生物群分析，同样观察到群落组成差异：牛和绵羊的阴道微生物群中，脲原体属和嗜血杆菌属（Histophilus）的丰度更高；而与其他家畜样本相比，猪的阴道微生物群中梭杆菌属（Fusobacterium）和帕维莫纳斯菌属（Parvimonas）的丰度更为突出。在牛样本中，有120个操作分类单元（Operational Taxonomic Unit，OTU）和82个菌属在70%的阴道样本中被检出。采用相同阈值标准，猪样本的核心OTU数量为40个、核心菌属为63个，绵羊样本的核心OTU数量为22个、核心菌属为50个。在三个家畜物种中，共有19个共享的核心阴道菌属。核心阴道OTU大多具有物种特异性，但存在8个共享的OTU，这些共享OTU包括链球菌属（OTU 21）、狭义梭菌属1群（Clostridium sensu stricto 1，OTU 18）以及棒状杆菌属（Corynebacterium，OTU 6），它们同时也是家畜核心阴道微生物群中丰度最高的成员之一。未来若要阐明单一微生物对家畜繁殖效率的功能意义，需先深入理解家畜阴道微生物群的相关特性。本次分析所鉴定出的核心阴道菌属，将有助于后续研究探索单一微生物调控或阻碍动物繁殖效率的作用机制与通路。