Table_5_Transmission of the gut microbiome in cohousing goats and pigs.xlsx

Social interaction facilitates the horizontal transmission of the microbiota between different individuals. However, little is known about the level of microbiota transmission in different livestock animals and different digestive tracts. The Hainan black goat and Wuzhishan pig are typical tropical local breeds on Hainan Island in China. Thus, we sampled and analyzed the gut microbiome in Hainan black goats (cecum and rumen) and Wuzhishan pigs (cecum) to study horizontal transmission by rearing them in the same pen (six goats and six pigs) or separate pens (nine goats and nine pigs). De novo assembly and binning recovered 3,262 strain-level and 2,488 species-level metagenome-assembled genomes (MAGs) using ∼1.3 Tb sequencing data. Of these MAGs, 1,856 MAGs were identified as novel strain. Compared with goats living in separate pens, social interaction in the same pen promotes community homogeneity in the rumen microbiome (P < 0.05) and the cecum microbiome (P < 0.05), respectively. Notably, approximately 7.08% (231/3262) of the gut microbial population could transmit during cohousing, 12 strains only in inter-species transmission, versus 190 strains only in intra-species transmission, and 10 strains only in foregut and hindgut transmission. In addition, the social contact group has high transmitted strain abundance, which is correlated with community composition. This study provided a new insight into the influence of social interaction on the animal gut microbiota.

社会互动可促进不同个体间微生物群的水平传播。然而，目前对不同家畜及不同消化道内的微生物群传播水平尚缺乏了解。海南黑山羊与五指山猪是中国海南岛典型的热带地方品种。为此，本研究对海南黑山羊（盲肠与瘤胃）及五指山猪（盲肠）的肠道微生物组进行采样分析，通过将二者混栏饲养（6只山羊与6只猪）或分栏饲养（9只山羊与9只猪）以探究微生物群的水平传播规律。本研究通过从头组装（de novo assembly）与分箱（binning）分析，基于约1.3 TB的测序数据，共获得3262个菌株级、2488个物种级的宏基因组组装基因组（metagenome-assembled genomes, MAGs）。其中1856个MAGs被鉴定为新型菌株。与分栏饲养的山羊相比，混栏饲养带来的社会互动分别提升了瘤胃微生物组（P < 0.05）与盲肠微生物组（P < 0.05）的群落均一性。值得注意的是，混栏饲养期间约有7.08%（231/3262）的肠道微生物类群发生了传播，其中仅发生跨物种传播的菌株有12株，仅发生种内传播的菌株有190株，另有10株仅在前肠与后肠间发生传播。此外，社会互动组的传播菌株丰度更高，且该丰度与群落组成显著相关。本研究为解析社会互动对动物肠道微生物群的影响提供了全新视角。