Causal estimation of maternal-offspring gut commensal bacterial associations under livestock grazing management conditions

The maternal gut bacteriome influences the microbiota and physiological functions of her offspring, but the flow of microbiota transfer under livestock grazing management has not been fully elucidated. Here, maternal-offspring associations of the gut bacteriome were investigated in Japanese black cattle of different genetic backgrounds as a livestock animal model, especially under open environmental conditions. Statistical analysis of faecal bacterial diversity revealed significant differences between dams and their calves before and after weaning (at 90 days of age). Furthermore, machine learning classification, factor analysis, and causal inference estimates that the faecal bacterial composition of dams has a weaker effect on calves in the preweaning period and a more pronounced effect on those in the postweaning period. Minimally, the genera Allobaculum , Bifidobacterium , Blautia , Bulleidia , CF231 , Clostridium , Collinsella , Coprococcus , Faecalibacterium, Methanobrevibacter , Lactobacillus , Sharpea , and Streptococcus in dams are highly linked to the faecal bacteria of postweaning calves. In terms of the metabolisms of faecal short-chain fatty acids, the genera Bifidobacterium and Faecalibacterium were associated with dams and postweaning calves. These computational observations highlight a nongenetic causal link from dam to pre- and postweaning calves regarding the potential shaping of the gut bacteriome, although the association appears to be discontinuous.