Taxonomic and functional adaption of the gastrointestinal microbiome of goats kept at high altitude (4800 m) under intensive or extensive rearing conditions

ABSTRACT The gut microbiota composition is influenced by the diet as well environment in both wild and domestic animals. We studied effects of two feeding systems on rumen hindgut microbiome semi-feral Tibetan goats kept at high altitude (∼4800 m) using 16S rRNA gene metagenomic sequencing. Intensive drylot resulted significantly higher zootechnical performance, narrower ruminal acetate: propionate ratios a drop average pH slaughter to ∼5.04. Hindgut microbial adaption appeared be more diverse group suggesting influx undegraded complex non-starch polysaccharides from rumen. Despite their fiber levels diet, grazing exhibited lower counts Methanobrevibacter genes associated with hydrogenotrophic methanogenesis pathway, presumably reflecting scarce dietary conditions (low energy density) when rearing pasture extreme alpine environments. These promote relevant abundance bacitracin genes. In parallel, we recognized significant increase antibiotic resistance digestive tracts summary, this study provides deeper insight into metataxonomic functional gastrointestinal subject intensive extensive altitude.