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

Abstract Background: The gut microbiota composition is influenced by the diet as well as the environment in both wild and domestic animals. Although the rumen microbiome in herbivorous ruminants has been studied intensively, there is a lack of data regarding the simultaneous adaption of the rumen and hindgut metagenome as affected by different feeding systems in extreme environments. Therefore, we studied the effects of two feeding systems, grazing and drylot, on the rumen and hindgut microbiome composition of semi-feral Tibetan goats kept at high altitude (~4800 m). 16S rRNA gene sequencing and metagenomic analysis were conducted on DNA extracts from the contents and mucosal layer of different sections of the gastrointestinal tract (rumen, cecum, and colon).Results: Intensive drylot feeding resulted in significantly higher zootechnical performance, narrower ruminal acetate: propionate ratios and a drop in the average rumen pH at slaughter to ~5.04. In response, the ruminal microbiome of drylot goats expressed a significantly lower diversity compared to the grazing animals. Otherwise, hindgut microbial adaption appeared to more diverse in the drylot group suggesting a higher influx of undegraded complex non-starch polysaccharides from the rumen. Despite their higher fiber levels in the diet, grazing goats exhibited lower counts of Methanobrevibacter and genes associated with the hydrogenotrophic methanogenesis pathway, presumably reflecting the scarce dietary conditions (low energy density) when rearing goats on pasture from extreme alpine environments. These conditions appeared to promote a relevant abundance of bacitracin genes, which potentially benefits the host's adaption to harsh environmental conditions. In parallel, we recognized a significant increase in the abundance of antibiotic resistance genes in the digestive tracts of drylot animals.Conclusion: In summary, this study provides a deeper insight in the phylogenetic and functional adaption of the gastrointestinal microbiome of goats subject to intensive drylot and extensive pasture rearing conditions at high altitude.