Microbial ecology along the buffalo digestive tract provides insights to their functions and interactions with the host

Abstract Buffalo is an important livestock in Asia. Like other ruminants, its digestive tract (DT) is the key to the quality and wellbeing of buffalo and heavily interact with microbes. Here, we present a comprehensive survey on the microbial ecology along buffalo’s DT, including eight sites in three sections (i.e., stomach, intestine and rectum). We collected 695 samples, performed metagenomic sequencing and obtained 4,960 high-quality metagenome-assembled genomes (MAGs), to which ~ 85% of the raw reads could be mapped. 90.7% of the MAGs are previously unidentified at species level. Overall, Firmicutes and Bacteroidetes are the most abundant phyla; their ratios showed an increasing trend along the DT, consistent with their functions in the DT sections. We identified known interactions between microbes and DT sites including the enrichment of fiber-digesting and methane-producing microbes in the stomach. Strikingly, archaea were highly abundant in both stomach and intestine and showed positive-correlations with Fibrobacter, indicating their roles in methane-production and fiber-degradation at both sections. We annotated 5,862,748 non-redundant proteins from the MAGs, many of which also showed different abundances and were related to site-specific functions. By comparing with the rumen microbiota of cattle, we found higher abundances of microbes in fiber degradation and but lower in methane production. Our catalog of microbial genomes and encoded-proteins provides insight to their functions and interactions with distinct DT sites, and pave the way to microbial interventions for better buffalo quality.