Rumen Microbiota in Cattle and Buffaloes: Insights into Host-Specific Bacterial Diversity

The present investigation was designed to elucidate the comparative collective diversity of bacteria in the rumen of buffalo and cattle. For this study, a total of 14,913 16S rRNA gene (rrn) sequences generated through Sanger sequencing of ruminal bacteria deposited in the GenBank database were analyzed, of which 13,432 sequences were from cattle and 1481 sequences were from buffalo. Bacterial sequences of cattle origin represented 18 existing phyla and 165 genera, and those of buffalo origin represented 12 phyla and 67 genera. According to Ribosomal Database Project (RDP) classifier, Firmicutes was the dominant phylum in cattle, representing 47.9% of all sequences. Bacteroidetes was the second most abundant phylum (32.3% of sequences), while Proteobacteria accounted for 8.6% of total sequences. In buffalo, Firmicutes was the dominant phylum with 47.2% of total sequences. Bacteroidetes and Proteobacteria phyla constituted 38.3% and 4.6% of total sequences, respectively. We identified 172 shared non-rare species-level operational taxonomic units (OTUs) between buffalo and cattle, with 17 unique to buffalo belonging to three phyla: Bacteroidetes, Firmicutes, and Fibrobacteres. In cattle, 774 OTUs of unique sequences were assigned to six phyla, namely, Firmicutes (422 OTUs), Bacteroidetes (234 OTUs), Fibrobacteres (99 OTUs), Actinobacteria (7 OTUs), Cyanobacteria (5 OTUs), and SR1 (7 OTUs). This study revealed significant differences in rumen bacterial diversity between buffaloes and cattle, supporting the development of species-specific strategies to enhance fibrous feed utilization.