Bacterial Diversity Dynamics Associated with Different Diets and Different Primer Pairs in the Rumen of Kankrej Cattle
Pyrosequencing of 16S rRNA gene targeting bacteria was applied to identify diet-induced shifts in the microbiome of both solid and liquid ruminal fractions retrieved from water buffalo fed different diets. The depth of coverage of metabolically active bacteria in a community using different primer pairs was also investigated. To assess reproducibility, animal to animal variation was considered in all phylogenetic and community comparisons. The experiment included four non-lactating water buffaloes fed three different diets for six weeks each; diets were M1 (50% concentrate: 50% dry roughage), M2 (25% concentrate: 75% dry roughage) and M3 (100% dry roughage). A total of 333, 851 pyrotags were analyzed in this study. Phylogenetic analysis revealed significant differences in the rumen microbiome mediated by primer and diet (P < 0.05). Differences in community composition due to primer, diet, fraction and animal were compared using unweighted and weighted UniFrac analysis. Clustering of communities was largely explained by primer differences in both weighted and unweighted UniFrac analyses (P < 0.001). In the weighted analysis, communities clustered by diets (P < 0.05) and fractions (P < 0.08) while no inter-animal variation was observed. The identified repertoire of bacterial populations was dependent on the primer pair, as targeting the V4-V5 region resulted in greater diversity profiles of the microbiome. Within each primer pair, dietary changes altered the community composition with noticeable shifts at genus level. Genera such as Ruminococcus and Fibrobacter (P < 0.05) were higher in abundance on M3 diet while Prevotella dominated (P < 0.05) on M1 diet.