Functional Characterization Reveals Novel Putative Coding Sequences in Prevotella ruminicola Genome Extracted from Rumen Metagenomic Studies

Aim: To reassemble Prevotella ruminicola genome from rumen metagenomic data of cattle and buffalo and compare with the published reference genome. Method: Rumen microbial communities from Mehsani buffaloes (n = 8) and Kankrej cattle (n = 8), each adapted to different proportions of a dry or green roughage diet, were subjected to metagenomic sequencing by Ion Torrent PGM, and subsequent reads were analyzed by MG-RAST. Using reference-guided assembly of the sequences against the published P. ruminicola strain 23, draft genomes of 2.56 and 2.46 Mb were reconstructed from Mehsani buffalo and Kankrej cows, respectively. The genomes were annotated using the RAST Server and carbohydrate active enzyme (CAZyme) analysis. Results: Taxonomic analysis by MG-RAST revealed P. ruminicola to be the most abundant species present among the rumen microflora. Functional annotation of reconstructed genomes using the RAST Server depicted the maximum assignment of coding sequences involved in the subsystems amino acid and derivatives and carbohydrate metabolism. CAZyme profiling revealed the glycoside hydrolases ( GH) family to be the most abundant. GH family subclassification revealed that the extracted genomes had more sequence hits for GH2, GH3, GH92 and GH97 as compared to the reference. Conclusion: The results reflect the metabolic significance of rumen-adapted P. ruminicola in utilizing a coarse diet for animals based on acquisition of novel genetic elements. (C) 2015 S. Karger AG, Basel