title: In depth analysis of rumen microbial and carbohydrate-active enzymes profile in Indian crossbred cattle.
abstract: Rumen houses a plethora of symbiotic microorganisms empowering the host to hydrolyze plant lignocellulose. In this study, NGS based metagenomic approach coupled with bioinformatic analysis was employed to gain an insight into the deconstruction of lignocellulose by carbohydrate-active enzymes (CAZymes) in Indian crossbred Holstein-Friesian cattle. Cattle rumen metagenomic DNA was sequenced using Illumina-MiSeq and 1.9 gigabases of data generated with an average read length of 871 bp. Analysis of the assembled sequences by Pfam-based Carbohydrate-active enzyme Analysis Toolkit identified 17,164 putative protein-encoding CAZymes belonging to different families of glycoside hydrolases (7574), glycosyltransferases (5185), carbohydrate-binding modules (2418), carbohydrate esterases (1516), auxiliary activities (434) and polysaccharide lyases (37). Phylogenetic analysis of putative CAZymes revealed that a significant proportion of CAZymes were contributed by bacteria belonging to the phylum Bacteroidetes (40%), Firmicutes (30%) and Proteobacteria (10%). The comparative analysis of HF cross rumen metagenome with other herbivore metagenomes indicated that Indian crossbred cattle rumen is endowed with a battery of CAZymes that may play a central role in lignocellulose deconstruction. The extensive catalog of enzymes reported in our study that hydrolyzes plant lignocellulose biomass, can be further explored for the better feed utilization in ruminants and also for different industrial applications.
authors.affiliation: Rumen Microbiology Laboratory, Animal Nutrition Division, National Institute of Animal Nutrition and Physiology, Bangalore, India; Department of Biotechnology, Jain University, Bangalore, India.
authors.forename: V Lyju
authors.initials: VL
authors.lastname: Jose
authors.affiliation: Bioinformatics Laboratory, Division of Molecular Entomology, National Bureau of Agricultural Insect Resources, Bangalore, India.
authors.forename: Ravi P
authors.initials: RP
authors.lastname: More
authors.affiliation: Rumen Microbiology Laboratory, Animal Nutrition Division, National Institute of Animal Nutrition and Physiology, Bangalore, India. Electronic address: thulasi.appoothy@gmail.com.
authors.forename: Thulasi
authors.initials: T
authors.lastname: Appoothy
authors.affiliation: Wildlife SOS, Bannerghatta Bear Rescue Centre, Bangalore, India.
authors.forename: A Sha
authors.initials: AS
authors.lastname: Arun
mesh_terms: D000818:Animals; D044822:Biodiversity; D002417:Cattle; D016000:Cluster Analysis; D057225:Data Mining; D006867:Hydrolases / Q000145:classification / Q000235:genetics; D054892:Metagenome; D056186:Metagenomics; D064307:Microbiota; D012417:Rumen / Q000382:microbiology*
chemical_list: D006867:Hydrolases
keywords: CAZymes; HF cross; Metagenomics; MiSeq; Pfam; Rumen