title: Microbial and Carbohydrate Active Enzyme profile of buffalo rumen metagenome and their alteration in response to variation in the diet.
abstract: Rumen microbiome represents rich source of enzymes degrading complex plant polysaccharides. We describe here analysis of Carbohydrate Active Enzymes (CAZymes) from 3.5 gigabase sequences of metagenomic data from rumen samples of Mehsani buffaloes fed on different proportions of green or dry roughages to concentrate ration. A total of 2597 contigs encoding putative CAZymes were identified by CAZyme Analysis Toolkit (CAT). The phylogenetic analysis of these contigs by MG-RAST revealed predominance of Bacteroidetes, followed by Firmicutes, Proteobacteria, and Actinobacteria phyla. Moreover, a higher abundance of oligosaccharide degrading and debranching enzymes in buffalo rumen metagenome and that of cellulases and hemicellulases in termite hindgut was observed when we compared glycoside hydrolase (GH) profile of buffalo rumen metagenome with cow rumen, termite hindgut and chicken caecum metagenome. Further, comparison of microbial profile of green or dry roughage fed animals showed significantly higher abundance (p-value<0.05) of various polysaccharide degrading bacterial genera like Fibrobacter, Prevotella, Bacteroides, Clostridium and Ruminococcus in green roughage fed animals. In addition, we found a significantly higher abundance (p-value<0.05) of enzymes associated with pectin digestion such as pectin lyase (PL) 1, PL10 and GH28 in green roughage fed animals. Our study outlines CAZyme profile of buffalo rumen metagenome and provides a scope to study the role of abundant enzyme families (oligosaccharide degrading and debranching enzymes) in digestion of coarse feed.
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388001, Gujarat, India; Department of Biochemistry and Molecular Biology, Georgetown University, Washington, D.C. 20007, USA.
authors.forename: Dishita D
authors.initials: DD
authors.lastname: Patel
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388001, Gujarat, India.
authors.forename: Amrutlal K
authors.initials: AK
authors.lastname: Patel
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388001, Gujarat, India.
authors.forename: Nidhi R
authors.initials: NR
authors.lastname: Parmar
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388001, Gujarat, India.
authors.forename: Tejas M
authors.initials: TM
authors.lastname: Shah
authors.affiliation: Department of Animal Nutrition, Livestock Research Station, Sardar Krushinagar Dantiwada Agricultural University, Sardar Krushinagar 385506, Gujarat, India.
authors.forename: Jethabhai B
authors.initials: JB
authors.lastname: Patel
authors.affiliation: Animal Nutrition Research Station, Anand Agricultural University, Anand 388001, Gujarat, India.
authors.forename: Paresh R
authors.initials: PR
authors.lastname: Pandya
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388001, Gujarat, India. Electronic address: cgjoshi@aau.in.
authors.forename: Chaitanya G
authors.initials: CG
authors.lastname: Joshi
mesh_terms: D000821:Animal Feed; D000818:Animals; D041963:Bacteroidetes / Q000201:enzymology / Q000235:genetics; D002020:Buffaloes / Q000235:genetics* / Q000382:microbiology*; D050260:Carbohydrate Metabolism; D004032:Diet; D054892:Metagenome; D064307:Microbiota; D010802:Phylogeny; D012417:Rumen / Q000201:enzymology* / Q000382:microbiology*
keywords: Buffalo rumen metagenome; CAZymes; Roughage; Shotgun assembly