title: Functional gene profiling through metaRNAseq approach reveals diet-dependent variation in rumen microbiota of buffalo (Bubalus bubalis).
abstract: Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection. Metatranscriptomes from rumen fiber adherent and fiber-free active bacteria were sequenced using Ion Torrent PGM platform followed by annotation using MG-RAST server and CAZYmes (Carbohydrate active enzymes) analysis toolkit. In all the samples Bacteroidetes was the most abundant phylum followed by Firmicutes. Functional analysis using KEGG Orthology database revealed Metabolism as the most abundant category at level 1 within which Carbohydrate metabolism was dominating. Diet treatments also exerted significant differences in proportion of enzymes involved in metabolic pathways for VFA production. Carbohydrate Active Enzyme(CAZy) analysis revealed the abundance of genes encoding glycoside hydrolases with the highest representation of GH13 CAZy family in all the samples. The findings provide an overview of the activities occurring in the rumen as well as active bacterial population and the changes occurring through different dietary treatments.
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India.
authors.forename: Ankit T
authors.initials: AT
authors.lastname: Hinsu
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, 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 (AAU), Anand, Gujarat, India.
authors.forename: Neelam M
authors.initials: NM
authors.lastname: Nathani
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India.
authors.forename: Ramesh J
authors.initials: RJ
authors.lastname: Pandit
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India.
authors.forename: Anand B
authors.initials: AB
authors.lastname: Patel
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, 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 (AAU), Anand, Gujarat, India. Electronic address: cgjoshi@rediffmail.com.
authors.forename: Chaitanya G
authors.initials: CG
authors.lastname: Joshi
mesh_terms: D000821:Animal Feed; D000818:Animals; D002020:Buffaloes / Q000382:microbiology*; D019295:Computational Biology; D004032:Diet / Q000379:methods*; D000069196:Gastrointestinal Microbiome; D020869:Gene Expression Profiling; D056186:Metagenomics; D012417:Rumen / Q000382:microbiology*
keywords: Buffalo; CAZyme; Metatranscriptomics; Microbiome; Rumen