title: The effect of a high-roughage diet on the metabolism of aromatic compounds by rumen microbes: a metagenomic study using Mehsani buffalo (Bubalus bubalis).
abstract: In developing countries, livestock are often fed a high-lignin, low-nutrient diet that is rich in aromatic compounds. It is therefore important to understand the structure of the microbial community responsible for the metabolism of these substances. A metagenomic analysis was therefore carried out to assess the microbial communities associated with the liquid and solid fractions of rumen biomaterial from domestic Mehsani buffalo (Bubalus bubalis) fed with varying proportions of roughage. The experimental design consisted of three feeding regimes (50, 75 and 100 % roughage) and two roughage types (green and dry). Genes associated with aromatic compound degradation were assessed via high-throughput DNA sequencing. A total of 3914.94 Mb data were generated from all treatment groups. Genes coding for functional responses associated with aromatic compound metabolism were more prevalent in the liquid fraction of rumen samples than solid fractions. Statistically significant differences (p < 0.05) were also observed between treatment groups. These differences were dependent on the proportion of roughage fed to the animal, with the type of roughage having little effect. The genes present in the highest abundance in all treatment groups were those related to aromatic compound catabolism. At the phylum level, Bacteroidetes were dominant in all treatments closely followed by the Firmicutes. This study demonstrates the use of feed type to selectively enrich microbial communities capable of metabolizing aromatic compounds in the rumen of domestic buffalo. The results may help to improve nutrient utilization efficiency in livestock and are thus of interest to farming industries, particularly in developing countries, worldwide.
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India.
authors.forename: Vimalkumar S
authors.initials: VS
authors.lastname: Prajapati
authors.affiliation: Environmental Genomics Division, National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, Maharashtra, India.
authors.forename: Hemant J
authors.initials: HJ
authors.lastname: Purohit
authors.affiliation: MDS Bio-Analytics Pvt. Ltd., Nagpur, Maharashtra, India.
authors.forename: Dhananjay V
authors.initials: DV
authors.lastname: Raje
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India.
authors.forename: Nidhi
authors.initials: N
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: Anand B
authors.initials: AB
authors.lastname: Patel
authors.affiliation: Australian Centre for Research on Separation Science (ACROSS), School of Applied Sciences, RMIT University, GPO Box 2476, Melbourne, VIC, 3001, Australia.
authors.forename: Oliver A H
authors.initials: OAH
authors.lastname: Jones
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India. cgjoshi@aau.in.
authors.forename: Chaitanya G
authors.initials: CG
authors.lastname: Joshi
mesh_terms: D000821:Animal Feed / Q000032:analysis*; D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D044822:Biodiversity; D002020:Buffaloes / Q000378:metabolism / Q000382:microbiology*; D004043:Dietary Fiber / Q000378:metabolism*; D000069196:Gastrointestinal Microbiome; D056186:Metagenomics; D010802:Phylogeny; D012417:Rumen / Q000378:metabolism / Q000382:microbiology*; D055549:Volatile Organic Compounds / Q000378:metabolism*
chemical_list: D004043:Dietary Fiber; D055549:Volatile Organic Compounds
keywords: Aromatic compound metabolism; Bubalus bubalis; MG-RAST; Metagenome; Personal genome machine