title: Exploring the sheep rumen microbiome for carbohydrate-active enzymes.
abstract: The rumen is a complex ecosystem enriched for microorganisms able to degrade biomass during the animal's digestion process. The recovery of new enzymes from naturally evolved biomass-degrading microbial communities is a promising strategy to overcome the inefficient enzymatic plant destruction in industrial production of biofuels. In this context, this study aimed to describe the bacterial composition and functions in the sheep rumen microbiome, focusing on carbohydrate-active enzymes (CAE). Here, we used phylogenetic profiling analysis (inventory of 16S rRNA genes) combined with metagenomics to access the rumen microbiome of four sheep and explore its potential to identify fibrolytic enzymes. The bacterial community was dominated by Bacteroidetes and Firmicutes, followed by Proteobacteria. As observed for other ruminants, Prevotella was the dominant genus in the microbiome, comprising more than 30 % of the total bacterial community. Multivariate analysis of the phylogenetic profiling data and chemical parameters showed a positive correlation between the abundance of Prevotellaceae (Bacteroidetes phylum) and organic matter degradability. A negative correlation was observed between Succinivibrionaceae (Proteobacteria phylum) and methane production. An average of 2 % of the shotgun metagenomic reads was assigned to putative CAE when considering nine protein databases. In addition, assembled contigs allowed recognition of 67 putative partial CAE (NCBI-Refseq) representing 12 glycosyl hydrolase families (Pfam database). Overall, we identified a total of 28 lignocellulases, 22 amylases and 9 other putative CAE, showing the sheep rumen microbiome as a promising source of new fibrolytic enzymes.
authors.affiliation: Laboratory of Environmental Microbiology, Embrapa Environment, Rod. SP340 km 127.5, Jaguaríuna, SP, Zip Code 13820-000, Brazil.
authors.forename: Lucas Dantas
authors.initials: LD
authors.lastname: Lopes
authors.forename: André Oliveira
authors.initials: AO
authors.lastname: de Souza Lima
authors.forename: Rodrigo Gouvêa
authors.initials: RG
authors.lastname: Taketani
authors.forename: Phillip
authors.initials: P
authors.lastname: Darias
authors.forename: Lília Raquel Fé
authors.initials: LR
authors.lastname: da Silva
authors.forename: Emiliana Manesco
authors.initials: EM
authors.lastname: Romagnoli
authors.forename: Helder
authors.initials: H
authors.lastname: Louvandini
authors.forename: Adibe Luiz
authors.initials: AL
authors.lastname: Abdalla
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Mendes
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000201:enzymology*; D050260:Carbohydrate Metabolism; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D006026:Glycoside Hydrolases / Q000235:genetics / Q000378:metabolism*; D064307:Microbiota; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012417:Rumen / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D012756:Sheep
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D006026:Glycoside Hydrolases