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.

Diversity and functions of the sheep faecal microbiota: a multi‐omic characterization

“…When comparing our data with the existing studies reporting a metagenomic analysis of faecal samples from other ruminants, we could find a general predominance of Firmicutes over Bacteroidetes in cattle, with Ruminococcaceae and Lachnospiraceae being the most representative microbial families of the former phylum (Durso et al ., , ; Shanks et al ., ; Kim et al ., ), in line with our results obtained in sheep. Conversely, Bacteroidetes was the most abundant phylum in the sheep rumen according to the literature (Castro‐Carrera et al ., ; de la Fuente et al ., ; Kittelmann et al ., ; Lopes et al ., ; Morgavi et al ., ). Consistently, a marked increase in the F/B ratio from rumen to colon was recently described in cow (Mao et al ., ).…”

Applying functional metagenomics to search for novel lignocellulosic enzymes in a microbial consortium derived from a thermophilic composting phase of sugarcane bagasse and cow manure

“…The use of function-based metagenomic approaches to search for novel lignocellulosic enzymes have led to the discovery of novel b-galactosidases/a-arabinopyranosidases (Beloqui et al 2010), cellulases Kim et al 2008;Lopes et al 2015;Pandey et al 2016), xylanases (Hu et al 2008;Kanokratana et al 2015), xylose isomerases (Parachin and Gorwa-Grauslund 2011), b-xylosidase/a-arabinofuranosidase (Matsuzawa et al 2015) and b-glucosidases (Del Pozo et al 2012;Biver et al 2014), supporting this strategy as a powerful activity-based screening tool to identify entirely new classes of gene sequences encoding new or known functions (Handelsman 2004;Parachin and Gorwa-Grauslund 2011). Several sources of potential cellullose-and hemicellulosedepleting microbial communities are being used for metagenomic analysis.…”

“…The successful discovery of biomass-degrading genes from various environmental samples including cow rumen (Hess et al 2011;Lopes et al 2015), compost soils ), composts (Matsuzawa et al 2015), sugar cane bagasse (Kanokratana et al 2015) and termite gut (Warnecke et al 2007) encouraged us to investigate complex and unexploited microbial communities obtained by mixing different samples enriched for microorganisms capable of degrading cellulose. In addition, the screening of microbial genomes in their natural environments can accelerate the discovery of new genes.…”

Dinâmica do microbioma ruminal de ovinos (<i>Ovis aries</i>) e sua relação com a degradação de biomassa

“…Youssef et al (2013) Em relação ao método empregado, inúmeros trabalhos têm usado esta sistemática para inferir sobre importantes parâmetros da estruturação de comunidades microbianas, principalmente sobre as comunidades microbianas e metabolitos associados ao rúmen, os quais são importantes para a compreensão da saúde e desempenho de animais ruminantes (LEE et al, 2012). Lopes et al (2015) utilizaram este método para inferir sobre os principais fatores que afetam a estrutura da comunidade bacteriana no rúmen de O. aries. Eles observaram correlações positivas entre a abundância relativa da família Prevotellaceae com a degradabilidade da matéria orgânica.…”