Exploring the sheep rumen microbiome for carbohydrate-active enzymes

Author(s)

Lopes, Lucas Dantas ^[1] ; de Souza Lima, Andre Oliveira ^[2] ; Taketani, Rodrigo Gouvea ^[1] ; Darias, Phillip ^[2] ; Fe da Silva, Lilia Raquel ^[3] ; Romagnoli, Emiliana Manesco ^[1] ; Louvandini, Helder ^[4] ; Abdalla, Adibe Luiz ^[4] ; Mendes, Rodrigo ^[1]

Affiliation

^[1] Embrapa Environm, Lab Environm Microbiol, BR-13820000 Jaguariuna, SP - Brazil

^[2] Univ Vale Itajai, Ctr Technol Sci Earth & Sea, BR-88302202 Itajai, SC - Brazil

^[3] Univ Fed Piaui, BR-64049550 Bairro Ininga, Teresina - Brazil

^[4] Univ Sao Paulo, Ctr Nucl Energy Agr, BR-13400970 Piracicaba, SP - Brazil

• Document type: Journal article
• Source: ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY; v. 108, n. 1, p. 15-30, JUL 2015.
• Web of Science Citations: 12

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. (AU)

• FAPESP's process: 12/03848-8 - Rumen microbiome metagenomics and metatranscriptomics for biomass degrading genes discovery
• Grantee: Rodrigo Mendes
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Young Investigators Grants
• FAPESP's process: 12/24588-4 - Dynamics of the sheep (Ovis aries) rumen microbiome and its relationship with biomass degradation
• Grantee: Emiliana Manesco Romagnoli
• Support Opportunities: Scholarships in Brazil - Doctorate