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Exploring the sheep rumen microbiome for carbohydrate-active enzymes

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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.

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Acknowledgments

This work was funded by FAPESP grant 2012/03848-8 and we also thank FAPESP for scholarship support provided to R. G. T. (2010/50799-7) and E. M. R. (2012/24588-4) and CNPq for supporting L. D. L. (135815/2011-8). Also, FAPESC grant 3422/2012 and CNPq grant 565062/2010-7 (INCT-Mar COI), supported this work.

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Authors and Affiliations

  1. Laboratory of Environmental Microbiology, Embrapa Environment, Rod. SP340 km 127.5, Jaguaríuna, SP, Zip Code 13820-000, Brazil

    Lucas Dantas Lopes, Rodrigo Gouvêa Taketani, Emiliana Manesco Romagnoli & Rodrigo Mendes

  2. Center of Technological Sciences of Earth and Sea, University of Vale do Itajaí, R. Uruguai 458, Itajaí, SC, Zip Code 88302-202, Brazil

    André Oliveira de Souza Lima & Phillip Darias

  3. Federal University of Piauí, Socopo Campus, Bairro Ininga, Teresina, PI, Zip Code 64049-550, Brazil

    Lília Raquel Fé da Silva

  4. Center for Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário 303, Piracicaba, SP, Zip Code 13400-970, Brazil

    Helder Louvandini & Adibe Luiz Abdalla

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  1. Lucas Dantas Lopes
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  2. André Oliveira de Souza Lima
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  3. Rodrigo Gouvêa Taketani
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  8. Adibe Luiz Abdalla
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  9. Rodrigo Mendes
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Correspondence to Rodrigo Mendes.

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Lopes, L.D., de Souza Lima, A.O., Taketani, R.G. et al. Exploring the sheep rumen microbiome for carbohydrate-active enzymes. Antonie van Leeuwenhoek 108, 15–30 (2015). https://doi.org/10.1007/s10482-015-0459-6

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