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Open Access Research

De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes

Aaron Weimann13, Yulia Trukhina13, Phillip B Pope2, Sebastian GA Konietzny13 and Alice C McHardy13*

Author Affiliations

1 Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, Saarbrücken, 66123, Germany

2 Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Post Office Box 5003, Ås, 1432, Norway

3 Department of Algorithmic Bioinformatics, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany

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Biotechnology for Biofuels 2013, 6:24  doi:10.1186/1754-6834-6-24

Published: 15 February 2013

Abstract

Background

Understanding the biological mechanisms used by microorganisms for plant biomass degradation is of considerable biotechnological interest. Despite of the growing number of sequenced (meta)genomes of plant biomass-degrading microbes, there is currently no technique for the systematic determination of the genomic components of this process from these data.

Results

We describe a computational method for the discovery of the protein domains and CAZy families involved in microbial plant biomass degradation. Our method furthermore accurately predicts the capability to degrade plant biomass for microbial species from their genome sequences. Application to a large, manually curated data set of microbial degraders and non-degraders identified gene families of enzymes known by physiological and biochemical tests to be implicated in cellulose degradation, such as GH5 and GH6. Additionally, genes of enzymes that degrade other plant polysaccharides, such as hemicellulose, pectins and oligosaccharides, were found, as well as gene families which have not previously been related to the process. For draft genomes reconstructed from a cow rumen metagenome our method predicted Bacteroidetes-affiliated species and a relative to a known plant biomass degrader to be plant biomass degraders. This was supported by the presence of genes encoding enzymatically active glycoside hydrolases in these genomes.

Conclusions

Our results show the potential of the method for generating novel insights into microbial plant biomass degradation from (meta-)genome data, where there is an increasing production of genome assemblages for uncultured microbes.