Environmental shaping of codon usage and functional adaptation across microbial communities.
Microbial communities represent the largest portion of the Earth's biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the biosphere. Metagenome studies are generally based on (i) classifying and ranking functions of identified genes; and (ii) estimating the phyletic distribution of constituent microbial species. To understand microbial communities at the systems level, it is necessary to extend these studies beyond the species' boundaries and capture higher levels of metabolic complexity. We evaluated 11 metagenome samples and demonstrated that microbes inhabiting the same ecological niche share common preferences for synonymous codons, regardless of their phylogeny. By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifestyle-specific genes across the entire microbial community, effectively considering microbial communities as meta-genomes. These findings set up a 'functional metagenomics' platform for the identification of genes relevant for adaptations of entire microbial communities to environments. Our results provide valuable arguments in defining the concept of microbial species through the context of their interactions within the community.
Bioinformatics Group, Department of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári körút 62, H-6726 Szeged, Hungary, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK and Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316 Oslo, Norway.
Masa
M
Roller
Vedran
V
Lucić
István
I
Nagy
Tina
T
Perica
Kristian
K
Vlahovicek
D000220:Adaptation, Biological / Q000235:genetics*; D000818:Animals; D003062:Codon; D017753:Ecosystem; D016680:Genome, Bacterial; D006801:Humans; D054892:Metagenome; D056186:Metagenomics; D051379:Mice; D010802:Phylogeny; D040901:Proteomics
D003062:Codon