Environmental Shaping of Codon Usage and Functional Adaptation Across Microbial Communities
Whole microbial communities exhibit patterns similar to those of single microbial species in terms of synonymous codon usage, regardless of their phyletic composition. Therefore, methods applicable on single microbial genomes to predict for functionally important and lifestyle-relevant genes based on translational optimization of synonymous codons can be applied to the study of the entire metagenomes. Using these predictions opens up a possibility to discover new and functionally unannotated genes relevant for the community metabolism and overall adaptation to a particular environment. This approach presents an integrated approach to the study of microbial community genomic information and provides an in silico functional metagenomic platform to complement metaproteomic studies.
Environmental diversity studies have bypassed the common problem where less than 1% of microbes are amenable to cultivation in laboratory conditions (Staley and Konopka 1985) by instead...
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