engleski

Codon usage bias in metagenomes

Codon usage (CU) bias is an effect predominant in prokaryotes whereby synonymous codons are used with different frequencies between different species and even between genes within a single genome. This effect is related to tRNA abundance and can be used to predict expressivity of proteins by comparing their CU with that of a reference set of housekeeping genes. Our aim was to investigate codon usage patterns within metagenomic sequences and test for a presence or absence of CU bias at the level of a microbial community. We investigated synonymous CU frequencies in three metagenome samples and have demonstrated that a) different metagenomes exhibit different patterns in codon usage, and b) gene functions within a metagenome with high predicted expressivity (compared to the meta-ribosomal set) correlate well with the ecological requirements within the environment, suggesting that different species within a microbial community indeed behave as a meta-genome.

metagenomes; codon; bias; bioinformatics

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