Encyclopedia of Metagenomics

2015 Edition
| Editors: Karen E. Nelson

Environmental Shaping of Codon Usage and Functional Adaptation Across Microbial Communities

  • Vedran Lucić
  • Masa Roller
  • Istvan Nagy
  • Kristian Vlahoviček
Reference work entry
DOI: https://doi.org/10.1007/978-1-4899-7478-5_562

Definition

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.

Introduction

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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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Vedran Lucić
    • 1
  • Masa Roller
    • 2
  • Istvan Nagy
    • 3
  • Kristian Vlahoviček
    • 2
  1. 1.Molecular Biology Department, Division of Biology, Faculty of ScienceUniversity of ZagrebZagrebCroatia
  2. 2.Bioinformatics Group, Molecular Biology Department, Division of Biology, Faculty of ScienceUniversity of ZagrebZagrebCroatia
  3. 3.Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of SciencesSzegedHungary