Journal
ACTA BIOCHIMICA POLONICA
Volume 62, Issue 1, Pages 161-166Publisher
ACTA BIOCHIMICA POLONICA
DOI: 10.18388/abp.2014_917
Keywords
function-based metagenomics; metagenomic library screening; gene expression; microbials; databases; codon usage bias; cell accumulation
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Funding
- European Commission [245137, KBBE-2009-3-2-01]
- Ministry of Science and Higher Education, Poland [1544/7.PR UE/2010/7]
- National Science Center, Poland [2011/01/D/NZ2/04817]
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Metagenomics is a powerful tool to better understand the microbial niches, especially these from extreme habitats like oceans and seas, hot springs or deserts. However, one who is going to face the metagenomic studies should realize the challenges which might occur in the course of experiments. This manuscript indicates common problems in function-driven metagenomics, especially factors that influence gene expression are taken into account. Codon usage bias, internal cell accumulation, correct protein folding or presence of proper initiation factors are discussed and possible ways to overcome these problems are proposed. Finally, the annotation process is described, including possible limitations that one should take under consideration. What is more, the most popular databases for metagenomic data are mentioned and discussed.
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