Encyclopedia of Metagenomics

Living Edition
| Editors: Karen E. Nelson

Protein-Coding Genes as Alternative Markers in Microbial Diversity Studies

  • Martin Wu
Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-6418-1_734-3



The small ribosomal unit RNA (SSU rRNA or 16S rRNA) has been widely used in microbial systematic and diversity studies. The appeal of using 16S rRNA gene as a marker gene is numerous. First of all, it is distributed in every single cellular organism. Secondly, because regions of 16S rRNA sequence are highly conserved, 16S rRNA gene can be PCR amplified from a wide diversity of taxa using “universal” primers and sequenced, bypassing the need to isolate and culture the organisms in question. Consequently, millions of 16S rRNA reference sequences are available for microbial classification and identification (Cole 2009).

Although 16S rRNA has been the “gold standard” in microbial diversity studies, it has several shortcomings. First, because 16S rRNA only makes up a tiny fraction of a genome (~0.1 %), its application as a marker gene in classifying metagenomic sequences is seriously limited. Secondly, the widely...


Hide Markov Model Marker Gene Lateral Gene Transfer Metagenomic Sequence Evolutionary Rate Variation 
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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.Department of BiologyUniversity of VirginiaCharlottesvilleUSA