Encyclopedia of Metagenomics

2015 Edition
| Editors: Karen E. Nelson

Metaxa, Overview

  • Johan Bengtsson-Palme
  • Martin Hartmann
  • K. Martin Eriksson
  • R. Henrik Nilsson
Reference work entry
DOI: https://doi.org/10.1007/978-1-4899-7478-5_239


16S extraction; rRNA extraction; SSU extraction; Taxonomic assignment


Metaxa is a software tool for extracting full-length and partial ribosomal small subunit (SSU; 16S/18S/12S) sequences from metagenomic datasets and for classifying the extracted sequences to taxonomic domains and organelle of origin. Metaxa is freely available from http://microbiology.se/software/metaxa/.


A common question in metagenomic studies concerns the species composition of the community sampled (Desai et al. 2012). This is frequently addressed using a specific genetic marker, typically the ribosomal RNA (rRNA) small subunit (SSU) gene sequence (also referred to as the 16S, 18S, or 12S subunit depending on the lineage under scrutiny). In some studies, the SSU gene is amplified by PCR and sequenced separately in order to study microbial diversity. However, even if the SSU sequences are not targeted for separate sequencing, it is still possible to identify and extract the SSU...

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Johan Bengtsson-Palme
    • 1
  • Martin Hartmann
    • 2
  • K. Martin Eriksson
    • 3
  • R. Henrik Nilsson
    • 3
  1. 1.Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of GothenburgGöteborgSweden
  2. 2.Molecular Ecology, Agroscope Reckenholz-Tänikon Research Station ARTZurichSwitzerland
  3. 3.Department of Biological and Environmental SciencesUniversity of GothenburgGöteborgSweden