Living Reference Work Entry

Encyclopedia of Metagenomics

pp 1-5

Date: Latest Version

Metaxa, Overview

  • Johan Bengtsson-PalmeAffiliated withInstitute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg Email author 
  • , Martin HartmannAffiliated withMolecular Ecology, Agroscope Reckenholz-Tänikon Research Station ART
  • , K. Martin ErikssonAffiliated withDepartment of Biological and Environmental Sciences, University of Gothenburg
  • , R Henrik NilssonAffiliated withDepartment of Biological and Environmental Sciences, University of Gothenburg


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 componen ...

This is an excerpt from the content