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

Synonyms

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

Definition

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/.

Introduction

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...

This is a preview of subscription content, log in to check access.

References

  1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389–402.PubMedCentralPubMedGoogle Scholar
  2. Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet G-A, Abarenkov K, Petri A, Alm Rosenblad M, Nilsson RH. Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets. Antonie van Leeuwenhoek. 2011;100(3):471–5.PubMedGoogle Scholar
  3. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2009;37(Database issue):D26–31.Google Scholar
  4. Bidartondo MI. Preserving accuracy in GenBank. Science (New York). 2008;319(5870):1616.Google Scholar
  5. Cannone JJ, Subramanian S, Schnare MN, Collett JR, D’Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics. 2002;3:2.PubMedCentralPubMedGoogle Scholar
  6. Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res. 2007;35(Database issue):D169–72.Google Scholar
  7. Desai N, Antonopoulos DA, Gilbert JA, Glass EM, Meyer F. From genomics to metagenomics. Curr Opin Biotechnol. 2012;23(1):72–6.PubMedGoogle Scholar
  8. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72(7):5069–72.PubMedCentralPubMedGoogle Scholar
  9. Eddy S. HMMER. http://hmmer.janelia.org (2010), Accessed 2012-05-15.
  10. Hartmann M, Howes CG, Abarenkov K, Mohn WW, Nilsson RH. V-Xtractor: an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences. J Microbiol Method. 2010;83(2):250–3.Google Scholar
  11. Hartmann M, Howes CG, Veldre V, Schneider S, Vaishampayan PA, Yannarell AC, Quince C, Johansson P, Björkroth KJ, Abarenkov K, Hallam SJ, Mohn WW, Nilsson RH. V-REVCOMP: automated high-throughput detection of reverse complementary 16S rRNA gene sequences in large environmental and taxonomic datasets. FEMS Microbiol Lett. 2011;319(2):140–5.PubMedGoogle Scholar
  12. Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 2008;9(4):286–98.PubMedGoogle Scholar
  13. Lupi R, de Meo PD, Picardi E, D’Antonio M, Paoletti D, Castrignanò T, Pesole G, Gissi C. MitoZoa: a curated mitochondrial genome database of metazoans for comparative genomics studies. Mitochondrion. 2010;10(2):192–9.PubMedGoogle Scholar
  14. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007;35(21):7188–96.PubMedCentralPubMedGoogle Scholar

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