Minimum taxonomic criteria for bacterial genome sequence depositions and announcements

J Microbiol Methods. 2012 Apr;89(1):18-21. doi: 10.1016/j.mimet.2012.02.008. Epub 2012 Feb 16.


Multiple bioinformatic methods are available to analyse the information encoded within the complete genome sequence of a bacterium and accurately assign its species status or nearest phylogenetic neighbour. However, it is clear that even now in what is the third decade of bacterial genomics, taxonomically incorrect genome sequence depositions are still being made. We outline a simple scheme of bioinformatic analysis and a set of minimum criteria that should be applied to all bacterial genomic data to ensure that they are accurately assigned to the species or genus level prior to database deposition. To illustrate the utility of the bioinformatic workflow, we analysed the recently deposited genome sequence of Lactobacillus acidophilus 30SC and demonstrated that this DNA was in fact derived from a strain of Lactobacillus amylovorus. Using these methods researchers can ensure that the taxonomic accuracy of genome sequence depositions is maintained within the ever increasing nucleic acid datasets.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / classification*
  • Bacteria / genetics*
  • Computational Biology / methods*
  • Computational Biology / standards*
  • Genome, Bacterial*
  • Phylogeny