The Library
Defining bacterial species in the genomic era : insights from the genus Acinetobacter
Tools
Chan, Jacqueline, Halachev, Mihail R., Loman, Nicholas J., Constantinidou, Chrystala and Pallen, Mark J. (2012) Defining bacterial species in the genomic era : insights from the genus Acinetobacter. BMC Microbiology, 12 (1). 302. doi:10.1186/1471-2180-12-302 ISSN 1471-2180.
|
Text
WRAP_Pallen1471-2180-12-302.pdf - Published Version Available under License Creative Commons Attribution 2.0.. Download (904Kb) | Preview |
Official URL: http://dx.doi.org/10.1186/1471-2180-12-302
Abstract
Background:
Microbial taxonomy remains a conservative discipline, relying on phenotypic information derived from growth in pure culture and techniques that are time-consuming and difficult to standardize, particularly when compared to the ease of modern high-throughput genome sequencing. Here, drawing on the genus Acinetobacter as a test case, we examine whether bacterial taxonomy could abandon phenotypic approaches and DNA-DNA hybridization and, instead, rely exclusively on analyses of genome sequence data.
Results:
In pursuit of this goal, we generated a set of thirteen new draft genome sequences, representing ten species, combined them with other publically available genome sequences and analyzed these 38 strains belonging to the genus. We found that analyses based on 16S rRNA gene sequences were not capable of delineating accepted species. However, a core genome phylogenetic tree proved consistent with the currently accepted taxonomy of the genus, while also identifying three misclassifications of strains in collections or databases. Among rapid distance-based methods, we found average-nucleotide identity (ANI) analyses delivered results consistent with traditional and phylogenetic classifications, whereas gene content based approaches appear to be too strongly influenced by the effects of horizontal gene transfer to agree with previously accepted species.
Conclusion:
We believe a combination of core genome phylogenetic analysis and ANI provides an appropriate method for bacterial species delineation, whereby bacterial species are defined as monophyletic groups of isolates with genomes that exhibit at least 95% pair-wise ANI. The proposed method is backwards compatible; it provides a scalable and uniform approach that works for both culturable and non-culturable species; is faster and cheaper than traditional taxonomic methods; is easily replicable and transferable among research institutions; and lastly, falls in line with Darwin’s vision of classification becoming, as far as is possible, genealogical.
Item Type: | Journal Article | ||||
---|---|---|---|---|---|
Subjects: | Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics |
||||
Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
||||
Library of Congress Subject Headings (LCSH): | Acinetobacter, Bacteria -- Classification, Genomes , Genomics | ||||
Journal or Publication Title: | BMC Microbiology | ||||
Publisher: | BioMed Central Ltd. | ||||
ISSN: | 1471-2180 | ||||
Official Date: | 2012 | ||||
Dates: |
|
||||
Volume: | 12 | ||||
Number: | 1 | ||||
Article Number: | 302 | ||||
DOI: | 10.1186/1471-2180-12-302 | ||||
Status: | Peer Reviewed | ||||
Publication Status: | Published | ||||
Access rights to Published version: | Restricted or Subscription Access | ||||
Date of first compliant deposit: | 26 December 2015 | ||||
Date of first compliant Open Access: | 26 December 2015 | ||||
Funder: | Medical Research Council (Great Britain) (MRC), National Institute for Health Research (Great Britain) (NIHR), Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC) | ||||
Grant number: | G0901717 (MRC) ; BBE0111791 (BBSRC) |
Request changes or add full text files to a record
Repository staff actions (login required)
View Item |
Downloads
Downloads per month over past year