Imperial College London
Alternate

DrWilliamHanage

Faculty of Medicine, School of Public Health

Visiting Reader
 
 
 
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Contact

 

+44 (0)20 7594 3622w.hanage

 
 
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Location

 

Norfolk PlaceSt Mary's Campus

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Summary

 

Publications

Citation

BibTex format

@article{Bishop:2009:10.1186/1741-7007-7-3,
author = {Bishop, CJ and Aanensen, DM and Jordan, GE and Kilian, M and Hanage, WP and Spratt, BG},
doi = {10.1186/1741-7007-7-3},
journal = {BMC Biology},
title = {Assigning strains to bacterial species via the internet},
url = {http://dx.doi.org/10.1186/1741-7007-7-3},
volume = {7},
year = {2009}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - BackgroundMethods for assigning strains to bacterial species are cumbersome and no longer fit for purpose. The concatenated sequences of multiple house-keeping genes have been shown to be able to define and circumscribe bacterial species as sequence clusters. The advantage of this approach (multilocus sequence analysis; MLSA) is that, for any group of related species, a strain database can be produced and combined with software that allows query strains to be assigned to species via the internet. As an exemplar of this approach, we have studied a group of species, the viridans streptococci, which are very difficult to assign to species using standard taxonomic procedures, and have developed a website that allows species assignment via the internet.ResultsSeven house-keeping gene sequences were obtained from 420 streptococcal strains to produce a viridans group database. The reference tree produced using the concatenated sequences identified sequence clusters which, by examining the position on the tree of the type strain of each viridans group species, could be equated with species clusters. MLSA also identified clusters that may correspond to new species, and previously described species whose status needs to be re-examined. A generic website and software for electronic taxonomy was developed. This site http://www.eMLSA.net allows the sequences of the seven gene fragments of a query strain to be entered and for the species assignment to be returned, according to its position within an assigned species cluster on the reference tree.ConclusionThe MLSA approach resulted in the identification of well-resolved species clusters within this taxonomically challenging group and, using the software we have developed, allows unknown strains to be assigned to viridans species via the internet. Submission of new strains will provide a growing resource for the taxonomy of viridans group streptococci, allowing the recognition of potential new species and taxonomic anomalies. M
AU  - Bishop,CJ
AU  - Aanensen,DM
AU  - Jordan,GE
AU  - Kilian,M
AU  - Hanage,WP
AU  - Spratt,BG
DO  - 10.1186/1741-7007-7-3
PY  - 2009///
SN  - 1741-7007
TI  - Assigning strains to bacterial species via the internet
T2  - BMC Biology
UR  - http://dx.doi.org/10.1186/1741-7007-7-3
UR  - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000264027900001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
UR  - http://hdl.handle.net/10044/1/30064
VL  - 7
ER  -
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