The Library
Multilocus sequence typing breathes life into a microbial metagenome
Tools
Mahenthiralingam, Eshwar, Baldwin, Adam, Drevinek, Pavel, Vanlaere, Elke, Vandamme, Peter, LiPuma, John J. and Dowson, Christopher G. (2006) Multilocus sequence typing breathes life into a microbial metagenome. PLoS One, Vol.1 (No.1). doi:10.1371/journal.pone.0000017 ISSN 1932-6203.
|
PDF
WRAP_Baldwin_journal.pone.0000017%5B1%5D.pdf - Requires a PDF viewer. Download (282Kb) |
Official URL: http://dx.doi.org/10.1371/journal.pone.0000017
Abstract
Shot-gun sequencing of DNA isolated from the environment and the assembly of metagenomes from the resulting data has considerably advanced the study of microbial diversity. However, the subsequent matching of these hypothetical metagenomes to cultivable microorganisms is a limitation of such cultivation-independent methods of population analysis. Using a nucleotide sequence-based genetic typing method, multilocus sequence typing, we were able for the first time to match clonal cultivable isolates to a published and controversial bacterial metagenome, Burkholderia SAR-1, which derived from analysis of the Sargasso Sea. The matching cultivable isolates were all associated with infection and geographically widely distributed; taxonomic analysis demonstrated they were members of Burkholderia cepacia complex Group K. Comparison of the Burkholderia SAR-1 metagenome to closely related B. cepacia complex genomes indicated that it was greater than 98% intact in terms of conserved genes, and it also shared complete sequence identity with the cultivable isolates at random loci beyond the genes sampled by the multilocus sequence typing. Two features of the extant cultivable clones support the argument that the Burkholderia SAR-1 sequence may have been a contaminant in the original metagenomic survey: (i) their growth in conditions reflective of sea water was poor, suggesting the ocean was not their preferred habitat, and (ii) several of the matching isolates were epidemiologically linked to outbreaks of infection that resulted from contaminated medical devices or products, indicating an adaptive fitness of this bacterial strain towards contamination-associated environments. The ability to match identical cultivable strains of bacteria to a hypothetical metagenome is a unique feature of nucleotide sequence-based microbial typing methods; such matching would not have been possible with more traditional methods of genetic typing, such as those based on pattern matching of genomic restriction fragments or amplified DNA fragments. Overall, we have taken the first steps in moving the status of the Burkholderia SAR-1 metagenome from a hypothetical entity towards the basis for life of cultivable strains that may now be analysed in conjunction with the assembled metagenomic sequence data by the wider scientific community.
Item Type: | Journal Article | ||||
---|---|---|---|---|---|
Subjects: | Q Science > QR Microbiology | ||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) > Biological Sciences ( -2010) | ||||
Library of Congress Subject Headings (LCSH): | Nucleotide sequence, Gene mapping, Marine microbiology | ||||
Journal or Publication Title: | PLoS One | ||||
Publisher: | Public Library of Science | ||||
ISSN: | 1932-6203 | ||||
Official Date: | 20 December 2006 | ||||
Dates: |
|
||||
Volume: | Vol.1 | ||||
Number: | No.1 | ||||
Number of Pages: | 8 | ||||
DOI: | 10.1371/journal.pone.0000017 | ||||
Status: | Peer Reviewed | ||||
Publication Status: | Published | ||||
Access rights to Published version: | Open Access (Creative Commons) | ||||
Funder: | Natural Environment Research Council (Great Britain) (NERC), Wellcome Trust (London, England), Stichting Kapteinfonds, Nederlandse Cystic Fibrosis Stichting, Cystic Fibrosis Foundation | ||||
Grant number: | 072853 (WT), 075586 (WT), NER/T/S/2001/0299 (NERC) |
Data sourced from Thomson Reuters' Web of Knowledge
Request changes or add full text files to a record
Repository staff actions (login required)
View Item |
Downloads
Downloads per month over past year