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Multilocus sequence typing breathes life into a microbial metagenome

Eshwar Mahenthiralingam, Adam Baldwin, Pavel Drevinek, Elke Vanlaere, Peter Vandamme UGent, John J LiPuma and Chris G Dowson (2006) PLOS ONE. 1(1).
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
journal title
PLOS ONE
PLoS One
volume
1
issue
1
article number
e17
Web of Science type
Article
Web of Science id
000207443600017
ISSN
1932-6203
DOI
10.1371/journal.pone.0000017
language
English
UGent publication?
yes
classification
A1
id
370301
handle
http://hdl.handle.net/1854/LU-370301
date created
2007-06-20 14:38:00
date last changed
2016-12-21 15:42:15
@article{370301,
  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.},
  articleno    = {e17},
  author       = {Mahenthiralingam, Eshwar and Baldwin, Adam and Drevinek, Pavel and Vanlaere, Elke and Vandamme, Peter and LiPuma, John J and Dowson, Chris G},
  issn         = {1932-6203},
  journal      = {PLOS ONE},
  language     = {eng},
  number       = {1},
  title        = {Multilocus sequence typing breathes life into a microbial metagenome},
  url          = {http://dx.doi.org/10.1371/journal.pone.0000017},
  volume       = {1},
  year         = {2006},
}

Chicago
Mahenthiralingam, Eshwar, Adam Baldwin, Pavel Drevinek, Elke Vanlaere, Peter Vandamme, John J LiPuma, and Chris G Dowson. 2006. “Multilocus Sequence Typing Breathes Life into a Microbial Metagenome.” Plos One 1 (1).
APA
Mahenthiralingam, Eshwar, Baldwin, A., Drevinek, P., Vanlaere, E., Vandamme, P., LiPuma, J. J., & Dowson, C. G. (2006). Multilocus sequence typing breathes life into a microbial metagenome. PLOS ONE, 1(1).
Vancouver
1.
Mahenthiralingam E, Baldwin A, Drevinek P, Vanlaere E, Vandamme P, LiPuma JJ, et al. Multilocus sequence typing breathes life into a microbial metagenome. PLOS ONE. 2006;1(1).
MLA
Mahenthiralingam, Eshwar, Adam Baldwin, Pavel Drevinek, et al. “Multilocus Sequence Typing Breathes Life into a Microbial Metagenome.” PLOS ONE 1.1 (2006): n. pag. Print.