Multilocus Sequence Typing Breathes Life into a Microbial Metagenome
Publication Date
December 20, 2006
Journal
PLOS ONE
Authors
Eshwar Mahenthiralingam, Adam Baldwin, Pavel Drevinek, Elke Vanlaere, et al
Volume
1
Issue
1
Pages
e17
DOI
http://doi.org/10.1371/journal.pone.0000017
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0000017
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/17183643
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1762331
Europe PMC
http://europepmc.org/abstract/MED/17183643
Web of Science
000207443600017
Scopus
34547701247
Mendeley
http://www.mendeley.com/research/multilocus-sequence-typing-breathes-life-microbial-metagenome
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Mendeley | Further Information

{"title"=>"Multilocus sequence typing breathes life into a microbial metagenome", "type"=>"journal", "authors"=>[{"first_name"=>"Eshwar", "last_name"=>"Mahenthiralingam", "scopus_author_id"=>"7004442378"}, {"first_name"=>"Adam", "last_name"=>"Baldwin", "scopus_author_id"=>"8832426500"}, {"first_name"=>"Pavel", "last_name"=>"Drevinek", "scopus_author_id"=>"6603477890"}, {"first_name"=>"Elke", "last_name"=>"Vanlaere", "scopus_author_id"=>"8537971000"}, {"first_name"=>"Peter", "last_name"=>"Vandamme", "scopus_author_id"=>"56211244100"}, {"first_name"=>"John J.", "last_name"=>"LiPuma", "scopus_author_id"=>"7006417100"}, {"first_name"=>"Chris G.", "last_name"=>"Dowson", "scopus_author_id"=>"7004517413"}], "year"=>2006, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-34547701247", "pui"=>"352589018", "pmid"=>"17183643", "doi"=>"10.1371/journal.pone.0000017", "sgr"=>"34547701247", "isbn"=>"1932-6203", "issn"=>"19326203"}, "id"=>"e0baab37-94df-3540-9799-5204ec7d6076", "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.", "link"=>"http://www.mendeley.com/research/multilocus-sequence-typing-breathes-life-microbial-metagenome", "reader_count"=>90, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>5, "Researcher"=>27, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>2, "Student > Master"=>9, "Other"=>2, "Student > Bachelor"=>8, "Lecturer"=>1, "Professor"=>7}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>5, "Researcher"=>27, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>2, "Student > Master"=>9, "Other"=>2, "Student > Bachelor"=>8, "Lecturer"=>1, "Professor"=>7}, "reader_count_by_subject_area"=>{"Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>77, "Medicine and Dentistry"=>2, "Chemistry"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>77}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Environmental Science"=>{"Environmental Science"=>3}}, "reader_count_by_country"=>{"United States"=>5, "United Kingdom"=>2, "Portugal"=>3, "India"=>1, "New Zealand"=>1, "Canada"=>2, "Sweden"=>2, "Austria"=>1, "Belgium"=>1, "Poland"=>2, "Brazil"=>1, "Mexico"=>1, "France"=>2, "Chile"=>1, "Germany"=>1}, "group_count"=>3}

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  • {"files"=>["https://ndownloader.figshare.com/files/954353"], "description"=>"<div><p>Phylogenetic analysis of the concatenated MLST loci was performed on a collection of representative <i>B. cepacia</i> complex strains as described <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000017#pone.0000017-Baldwin1\" target=\"_blank\">[11]</a>.</p>\n <p>\n <i>B. cepacia</i> complex Group K, its separation into two clusters (A and B), and the position of the ST102 clones and SAR-1 metagenome.</p>\n <p>The positions of the genome reference strains, <i>B. cepacia</i> complex Group K strain 383 and <i>B. cenocepacia</i> J2315, are also indicated.</p>\n <p>Bootstrap values and genetic distance scale are shown.</p></div>", "links"=>[], "tags"=>["sar-1", "cultivable", "st102"], "article_id"=>624640, "categories"=>["Molecular Biology", "Medicine", "Microbiology", "Genetics", "Infectious Diseases", "Biotechnology", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Eshwar Mahenthiralingam", "Adam Baldwin", "Pavel Drevinek", "Elke Vanlaere", "Peter Vandamme", "John J. LiPuma", "Chris G. Dowson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000017.g001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analysis_of_SAR_1_and_the_cultivable_ST102_isolates_/624640", "title"=>"Phylogenetic analysis of SAR-1 and the cultivable ST102 isolates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:58:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/954512"], "description"=>"<div><p>The distribution of homologous genes (blue) and absent genes (yellow) are shown for each <i>B. cepacia</i> complex Group K genome (indicated on the right).</p>\n <p>The panels correspond to the three J2315 chromosomes (chromosome number indicated on the left).</p></div>", "links"=>[], "tags"=>["sar-1", "383", "genes", "homologous"], "article_id"=>624798, "categories"=>["Molecular Biology", "Medicine", "Microbiology", "Genetics", "Infectious Diseases", "Biotechnology", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Eshwar Mahenthiralingam", "Adam Baldwin", "Pavel Drevinek", "Elke Vanlaere", "Peter Vandamme", "John J. LiPuma", "Chris G. Dowson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000017.g003", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genomic_distribution_of_Burkholderia_SAR_1_and_B_cepacia_383_genes_homologous_to_B_cenocepacia_J2315_/624798", "title"=>"Genomic distribution of <i>Burkholderia</i> SAR-1 and <i>B. cepacia</i> 383 genes homologous to <i>B. cenocepacia</i> J2315.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:59:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/954443"], "description"=>"<div><p>The genomic macrorestriction fingerprint profiles resulting from restriction digestion with <i>Spe</i>I (Panel A) and <i>Xba</i>I (Panel B) are shown for the following strains in each lane: 1, LMG 23255, 2, LMG 23250, 3, LMG 23251, and 4, LMG 23253.</p>\n <p>Molecular size markers were run in the lane M and the size of relevant bands is indicated in kb.</p></div>", "links"=>[], "tags"=>["cultivable", "st102"], "article_id"=>624732, "categories"=>["Molecular Biology", "Medicine", "Microbiology", "Genetics", "Infectious Diseases", "Biotechnology", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Eshwar Mahenthiralingam", "Adam Baldwin", "Pavel Drevinek", "Elke Vanlaere", "Peter Vandamme", "John J. LiPuma", "Chris G. Dowson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000017.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Macrorestriction_analysis_of_the_cultivable_ST102_strains_/624732", "title"=>"Macrorestriction analysis of the cultivable ST102 strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:58:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/470097", "https://ndownloader.figshare.com/files/470141"], "description"=>"<div><p>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, <em>Burkholderia</em> 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 <em>Burkholderia cepacia</em> complex Group K. Comparison of the <em>Burkholderia</em> SAR-1 metagenome to closely related <em>B. cepacia</em> 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 <em>Burkholderia</em> 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 <em>Burkholderia</em> 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.</p> </div>", "links"=>[], "tags"=>["multilocus", "typing", "breathes", "microbial", "metagenome"], "article_id"=>152641, "categories"=>["Molecular Biology", "Medicine", "Cancer", "Microbiology", "Genetics", "Biotechnology", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Eshwar Mahenthiralingam", "Adam Baldwin", "Pavel Drevinek", "Elke Vanlaere", "Peter Vandamme", "John J. LiPuma", "Chris G. Dowson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0000017.s001", "https://dx.doi.org/10.1371/journal.pone.0000017.s002"], "stats"=>{"downloads"=>11, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Multilocus_Sequence_Typing_Breathes_Life_into_a_Microbial_Metagenome/152641", "title"=>"Multilocus Sequence Typing Breathes Life into a Microbial Metagenome", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2006-12-20 00:44:01"}

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