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Mining virulence genes using metagenomics.

Belda-Ferre P, Cabrera-Rubio R, Moya A, Mira A - PLoS ONE (2011)

Bottom Line: When a bacterial genome is compared to the metagenome of an environment it inhabits, most genes recruit at high sequence identity.From an applied point of view, MIs of human pathogens (e.g. those identified in enterohaemorragic Escherichia coli against the gut metagenome or in pathogenic Neisseria meningitidis against the oral metagenome) include virulence genes that appear to be absent in related strains or species present in the microbiome of healthy individuals.Using this approach, we detect well-known pathogenicity islands and identify new potential virulence genes in several human pathogens.

View Article: PubMed Central - PubMed

Affiliation: Joint Unit of Research in Genomics and Health, Centre for Public Health Research-Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain.

ABSTRACT
When a bacterial genome is compared to the metagenome of an environment it inhabits, most genes recruit at high sequence identity. In free-living bacteria (for instance marine bacteria compared against the ocean metagenome) certain genomic regions are totally absent in recruitment plots, representing therefore genes unique to individual bacterial isolates. We show that these Metagenomic Islands (MIs) are also visible in bacteria living in human hosts when their genomes are compared to sequences from the human microbiome, despite the compartmentalized structure of human-related environments such as the gut. From an applied point of view, MIs of human pathogens (e.g. those identified in enterohaemorragic Escherichia coli against the gut metagenome or in pathogenic Neisseria meningitidis against the oral metagenome) include virulence genes that appear to be absent in related strains or species present in the microbiome of healthy individuals. We propose that this strategy (i.e. recruitment analysis of pathogenic bacteria against the metagenome of healthy subjects) can be used to detect pathogenicity regions in species where the genes involved in virulence are poorly characterized. Using this approach, we detect well-known pathogenicity islands and identify new potential virulence genes in several human pathogens.

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Detecting virulence plasmids by metagenomics.Protein recruitment plots obtained by comparing the healthy gut metagenome against plasmids of pathogenic Shigella flexneri and E. coli strains. The islands identify known virulence genes whereas genes involved in plasmid housekeeping functions display high recruitment (see Table S2).
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pone-0024975-g002: Detecting virulence plasmids by metagenomics.Protein recruitment plots obtained by comparing the healthy gut metagenome against plasmids of pathogenic Shigella flexneri and E. coli strains. The islands identify known virulence genes whereas genes involved in plasmid housekeeping functions display high recruitment (see Table S2).

Mentions: Given that many virulence genes are coded in extrachromosomal elements, the same approach was followed for well-characterized bacterial plasmids of enteric bacteria. Despite the promiscuous nature of many extrachromosomal replicons, most plasmids genes from pathogenic strains of E. coli showed an intense coverage (Figure 2), showing that these are frequent among natural populations of commensal enteric bacteria. However, clear islands were also identified. Examination of gene content in plasmids' MIs indicated that virulence genes were again absent from the recruitments (Table S2), whereas genes involved in replication, conjugation and other basic plasmid functions were well represented in the gut metagenome. Thus, metagenomic recruitments can prove useful to detect virulence plasmids and to determine which regions from an uncharacterized plasmid may be involved in pathogenicity.


Mining virulence genes using metagenomics.

Belda-Ferre P, Cabrera-Rubio R, Moya A, Mira A - PLoS ONE (2011)

Detecting virulence plasmids by metagenomics.Protein recruitment plots obtained by comparing the healthy gut metagenome against plasmids of pathogenic Shigella flexneri and E. coli strains. The islands identify known virulence genes whereas genes involved in plasmid housekeeping functions display high recruitment (see Table S2).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3198465&req=5

pone-0024975-g002: Detecting virulence plasmids by metagenomics.Protein recruitment plots obtained by comparing the healthy gut metagenome against plasmids of pathogenic Shigella flexneri and E. coli strains. The islands identify known virulence genes whereas genes involved in plasmid housekeeping functions display high recruitment (see Table S2).
Mentions: Given that many virulence genes are coded in extrachromosomal elements, the same approach was followed for well-characterized bacterial plasmids of enteric bacteria. Despite the promiscuous nature of many extrachromosomal replicons, most plasmids genes from pathogenic strains of E. coli showed an intense coverage (Figure 2), showing that these are frequent among natural populations of commensal enteric bacteria. However, clear islands were also identified. Examination of gene content in plasmids' MIs indicated that virulence genes were again absent from the recruitments (Table S2), whereas genes involved in replication, conjugation and other basic plasmid functions were well represented in the gut metagenome. Thus, metagenomic recruitments can prove useful to detect virulence plasmids and to determine which regions from an uncharacterized plasmid may be involved in pathogenicity.

Bottom Line: When a bacterial genome is compared to the metagenome of an environment it inhabits, most genes recruit at high sequence identity.From an applied point of view, MIs of human pathogens (e.g. those identified in enterohaemorragic Escherichia coli against the gut metagenome or in pathogenic Neisseria meningitidis against the oral metagenome) include virulence genes that appear to be absent in related strains or species present in the microbiome of healthy individuals.Using this approach, we detect well-known pathogenicity islands and identify new potential virulence genes in several human pathogens.

View Article: PubMed Central - PubMed

Affiliation: Joint Unit of Research in Genomics and Health, Centre for Public Health Research-Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain.

ABSTRACT
When a bacterial genome is compared to the metagenome of an environment it inhabits, most genes recruit at high sequence identity. In free-living bacteria (for instance marine bacteria compared against the ocean metagenome) certain genomic regions are totally absent in recruitment plots, representing therefore genes unique to individual bacterial isolates. We show that these Metagenomic Islands (MIs) are also visible in bacteria living in human hosts when their genomes are compared to sequences from the human microbiome, despite the compartmentalized structure of human-related environments such as the gut. From an applied point of view, MIs of human pathogens (e.g. those identified in enterohaemorragic Escherichia coli against the gut metagenome or in pathogenic Neisseria meningitidis against the oral metagenome) include virulence genes that appear to be absent in related strains or species present in the microbiome of healthy individuals. We propose that this strategy (i.e. recruitment analysis of pathogenic bacteria against the metagenome of healthy subjects) can be used to detect pathogenicity regions in species where the genes involved in virulence are poorly characterized. Using this approach, we detect well-known pathogenicity islands and identify new potential virulence genes in several human pathogens.

Show MeSH
Related in: MedlinePlus