Mining virulence genes using metagenomics.

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, representin...

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Autores principales:	Pedro Belda-Ferre, Raúl Cabrera-Rubio, Andrés Moya, Alex Mira
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ffe03dafd51948bb9b71d183514a3521
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spelling	oai:doaj.org-article:ffe03dafd51948bb9b71d183514a35212021-11-18T07:36:12ZMining virulence genes using metagenomics.1932-620310.1371/journal.pone.0024975https://doaj.org/article/ffe03dafd51948bb9b71d183514a35212011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22039404/?tool=EBIhttps://doaj.org/toc/1932-6203When 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.Pedro Belda-FerreRaúl Cabrera-RubioAndrés MoyaAlex MiraPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 10, p e24975 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Pedro Belda-Ferre Raúl Cabrera-Rubio Andrés Moya Alex Mira Mining virulence genes using metagenomics.
description	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.
format	article
author	Pedro Belda-Ferre Raúl Cabrera-Rubio Andrés Moya Alex Mira
author_facet	Pedro Belda-Ferre Raúl Cabrera-Rubio Andrés Moya Alex Mira
author_sort	Pedro Belda-Ferre
title	Mining virulence genes using metagenomics.
title_short	Mining virulence genes using metagenomics.
title_full	Mining virulence genes using metagenomics.
title_fullStr	Mining virulence genes using metagenomics.
title_full_unstemmed	Mining virulence genes using metagenomics.
title_sort	mining virulence genes using metagenomics.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/ffe03dafd51948bb9b71d183514a3521
work_keys_str_mv	AT pedrobeldaferre miningvirulencegenesusingmetagenomics AT raulcabrerarubio miningvirulencegenesusingmetagenomics AT andresmoya miningvirulencegenesusingmetagenomics AT alexmira miningvirulencegenesusingmetagenomics
_version_	1718423263971901440

Mining virulence genes using metagenomics.

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