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Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes
Gardnerella vaginalis has long been associated with bacterial vaginosis, a condition that increases the risk of women to preterm birth, sexually transmitted infections, and other adverse sequelae. However, G. vaginalis is also commonly found in healthy asymptomatic women of all ages. This raises the...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5881158/ https://www.ncbi.nlm.nih.gov/pubmed/29632552 http://dx.doi.org/10.1111/eva.12555 |
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author | Cornejo, Omar E. Hickey, Roxana J. Suzuki, Haruo Forney, Larry J. |
author_facet | Cornejo, Omar E. Hickey, Roxana J. Suzuki, Haruo Forney, Larry J. |
author_sort | Cornejo, Omar E. |
collection | PubMed |
description | Gardnerella vaginalis has long been associated with bacterial vaginosis, a condition that increases the risk of women to preterm birth, sexually transmitted infections, and other adverse sequelae. However, G. vaginalis is also commonly found in healthy asymptomatic women of all ages. This raises the question if genetic differences among strains might distinguish potentially pathogenic from commensal strains. To disentangle the diversity of G. vaginalis, we invoked the concept of ecotypes—lineages of genetically and ecologically distinct strains within a named species—to better understand their evolutionary history and identify functional characteristics. We compared the genomes of G. vaginalis to six species in the closely related Bifidobacterium genus and found that G. vaginalis has a large accessory genome relative to Bifidobacterium, including many unique genes possibly involved in metabolism, drug resistance, and virulence. We then performed a comparative genomic analysis of 35 strains of G. vaginalis to infer a phylogeny based on the combined analysis of the core genome, using nucleotide substitution models, and the accessory genome, using gene gain/loss models. With the inferred tree topology, we performed comparisons of functional gene content among lineages that diverged at varying depths in the phylogeny and found significant differences in the representation of genes putatively involved in pathogenicity. Our functional enrichment analysis suggests that some lineages of G. vaginalis may possess enhanced pathogenic capabilities, including genes involved in mucus degradation like sialidases, while others may be commensal strains, lacking many of these pathogenic capabilities. The combined phylogenetic evidence and functional enrichment analysis allowed us to identify distinct ecotypes that have evolved in G. vaginalis as the result of the differential gene gain/loss for specific functions, including the capability to cause disease. We finally discuss how this analysis framework could be used to gain insight into the etiology of bacterial vaginosis and improve diagnosis. |
format | Online Article Text |
id | pubmed-5881158 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-58811582018-04-09 Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes Cornejo, Omar E. Hickey, Roxana J. Suzuki, Haruo Forney, Larry J. Evol Appl Original Articles Gardnerella vaginalis has long been associated with bacterial vaginosis, a condition that increases the risk of women to preterm birth, sexually transmitted infections, and other adverse sequelae. However, G. vaginalis is also commonly found in healthy asymptomatic women of all ages. This raises the question if genetic differences among strains might distinguish potentially pathogenic from commensal strains. To disentangle the diversity of G. vaginalis, we invoked the concept of ecotypes—lineages of genetically and ecologically distinct strains within a named species—to better understand their evolutionary history and identify functional characteristics. We compared the genomes of G. vaginalis to six species in the closely related Bifidobacterium genus and found that G. vaginalis has a large accessory genome relative to Bifidobacterium, including many unique genes possibly involved in metabolism, drug resistance, and virulence. We then performed a comparative genomic analysis of 35 strains of G. vaginalis to infer a phylogeny based on the combined analysis of the core genome, using nucleotide substitution models, and the accessory genome, using gene gain/loss models. With the inferred tree topology, we performed comparisons of functional gene content among lineages that diverged at varying depths in the phylogeny and found significant differences in the representation of genes putatively involved in pathogenicity. Our functional enrichment analysis suggests that some lineages of G. vaginalis may possess enhanced pathogenic capabilities, including genes involved in mucus degradation like sialidases, while others may be commensal strains, lacking many of these pathogenic capabilities. The combined phylogenetic evidence and functional enrichment analysis allowed us to identify distinct ecotypes that have evolved in G. vaginalis as the result of the differential gene gain/loss for specific functions, including the capability to cause disease. We finally discuss how this analysis framework could be used to gain insight into the etiology of bacterial vaginosis and improve diagnosis. John Wiley and Sons Inc. 2017-11-16 /pmc/articles/PMC5881158/ /pubmed/29632552 http://dx.doi.org/10.1111/eva.12555 Text en © 2017 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Articles Cornejo, Omar E. Hickey, Roxana J. Suzuki, Haruo Forney, Larry J. Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes |
title | Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes |
title_full | Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes |
title_fullStr | Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes |
title_full_unstemmed | Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes |
title_short | Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes |
title_sort | focusing the diversity of gardnerella vaginalis through the lens of ecotypes |
topic | Original Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5881158/ https://www.ncbi.nlm.nih.gov/pubmed/29632552 http://dx.doi.org/10.1111/eva.12555 |
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