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Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease

The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular di...

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Autores principales: Liu, Bo, Faller, Lina L., Klitgord, Niels, Mazumdar, Varun, Ghodsi, Mohammad, Sommer, Daniel D., Gibbons, Theodore R., Treangen, Todd J., Chang, Yi-Chien, Li, Shan, Stine, O. Colin, Hasturk, Hatice, Kasif, Simon, Segrè, Daniel, Pop, Mihai, Amar, Salomon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3366996/
https://www.ncbi.nlm.nih.gov/pubmed/22675498
http://dx.doi.org/10.1371/journal.pone.0037919
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author Liu, Bo
Faller, Lina L.
Klitgord, Niels
Mazumdar, Varun
Ghodsi, Mohammad
Sommer, Daniel D.
Gibbons, Theodore R.
Treangen, Todd J.
Chang, Yi-Chien
Li, Shan
Stine, O. Colin
Hasturk, Hatice
Kasif, Simon
Segrè, Daniel
Pop, Mihai
Amar, Salomon
author_facet Liu, Bo
Faller, Lina L.
Klitgord, Niels
Mazumdar, Varun
Ghodsi, Mohammad
Sommer, Daniel D.
Gibbons, Theodore R.
Treangen, Todd J.
Chang, Yi-Chien
Li, Shan
Stine, O. Colin
Hasturk, Hatice
Kasif, Simon
Segrè, Daniel
Pop, Mihai
Amar, Salomon
author_sort Liu, Bo
collection PubMed
description The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Through the sequencing of the 16S rRNA gene and of whole community DNA we provide a glimpse at the global genetic, metabolic, and ecological changes associated with periodontitis in 15 subgingival plaque samples, four from each of two periodontitis patients, and the remaining samples from three healthy individuals. We also demonstrate the power of whole-metagenome sequencing approaches in characterizing the genomes of key players in the oral microbiome, including an unculturable TM7 organism. We reveal the disease microbiome to be enriched in virulence factors, and adapted to a parasitic lifestyle that takes advantage of the disrupted host homeostasis. Furthermore, diseased samples share a common structure that was not found in completely healthy samples, suggesting that the disease state may occupy a narrow region within the space of possible configurations of the oral microbiome. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. Despite a modest level of sequencing (∼2 lanes Illumina 76 bp PE) and high human DNA contamination (up to ∼90%) we were able to partially reconstruct several oral microbes and to preliminarily characterize some systems-level differences between the healthy and diseased oral microbiomes.
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spelling pubmed-33669962012-06-06 Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease Liu, Bo Faller, Lina L. Klitgord, Niels Mazumdar, Varun Ghodsi, Mohammad Sommer, Daniel D. Gibbons, Theodore R. Treangen, Todd J. Chang, Yi-Chien Li, Shan Stine, O. Colin Hasturk, Hatice Kasif, Simon Segrè, Daniel Pop, Mihai Amar, Salomon PLoS One Research Article The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Through the sequencing of the 16S rRNA gene and of whole community DNA we provide a glimpse at the global genetic, metabolic, and ecological changes associated with periodontitis in 15 subgingival plaque samples, four from each of two periodontitis patients, and the remaining samples from three healthy individuals. We also demonstrate the power of whole-metagenome sequencing approaches in characterizing the genomes of key players in the oral microbiome, including an unculturable TM7 organism. We reveal the disease microbiome to be enriched in virulence factors, and adapted to a parasitic lifestyle that takes advantage of the disrupted host homeostasis. Furthermore, diseased samples share a common structure that was not found in completely healthy samples, suggesting that the disease state may occupy a narrow region within the space of possible configurations of the oral microbiome. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. Despite a modest level of sequencing (∼2 lanes Illumina 76 bp PE) and high human DNA contamination (up to ∼90%) we were able to partially reconstruct several oral microbes and to preliminarily characterize some systems-level differences between the healthy and diseased oral microbiomes. Public Library of Science 2012-06-04 /pmc/articles/PMC3366996/ /pubmed/22675498 http://dx.doi.org/10.1371/journal.pone.0037919 Text en Liu et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Liu, Bo
Faller, Lina L.
Klitgord, Niels
Mazumdar, Varun
Ghodsi, Mohammad
Sommer, Daniel D.
Gibbons, Theodore R.
Treangen, Todd J.
Chang, Yi-Chien
Li, Shan
Stine, O. Colin
Hasturk, Hatice
Kasif, Simon
Segrè, Daniel
Pop, Mihai
Amar, Salomon
Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease
title Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease
title_full Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease
title_fullStr Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease
title_full_unstemmed Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease
title_short Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease
title_sort deep sequencing of the oral microbiome reveals signatures of periodontal disease
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3366996/
https://www.ncbi.nlm.nih.gov/pubmed/22675498
http://dx.doi.org/10.1371/journal.pone.0037919
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