Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing.

Periodontitis, one of the most common diseases in the world, is caused by a mixture of pathogenic bacteria and inflammatory host responses and often treated by antimicrobials as an adjunct to scaling and root planing (SRP). Our study aims to elucidate explorative and descriptive temporal shifts in b...

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Autores principales:	Sebastian Jünemann, Karola Prior, Rafael Szczepanowski, Inga Harks, Benjamin Ehmke, Alexander Goesmann, Jens Stoye, Dag Harmsen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/95c3b69907934b71bc799cb3c3e37a7d
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spelling	oai:doaj.org-article:95c3b69907934b71bc799cb3c3e37a7d2021-11-18T07:10:08ZBacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing.1932-620310.1371/journal.pone.0041606https://doaj.org/article/95c3b69907934b71bc799cb3c3e37a7d2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22870235/?tool=EBIhttps://doaj.org/toc/1932-6203Periodontitis, one of the most common diseases in the world, is caused by a mixture of pathogenic bacteria and inflammatory host responses and often treated by antimicrobials as an adjunct to scaling and root planing (SRP). Our study aims to elucidate explorative and descriptive temporal shifts in bacterial communities between patients treated by SRP alone versus SRP plus antibiotics. This is the first metagenomic study using an Ion Torrent Personal Genome Machine (PGM). Eight subgingival plaque samples from four patients with chronic periodontitis, taken before and two months after intervention were analyzed. Amplicons from the V6 hypervariable region of the 16S rRNA gene were generated and sequenced each on a 314 chip. Sequencing reads were clustered into operational taxonomic units (OTUs, 3% distance), described by community metrics, and taxonomically classified. Reads ranging from 599,933 to 650,416 per sample were clustered into 1,648 to 2,659 non-singleton OTUs, respectively. Increased diversity (Shannon and Simpson) in all samples after therapy was observed regardless of the treatment type whereas richness (ACE) showed no correlation. Taxonomic analysis revealed different microbial shifts between both therapy approaches at all taxonomic levels. Most remarkably, the genera Porphyromonas, Tannerella, Treponema, and Filifactor all harboring periodontal pathogenic species were removed almost only in the group treated with SPR and antibiotics. For the species T. forsythia and P. gingivalis results were corroborated by real-time PCR analysis. In the future, hypothesis free metagenomic analysis could be the key in understanding polymicrobial diseases and be used for therapy monitoring. Therefore, as read length continues to increase and cost to decrease, rapid benchtop sequencers like the PGM might finally be used in routine diagnostic.Sebastian JünemannKarola PriorRafael SzczepanowskiInga HarksBenjamin EhmkeAlexander GoesmannJens StoyeDag HarmsenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 8, p e41606 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sebastian Jünemann Karola Prior Rafael Szczepanowski Inga Harks Benjamin Ehmke Alexander Goesmann Jens Stoye Dag Harmsen Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing.
description	Periodontitis, one of the most common diseases in the world, is caused by a mixture of pathogenic bacteria and inflammatory host responses and often treated by antimicrobials as an adjunct to scaling and root planing (SRP). Our study aims to elucidate explorative and descriptive temporal shifts in bacterial communities between patients treated by SRP alone versus SRP plus antibiotics. This is the first metagenomic study using an Ion Torrent Personal Genome Machine (PGM). Eight subgingival plaque samples from four patients with chronic periodontitis, taken before and two months after intervention were analyzed. Amplicons from the V6 hypervariable region of the 16S rRNA gene were generated and sequenced each on a 314 chip. Sequencing reads were clustered into operational taxonomic units (OTUs, 3% distance), described by community metrics, and taxonomically classified. Reads ranging from 599,933 to 650,416 per sample were clustered into 1,648 to 2,659 non-singleton OTUs, respectively. Increased diversity (Shannon and Simpson) in all samples after therapy was observed regardless of the treatment type whereas richness (ACE) showed no correlation. Taxonomic analysis revealed different microbial shifts between both therapy approaches at all taxonomic levels. Most remarkably, the genera Porphyromonas, Tannerella, Treponema, and Filifactor all harboring periodontal pathogenic species were removed almost only in the group treated with SPR and antibiotics. For the species T. forsythia and P. gingivalis results were corroborated by real-time PCR analysis. In the future, hypothesis free metagenomic analysis could be the key in understanding polymicrobial diseases and be used for therapy monitoring. Therefore, as read length continues to increase and cost to decrease, rapid benchtop sequencers like the PGM might finally be used in routine diagnostic.
format	article
author	Sebastian Jünemann Karola Prior Rafael Szczepanowski Inga Harks Benjamin Ehmke Alexander Goesmann Jens Stoye Dag Harmsen
author_facet	Sebastian Jünemann Karola Prior Rafael Szczepanowski Inga Harks Benjamin Ehmke Alexander Goesmann Jens Stoye Dag Harmsen
author_sort	Sebastian Jünemann
title	Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing.
title_short	Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing.
title_full	Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing.
title_fullStr	Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing.
title_full_unstemmed	Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing.
title_sort	bacterial community shift in treated periodontitis patients revealed by ion torrent 16s rrna gene amplicon sequencing.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/95c3b69907934b71bc799cb3c3e37a7d
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Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing.

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