Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing.
Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing.
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DOI：
10.1371/journal.pone.0041606
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Harmsen D
中科院分区：
文献类型：
--
作者：
Jünemann S;Prior K;Szczepanowski R;Harks I;Ehmke B;Goesmann A;Stoye J;Harmsen D
牙周炎是世界上最常见的疾病之一，由病原菌和炎症宿主反应的混合物引起，并且通常通过抗菌剂作为洁治和根面平整（SRP）的辅助治疗。我们的研究旨在阐明探索性和描述性的时间变化之间的细菌群落的患者治疗SRP单独与SRP加抗生素。这是第一个使用离子激流个人基因组机器（PGM）的宏基因组研究。对4名慢性牙周炎患者的8个龈下菌斑样本进行了分析，分别在干预前和干预后2个月进行。产生来自16S rRNA基因的V6高变区的扩增子，并在314芯片上对每个扩增子进行测序。将测序读段聚类成操作分类单位（OTU，3%距离），通过群落度量描述，并进行分类学分类。将每个样品范围从599，933至650，416的读数分别聚类成1，648至2，659个非单例OTU。无论治疗类型如何，治疗后所有样本中的多样性（Shannon和Simpson）都有所增加，而丰富度（ACE）则没有显示出相关性。分类学分析揭示了两种治疗方法在所有分类学水平上的不同微生物变化。最值得注意的是，所有携带牙周致病菌的卟啉单胞菌属、坦那氏菌属、密螺旋体属和丝状菌属几乎仅在SPR和抗生素治疗组中被去除。对T.通过实时PCR分析证实了牙龈卟啉单胞菌和牙龈卟啉单胞菌的结果。在未来，无假设宏基因组分析可能是理解多微生物疾病的关键，并用于治疗监测。因此，随着读取长度持续增加和成本降低，快速台式测序仪如PGM可能最终用于常规诊断。
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.
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影响因子：
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作者：
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通讯作者：
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影响因子：
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作者：
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影响因子：
6.7
作者：
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