The Human Oral Microbiome
The Human Oral Microbiome
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DOI：
10.1128/jb.00542-10
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发表时间：
2010-10-01
影响因子：
3.2
通讯作者：
Wade, William G.
中科院分区：
文献类型：
--
作者：
Dewhirst, Floyd E.;Chen, Tuste;Wade, William G.
人类口腔包含许多不同的栖息地，包括牙齿、牙龈沟、舌头、脸颊、硬腭和软腭以及扁桃体，这些都是细菌的定植地。口腔微生物组在物种水平上由600多个流行的分类群组成，不同的亚群在不同的栖息地占主导地位。口腔微生物组已通过培养和非培养依赖性分子方法（如16S rRNA克隆）进行了广泛表征。不幸的是，绝大多数未命名的口腔分类群是由克隆编号或16S rRNA GenBank登录号引用的，通常没有分类锚。这项研究的第一个目的是将16S rRNA基因序列收集到一个基于遗传学的数据库中，即人类口腔微生物组数据库（HOMD），并使其可通过网络访问（www.homd.org）。HOMD包括13门中的619个分类群，如下：放线菌门、拟杆菌门、衣原体门、绿菌门、广古菌门、厚壁菌门、梭菌门、变形菌门、螺旋体门、SR1、增效菌门、Tenericutes和TM7。第二个目标是分析从口腔微生物群研究中分离的36，043个16S rRNA基因克隆，以确定分类群的相对丰度并鉴定新的候选分类群。分析确定了1，179个分类群，其中24%已命名，8%为栽培但未命名，68%为未栽培的植物类型。经过验证，434个新的，非单细胞分类群将被添加到HOMD。需要占90%，95%，或99%的克隆检查的分类群的数量分别为259，413，和875，。HOMD是人类相关微生物组的第一个策划描述，并为了解微生物组在健康和疾病中的作用提供了工具。
The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene sequences into a curated phylogeny-based database, the Human Oral Microbiome Database (HOMD), and make it web accessible (www.homd.org). The HOMD includes 619 taxa in 13 phyla, as follows: Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Euryarchaeota, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, SR1, Synergistetes, Tenericutes, and TM7. The second aim was to analyze 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa. The analysis identified 1,179 taxa, of which 24% were named, 8% were cultivated but unnamed, and 68% were uncultivated phylotypes. Upon validation, 434 novel, nonsingleton taxa will be added to the HOMD. The number of taxa needed to account for 90%, 95%, or 99% of the clones examined is 259, 413, and 875, respectively. The HOMD is the first curated description of a human-associated microbiome and provides tools for use in understanding the role of the microbiome in health and disease.