Individuality, Stability, and Variability of the Plaque Microbiome.
Individuality, Stability, and Variability of the Plaque Microbiome.
复制标题
DOI：
10.3389/fmicb.2016.00564
复制
发表时间：
2016
影响因子：
5.2
通讯作者：
Borisy GG
中科院分区：
文献类型：
--
作者：
Utter DR;Mark Welch JL;Borisy GG
牙菌斑是由一组特征生物体组成的细菌生物膜。关于牙菌斑微生物组时间动态的独立于培养的高通量分析的信息相对较少。我们使用最小熵分解（一种类似于寡分型的基于信息论的方法，提供单核苷酸分辨率）来分析先前发布的时间序列数据集，并研究斑块微生物组在各种分析和分类水平上的动态。在属和 97% 操作分类单位 (OTU) 分辨率水平上，每个个体内的变异范围与数据集中其他个体的变异范围重叠。然而，当在寡聚型水平上进行分析时，重叠很大程度上消失了，这表明单核苷酸分辨率能够使个体彼此明确区分。所有样本中的绝大多数菌斑群落由来自中等数量的菌斑典型属的细菌组成，表明整体群落框架在个体之间共享。这些属中的每一个都围绕一个稳定的平均值波动，该平均值在个体之间存在差异，其中一些属的个体间变异性高于其他属。因此，在属水平上，个体之间的差异不在于主要属的身份，而在于这些属的比例在不同嘴之间始终存在差异。然而，在寡型水平上，我们检测到了寡型“指纹”，这是一组高度个体特异性的持续丰富的寡型，随着时间的推移，在稳定的平均值附近波动。例如，在棒状杆菌属中，每个个体中都可以检测到十多种寡型，其中不同的子集在任何特定个体中都达到高丰度。这种模式表明，每张嘴都含有略有不同的生物群落。我们还将这里描述的中国牙菌斑群落与之前描述的西方牙菌斑群落进行了比较，如对人类微生物组项目的数据分析所代表的那样，发现中国和西方的龈上菌斑之间没有重大差异。总之，我们发现菌斑微生物组在寡型水平上高度个体化，其特征是群落成员的稳定性，以及个体之间和随着时间的推移群落成员的相对丰度的变化。
Dental plaque is a bacterial biofilm composed of a characteristic set of organisms. Relatively little information from cultivation-independent, high-throughput analyses has been published on the temporal dynamics of the dental plaque microbiome. We used Minimum Entropy Decomposition, an information theory-based approach similar to oligotyping that provides single-nucleotide resolution, to analyze a previously published time series data set and investigate the dynamics of the plaque microbiome at various analytic and taxonomic levels. At both the genus and 97% Operational Taxonomic Unit (OTU) levels of resolution, the range of variation within each individual overlapped that of other individuals in the data set. When analyzed at the oligotype level, however, the overlap largely disappeared, showing that single-nucleotide resolution enables differentiation of individuals from one another without ambiguity. The overwhelming majority of the plaque community in all samples was made up of bacteria from a moderate number of plaque-typical genera, indicating that the overall community framework is shared among individuals. Each of these genera fluctuated in abundance around a stable mean that varied between individuals, with some genera having higher inter-individual variability than others. Thus, at the genus level, differences between individuals lay not in the identity of the major genera but in consistently differing proportions of these genera from mouth to mouth. However, at the oligotype level, we detected oligotype “fingerprints,” a highly individual-specific set of persistently abundant oligotypes fluctuating around a stable mean over time. For example, within the genus Corynebacterium, more than a dozen oligotypes were detectable in each individual, of which a different subset reached high abundance in any given person. This pattern suggests that each mouth contains a subtly different community of organisms. We also compared the Chinese plaque community characterized here to previously characterized Western plaque communities, as represented by analyses of data emerging from the Human Microbiome Project, and found no major differences between Chinese and Western supragingival plaque. In conclusion, we found the plaque microbiome to be highly individualized at the oligotype level and characterized by stability of community membership, with variability in the relative abundance of community members between individuals and over time.