Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle.
Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle.
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DOI：
10.1186/s40168-016-0160-7
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发表时间：
2016-04-12
期刊：
影响因子：
15.5
通讯作者：
Huse SM
中科院分区：
文献类型：
--
作者：
Gorvitovskaia A;Holmes SP;Huse SM
在肠道微生物组的一系列研究中，“肠型”已被用于对在排序分析中聚集在一起的肠道微生物组样品进行分类。最初，描述了三种不同的肠型，尽管后来的研究将其减少到两个集群，一个由拟杆菌属或梭菌目物种主导，在西方（美国和西欧）受试者中更常见，另一个由普雷沃菌属主导，更常与非西方受试者相关。这两个分类群，拟杆菌属和普雷沃菌属，已被假定为代表一致的潜在微生物群落，但没有人已经证明存在额外的微生物分类群的研究，可以定义这些社区。我们分析了来自五大洲样本的五项先前研究的微生物组数据。我们清楚地表明，在所有研究中，没有一致的细菌类群与拟杆菌属或普雷沃菌属主导的群落相关。通过增加样本的数量和多样性，我们发现了拟杆菌和普雷沃菌的梯度，并且在最初提出的“肠型”假设中的主坐标图中缺乏明显的聚类。在许多排序图中观察到的样品的明显分离是由于样品的普雷沃氏菌和拟杆菌丰度的差异，并且不代表“肠型”内一致的微生物群落，并且与研究中的其他分类群无关。我们看到的投影与由拟杆菌和普雷沃菌的简单混合物产生的连续值一致;这两种生物标志物与投影轴显著相关。我们认为，以前的研究结果引用拟杆菌属和普雷沃菌为主的集群是由这两个类群在人类肠道和普雷沃菌丰富的样品的稀疏性比其他类群更大的相对丰度造成的工件的结果。我们认为，术语“肠型”是误导，因为它意味着一个潜在的一致性的社区类群和一个明确的分离套人类肠道样本，这两个都不支持更广泛的数据。我们建议使用“生物标志物”作为这些和其他与饮食，生活方式和疾病状态相关的分类群的更准确的描述。本文的在线版本（doi：10.1186/s40168-016-0160-7）包含补充材料，可供授权用户使用。
In a series of studies of the gut microbiome, “enterotypes” have been used to classify gut microbiome samples that cluster together in ordination analyses. Initially, three distinct enterotypes were described, although later studies reduced this to two clusters, one dominated by Bacteroides or Clostridiales species found more commonly in Western (American and Western European) subjects and the other dominated by Prevotella more often associated with non-Western subjects. The two taxa, Bacteroides and Prevotella, have been presumed to represent consistent underlying microbial communities, but no one has demonstrated the presence of additional microbial taxa across studies that can define these communities. We analyzed the combined microbiome data from five previous studies with samples across five continents. We clearly demonstrate that there are no consistent bacterial taxa associated with either Bacteroides- or Prevotella-dominated communities across the studies. By increasing the number and diversity of samples, we found gradients of both Bacteroides and Prevotella and a lack of the distinct clusters in the principal coordinate plots originally proposed in the “enterotypes” hypothesis. The apparent segregation of the samples seen in many ordination plots is due to the differences in the samples’ Prevotella and Bacteroides abundances and does not represent consistent microbial communities within the “enterotypes” and is not associated with other taxa across studies. The projections we see are consistent with a continuum of values created from a simple mixture of Bacteroides and Prevotella; these two biomarkers are significantly correlated to the projection axes. We suggest that previous findings citing Bacteroides- and Prevotella-dominated clusters are the result of an artifact caused by the greater relative abundance of these two taxa over other taxa in the human gut and the sparsity of Prevotella abundant samples. We believe that the term “enterotypes” is misleading because it implies both an underlying consistency of community taxa and a clear separation of sets of human gut samples, neither of which is supported by the broader data. We propose the use of “biomarker” as a more accurate description of these and other taxa that correlate with diet, lifestyle, and disease state. The online version of this article (doi:10.1186/s40168-016-0160-7) contains supplementary material, which is available to authorized users.