The human gut microbiome has been suggested to affect human health and thus has received considerable attention. To clarify the structure of the human gut microbiome, clustering methods are frequently applied to human gut taxonomic profiles. Enterotypes, i.e., clusters of individuals with similar microbiome composition, are well-studied and characterized. However, only a few detailed studies on assemblages, i.e., clusters of co-occurring bacterial taxa, have been conducted. Particularly, the relationship between the enterotype and assemblage is not well-understood. In this study, we detected gut microbiome assemblages using a latent Dirichlet allocation (LDA) method. We applied LDA to a large-scale human gut metagenome dataset and found that a 4-assemblage LDA model could represent relationships between enterotypes and assemblages with high interpretability. This model indicated that each individual tends to have several assemblages, three of which corresponded to the three classically recognized enterotypes. Conversely, the fourth assemblage corresponded to no enterotypes and emerged in all enterotypes. Interestingly, the dominant genera of this assemblage (Clostridium, Eubacterium, Faecalibacterium, Roseburia, Coprococcus, and Butyrivibrio) included butyrate-producing species such as Faecalibacterium prausnitzii. Indeed, the fourth assemblage significantly positively correlated with three butyrate-producing functions. We conducted an assemblage analysis on a large-scale human gut metagenome dataset using LDA. The present study revealed that there is an enterotype-independent assemblage.

中文翻译：

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使用潜在狄利克雷分配揭示人类肠道微生物组中的微生物组合结构。


人类肠道微生物群被认为会影响人类健康，因此受到了相当多的关注。为了阐明人类肠道微生物组的结构，聚类方法经常应用于人类肠道分类谱。肠型，即具有相似微生物组组成的个体簇，已得到充分研究和表征。然而，仅对组合（即共存细菌类群簇）进行了一些详细研究。特别是，肠型和组合之间的关系尚不清楚。在这项研究中，我们使用潜在狄利克雷分配（LDA）方法检测肠道微生物组组合。我们将 LDA 应用于大规模人类肠道宏基因组数据集，发现 4 组合 LDA 模型可以以高可解释性表示肠型和组合之间的关系。该模型表明，每个个体往往有多个组合，其中三个组合对应于三种经典的肠型。相反，第四种组合不对应于任何肠型，并且出现在所有肠型中。有趣的是，该组合的优势属（梭菌属、真杆菌属、粪杆菌属、罗斯伯利亚属、粪球菌属和丁酸弧菌属）包括产丁酸盐的物种，例如普拉斯尼茨粪杆菌属。事实上，第四个组合与三个丁酸生成功能显着正相关。我们使用 LDA 对大规模人类肠道宏基因组数据集进行了组合分析。本研究表明存在一种独立于肠型的组合。