Revealing the microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation.

ABSTRACT:

Background

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.

Results

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

SUBMITTER: Hosoda S 

PROVIDER: S-EPMC7313204 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature