ArticleMicrobiome2020
Revealing the microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation.
Article in Microbiome, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Trial
- LGTM: Gaussian process modulated neural topic modeling for longitudinal microbiome.Gut microbes · 2026Article
- Longitudinal modelling of microbiome subcommunities reveals parity-dependent dynamics during pregnancy and postpartum.Gut microbes · 2026Article
- A spectrum of gut microbiota signatures predicts long-term health status.Bioinformatics (Oxford, England) · 2026Article
- Enhancing the understanding of environmental microbiomes through topic modeling: a quantitative and qualitative analysis.Environmental microbiome · 2026Article
- Review
- Article
- Paired oral clinical specimens reveal the underlying ecology supporting the emergence of inflammophilic microbiome communities.bioRxiv : the preprint server for biology · 2026Article
- Data-driven enterosignatures link gut microbiome reorganization to heat stress responses in lactating sows.Frontiers in microbiology · 2026Article
- From forest to farm: the impact of a broad spectrum of lifestyles on the porcine gut microbiota.Current research in microbial sciences · 2026Article
- Detecting signatures underlying the composition of biological data.Nucleic acids research · 2025Article
- Latent Dirichlet Allocation reveals tomato root-associated bacterial interactions responding to hairy root disease.Environmental microbiome · 2025Article
- Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes.Cancer research · 2025Review
- Microbes Under Climate Refugia: Equable Subcommunity Rank Dynamics in Large-River Deltaic Estuaries.Ecology and evolution · 2025Article
- Exploring associations among pro-inflammatory cytokines, osteoarthritis, and gut microbiome composition in individuals with obesity using machine learning.Osteoarthritis and cartilage open · 2025Article
- Gut microbiome enterotypes and temporal variations during a six-month inulin-supplemented weight loss randomized controlled trial in Thai children with obesity.Computational and structural biotechnology journal · 2025Article
- Article
- A new approach to describe the taxonomic structure of microbiome and its application to assess the relationship between microbial niches.BMC bioinformatics · 2024Article
- An energy landscape approach reveals the potential key bacteria contributing to the development of inflammatory bowel disease.PloS one · 2024Article
- Gut microbiome diversity, variability, and latent community types compared with shifts in body weight during the freshman year of college in dormitory-housed adolescents.Gut microbes · 2023Observational
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsIn 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.
conclusionsWe 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. Video Abstract.
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