ArticleMicrobiome2024
Gut microbiome-metabolome interactions predict host condition.
Article in Microbiome, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- The FERM guild: a differentially correlated microbial module drives hypertension via metabolic flux perturbations.mSystems · 2026Article
- Common xenobiotics modulate gut microbial responses to low‑calorie sweeteners in vitro.Molecular systems biology · 2026Article
- Unlocking therapeutic impacts of the gut microbiota with computational tools.Current opinion in biotechnology · 2026Review
- Frontier research and clinical application prospects of microbiome biomarkers in autoimmune diseases.Frontiers in immunology · 2026Review
- The Interplay Between Lifestyle and Oral/Faecal Microbial Profiles Among Periodontal Disease Patients: A Cross-Sectional Study.Journal of clinical periodontology · 2026Article
- Predicted meta-omics: A potential solution to multi-omics data scarcity in microbiome studies.PloS one · 2026Article
- Review
- Effects of Fermentation and Enzymatic Hydrolysis of Cottonseed Protein on Rumen Fermentation Characteristics, Intestinal Barrier Function, and Hepatic Metabolism in Suckling Lambs.Animals : an open access journal from MDPI · 2025Article
- Deep Learning Transforms Phage-Host Interaction Discovery from Metagenomic Data.bioRxiv : the preprint server for biology · 2025Article
- Lipidomic signatures linked to gut microbiota alterations in children and adolescents with type 2 diabetes mellitus and metabolic syndrome.Scientific reports · 2025Article
- Sex-induced alterations in rumen microbial communities and metabolite profiles: implications for lamb body weight.BMC microbiology · 2025Article
- Metabolomic analysis reveals key changes in amino acid metabolism in colorectal cancer patients.Amino acids · 2025Article
- MicrobeRX: a tool for enzymatic-reaction-based metabolite prediction in the gut microbiome.Microbiome · 2025Article
- Microbiota-derived metabolites in inflammatory bowel disease.Seminars in immunopathology · 2025Review
- Advances in functional analysis of the microbiome: Integrating metabolic modeling, metabolite prediction, and pathway inference with Next-Generation Sequencing data.Journal of microbiology (Seoul, Korea) · 2025Review
- Gut microbiota in colorectal cancer: a review of its influence on tumor immune surveillance and therapeutic response.Frontiers in oncology · 2025Review
- Integrated analysis of microbiome and metabolome reveals insights into cervical neoplasia aggravation in a Chinese cohort.Frontiers in cellular and infection microbiology · 2025Article
- The impact of traditional Chinese medicine and dietary compounds on modulating gut microbiota in hepatic fibrosis: A review.Heliyon · 2024Review
- Microbial-Metabolomic Exploration of Tea Polyphenols in the Regulation of Serum Indicators, Liver Metabolism, Rumen Microorganisms, and Metabolism in Hu Sheep.Animals : an open access journal from MDPI · 2024Article
- Metagenomics-Metabolomics Exploration of Three-Way-Crossbreeding Effects on Rumen to Provide Basis for Crossbreeding Improvement of Sheep Microbiome and Metabolome of Sheep.Animals : an open access journal from MDPI · 2024Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe effect of microbes on their human host is often mediated through changes in metabolite concentrations. As such, multiple tools have been proposed to predict metabolite concentrations from microbial taxa frequencies. Such tools typically fail to capture the dependence of the microbiome-metabolite relation on the environment.
resultsWe propose to treat the microbiome-metabolome relation as the equilibrium of a complex interaction and to relate the host condition to a latent representation of the interaction between the log concentration of the metabolome and the log frequencies of the microbiome. We develop LOCATE (Latent variables Of miCrobiome And meTabolites rElations), a machine learning tool to predict the metabolite concentration from the microbiome composition and produce a latent representation of the interaction. This representation is then used to predict the host condition. LOCATE's accuracy in predicting the metabolome is higher than all current predictors. The metabolite concentration prediction accuracy significantly decreases cross datasets, and cross conditions, especially in 16S data. LOCATE's latent representation predicts the host condition better than either the microbiome or the metabolome. This representation is strongly correlated with host demographics. A significant improvement in accuracy (0.793 vs. 0.724 average accuracy) is obtained even with a small number of metabolite samples ([Formula: see text]).
conclusionThese results suggest that a latent representation of the microbiome-metabolome interaction leads to a better association with the host condition than any of the two separated or the simple combination of the two. Video Abstract.
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