ArticlemSystems2020
MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota.
Article in mSystems, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 178 papers, 1 of them a synthesis that pooled it.
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Who cites it
178 citing papers in PubMed, 1 synthesis or guideline pooled it, 276 citations in OpenAlex.
- Leveraging genome-scale metabolic models to understand aerobic methanotrophs.The ISME journal · 2024Pooled it
- Trial
- Multi-omic modelling of body mass index response to a dietary weight loss intervention.Gut microbes · 2026Article
- Metagenome-scale modeling to assess microbiome metabolic complementarity for precision microbiota transplantation therapies.Gut microbes · 2026Article
- Genome-scale metabolic models predict diet- and lifestyle-driven shifts of ecological interactions in the gut microbiome.Gut microbes · 2026Article
- The cervicovaginal gut microbiota axis as a key determinant of systemic physiology.Gut microbes · 2026Review
- The FERM guild: a differentially correlated microbial module drives hypertension via metabolic flux perturbations.mSystems · 2026Article
- Systems engineering of engineered live biotherapeutics: A discovery-to-translation framework for streamlining microbiome therapeutic development.Journal of controlled release : official journal of the Controlled Release Society · 2026Review
- The Biotechnological Applications of Marine Bacteria.Biology · 2026Review
- Article
- Designing fiber-gut microbiome interactions with active learning.Nature chemical biology · 2026Article
- Omics-based decoding of molecular and metabolic crosstalk in the skin barrier ecosystem.Cell death and differentiation · 2026Review
- Quartet: Disentangling positive and negative components of microbial interactions.PLoS computational biology · 2026Article
- Genome-scale metabolic modelling identifies vaginal microbiome members as potential probiotics.Nature microbiology · 2026Article
- Metabolic set theory: a generalized model of microbial interactions.NPJ systems biology and applications · 2026Article
- Short-Chain Fatty Acids: Bridging Gut Microbiota and Systemic Aging-Mechanisms, Interventions, and Current Challenges.Metabolites · 2026Review
- The Programmable Microbiome: Integrative AI and Multi-Omics Frameworks for Precision T2DM Management.Biology · 2026Review
- From diet to function: using synthetic microbial communities to map gut microbial interactions.NPJ biofilms and microbiomes · 2026Review
- Ecological and metabolic restructuring of anaerobic microbiomes under sulfate stress via magnetite-enhanced cooperative networks.Microbiome · 2026Article
- Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome.Nature communications · 2026Article
118 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Compositional changes in the gut microbiota have been associated with a variety of medical conditions such as obesity, Crohn's disease, and diabetes. However, connecting microbial community composition to ecosystem function remains a challenge. Here, we introduce MICOM, a customizable metabolic model of the human gut microbiome. By using a heuristic optimization approach based on L2 regularization, we were able to obtain a unique set of realistic growth rates that corresponded well with observed replication rates. We integrated adjustable dietary and taxon abundance constraints to generate personalized metabolic models for individual metagenomic samples. We applied MICOM to a balanced cohort of metagenomes from 186 people, including a metabolically healthy population and individuals with type 1 and type 2 diabetes. Model results showed that individual bacterial genera maintained conserved niche structures across humans, while the community-level production of short-chain fatty acids (SCFAs) was heterogeneous and highly individual specific. Model output revealed complex cross-feeding interactions that would be difficult to measure
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.