ArticleNucleic acids research2021
metaGEM: reconstruction of genome scale metabolic models directly from metagenomes.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers, 1 of them a synthesis that pooled it.
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Who cites it
63 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.Nature microbiology · 2026Pooled it
- 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
- Rainfall Drives Differentiation of Plant Rhizosphere Microbial Communities in Two Different Types of Alpine Wetlands: A Perspective Based on a Carbon-Water Coupling Framework.Microbial ecology · 2026Article
- Functional roles of degraders and non-degraders in anaerobic trophic networks converting lignocellulose into monocarboxylates.NPJ biofilms and microbiomes · 2026Article
- Continental-scale integration of soil metagenomes and organic matter chemistry reveals ubiquitous microbial capacity for chemically-recalcitrant carbon decomposition.Nature communications · 2026Article
- Genome-Scale Metabolic Models Guided Improvement of Fermented Milk Quality and Flavor byFoods (Basel, Switzerland) · 2026Article
- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- Metagenome-assembled genomes from the gut microbiome of spontaneous diabetic macaques provide insights into microbes associated with type 2 diabetes mellitus.BMC microbiology · 2026Article
- Predictive multispecies constraint-based metabolic modeling: case studies and best practices.Briefings in bioinformatics · 2026Review
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Unlocking therapeutic impacts of the gut microbiota with computational tools.Current opinion in biotechnology · 2026Review
- Moisture-mediated resource availability shapes rhizosphere and bulk soil microbial structure and function post-rainfall.Frontiers in microbiology · 2026Article
- Article
- Metagenomics-Toolkit: the flexible and efficient cloud-based metagenomics workflow featuring machine learning-enabled resource allocation.NAR genomics and bioinformatics · 2025Article
- Leveraging chemical synthesis to discover metabolites from the gut microbiome.Annals of the New York Academy of Sciences · 2025Review
- A survey of computational approaches for characterizing microbial interactions in microbial mats.Genome biology · 2025Review
- Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.eLife · 2025Article
- Moving from genome-scale to community-scale metabolic models for the human gut microbiome.Nature microbiology · 2025Review
- Genome-scale models in human metabologenomics.Nature reviews. Genetics · 2025Review
3 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Metagenomic analyses of microbial communities have revealed a large degree of interspecies and intraspecies genetic diversity through the reconstruction of metagenome assembled genomes (MAGs). Yet, metabolic modeling efforts mainly rely on reference genomes as the starting point for reconstruction and simulation of genome scale metabolic models (GEMs), neglecting the immense intra- and inter-species diversity present in microbial communities. Here, we present metaGEM (https://github.com/franciscozorrilla/metaGEM), an end-to-end pipeline enabling metabolic modeling of multi-species communities directly from metagenomes. The pipeline automates all steps from the extraction of context-specific prokaryotic GEMs from MAGs to community level flux balance analysis (FBA) simulations. To demonstrate the capabilities of metaGEM, we analyzed 483 samples spanning lab culture, human gut, plant-associated, soil, and ocean metagenomes, reconstructing over 14,000 GEMs. We show that GEMs reconstructed from metagenomes have fully represented metabolism comparable to isolated genomes. We demonstrate that metagenomic GEMs capture intraspecies metabolic diversity and identify potential differences in the progression of type 2 diabetes at the level of gut bacterial metabolic exchanges. Overall, metaGEM enables FBA-ready metabolic model reconstruction directly from metagenomes, provides a resource of metabolic models, and showcases community-level modeling of microbiomes associated with disease conditions allowing generation of mechanistic hypotheses.
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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.