ArticleCell reports methods2023
Metatranscriptomics-guided genome-scale metabolic modeling of microbial communities.
Article in Cell reports methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 1 of them a synthesis that pooled it.
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Who cites it
38 citing papers in PubMed, 1 synthesis or guideline pooled it, 72 citations in OpenAlex.
- Leveraging genome-scale metabolic models to understand aerobic methanotrophs.The ISME journal · 2024Pooled it
- Programming Gut Microbiome Function Through Cross-Feeding: From Ecological Mechanisms to Live Biotherapeutics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome.Nature communications · 2026Article
- Enhancing inference of differential gene expression in metatranscriptomes from human microbial communities.Nature communications · 2026Article
- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- Phage-Microbiota Interactions in the Gut: Implications for Health and Therapeutic Strategies.Probiotics and antimicrobial proteins · 2026Review
- Genome-scale metabolic modelling of human gut microbes to inform rational community design.Gut microbes · 2025Article
- Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.Microbiome · 2025Article
- Methane cycling microorganisms drive seasonal variation of methane emission in mangrove ecosystems.Environmental microbiome · 2025Article
- Biosynthesis of biobased products from lignocellulose using filamentous fungi-integrated microbial consortia.Biotechnology for biofuels and bioproducts · 2025Review
- Article
- Systematic evaluation of metatranscriptomic differential gene expressionbioRxiv : the preprint server for biology · 2025Article
- Metatranscriptomics-based metabolic modeling of patient-specific urinary microbiome during infection.NPJ biofilms and microbiomes · 2025Article
- Genome-scale metabolic model-guided systematic framework for designing customized live biotherapeutic products.NPJ systems biology and applications · 2025Review
- Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.Briefings in bioinformatics · 2025Review
- Designing synthetic microbial communities for enhanced anaerobic waste treatment.Applied and environmental microbiology · 2025Review
- Sustainable Food Waste Management in Anaerobic Digesters: Prediction of the Organic Load Impact by Metagenome-Scale Metabolic Modeling.Environmental science & technology · 2025Article
- UnifiedGreatMod: a new holistic modelling paradigm for studying biological systems on a complete and harmonious scale.Bioinformatics (Oxford, England) · 2025Article
- Impact of trace metal supplementation on anaerobic biological methanation under hydrogen and carbon dioxide starvation.NPJ biofilms and microbiomes · 2025Article
- Core cooperative metabolism in low-complexity CO2-fixing anaerobic microbiota.The ISME journal · 2025Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Multi-omics data integration via mechanistic models of metabolism is a scalable and flexible framework for exploring biological hypotheses in microbial systems. However, although most microorganisms are unculturable, such multi-omics modeling is limited to isolate microbes or simple synthetic communities. Here, we developed an approach for modeling microbial activity and interactions that leverages the reconstruction of metagenome-assembled genomes and associated genome-centric metatranscriptomes. At its core, we designed a method for condition-specific metabolic modeling of microbial communities through the integration of metatranscriptomic data. Using this approach, we explored the behavior of anaerobic digestion consortia driven by hydrogen availability and human gut microbiota dysbiosis associated with Crohn's disease, identifying condition-dependent amino acid requirements in archaeal species and a reduced short-chain fatty acid exchange network associated with disease, respectively. Our approach can be applied to complex microbial communities, allowing a mechanistic contextualization of multi-omics data on a metagenome scale.
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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.