ArticleCell systems2018
Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota.
Article in Cell systems, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed.
- Article
- Short-term oxycodone exposure produces delayed and persistent gut microbiome disruption in mice.bioRxiv : the preprint server for biology · 2026Article
- Generative approaches to kinetic parameter inference in metabolic networks via latent space exploration.Nature communications · 2026Article
- Modeling Microbiome Modulation of Tumor Metabolic Networks to Predict Synergistic Therapies.bioRxiv : the preprint server for biology · 2026Article
- Constraint-Based Modeling of Microbial Communities for Metabolite Production.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Article
- Article
- Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria.Microbiome · 2025Article
- Community living causes changes in metabolic behavior and is permitted by specific growth conditions in two bacterial co-culture systems.Journal of bacteriology · 2025Article
- Biombalance™, an Oligomeric Procyanidins-Enriched Grape Seed Extract, Prevents Inflammation and Microbiota Dysbiosis in a Mice Colitis Model.Antioxidants (Basel, Switzerland) · 2025Article
- An in silico framework for the rational design of vaginal probiotic therapy.PLoS computational biology · 2025Article
- Feruloylacetone and Its Analog Demethoxyferuloylacetone Mitigate Obesity-Related Muscle Atrophy and Insulin Resistance in Mice.Journal of agricultural and food chemistry · 2025Article
- Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile.Cell host & microbe · 2025Article
- Human gut microbiota interactions shape the long-term growth dynamics and evolutionary adaptations ofbioRxiv : the preprint server for biology · 2024Article
- Emerging tools and best practices for studying gut microbial community metabolism.Nature metabolism · 2024Review
- Deciphering metabolic crosstalk in context: lessons from inflammatory diseases.Molecular oncology · 2024Review
- Resource competition predicts assembly of gut bacterial communities in vitro.Nature microbiology · 2024Article
- Article
- Article
- Control points for design of taxonomic composition in synthetic human gut communities.Cell systems · 2023Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
The diversity and number of species present within microbial communities create the potential for a multitude of interspecies metabolic interactions. Here, we develop, apply, and experimentally test a framework for inferring metabolic mechanisms associated with interspecies interactions. We perform pairwise growth and metabolome profiling of co-cultures of strains from a model mouse microbiota. We then apply our framework to dissect emergent metabolic behaviors that occur in co-culture. Based on one of the inferences from this framework, we identify and interrogate an amino acid cross-feeding interaction and validate that the proposed interaction leads to a growth benefit in vitro. Our results reveal the type and extent of emergent metabolic behavior in microbial communities composed of gut microbes. We focus on growth-modulating interactions, but the framework can be applied to interspecies interactions that modulate any phenotype of interest within microbial communities.
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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.