ArticleApplied and environmental microbiology2015
Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico.
Article in Applied and environmental microbiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed, 137 citations in OpenAlex.
- Substrate utilization and cross-feeding synergistically determine microbiome resistance to pathogen invasion.Nature ecology & evolution · 2026Article
- Constraint-Based Modeling of Microbial Communities for Metabolite Production.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Boundary conditions for exploiting the cooperation ofApplied and environmental microbiology · 2025Article
- Toward the Next Generation of In Silico Modeling of Dynamic Host-Microbiota Interactions in the Skin.JID innovations : skin science from molecules to population health · 2025Review
- Competition and cooperation: The plasticity of bacterial interactions across environments.PLoS computational biology · 2025Article
- COmmunity and Single Microbe Optimisation System (COSMOS).NPJ systems biology and applications · 2025Article
- Sustainable Food Waste Management in Anaerobic Digesters: Prediction of the Organic Load Impact by Metagenome-Scale Metabolic Modeling.Environmental science & technology · 2025Article
- Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices.Biological reviews of the Cambridge Philosophical Society · 2025Review
- Effect of microbial interactions on performance of community metabolic modeling algorithms: flux balance analysis (FBA), community FBA (cFBA) and SteadyCom.Bioprocess and biosystems engineering · 2024Article
- Community metabolic modeling of host-microbiota interactions through multi-objective optimization.iScience · 2024Article
- GEM-based computational modeling for exploring metabolic interactions in a microbial community.PLoS computational biology · 2024Article
- Designing function-specific minimal microbiomes from large microbial communities.NPJ systems biology and applications · 2024Article
- Deciphering the impact of microbial interactions on COPD exacerbation: An in-depth analysis of the lung microbiome.Heliyon · 2024Article
- Flux sampling in genome-scale metabolic modeling of microbial communities.BMC bioinformatics · 2024Article
- Predicting microbial interactions with approaches based on flux balance analysis: an evaluation.BMC bioinformatics · 2024Article
- Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.Microbial biotechnology · 2024Review
- Probing interspecies metabolic interactions within a synthetic binary microbiome using genome-scale modeling.Microbiome research reports · 2024Article
- Flux Sampling in Genome-scale Metabolic Modeling of Microbial Communities.bioRxiv : the preprint server for biology · 2023Article
- Towards applications of genome-scale metabolic model-based approaches in designing synthetic microbial communities.Quantitative biology (Beijing, China) · 2023Review
- In silico prediction of potential indigenous microbial biomarkers in Penaeus vannamei identified through meta-analysis and genome-scale metabolic modelling.Environmental microbiome · 2023Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The human gut is inhabited by thousands of microbial species, most of which are still uncharacterized. Gut microbes have adapted to each other's presence as well as to the host and engage in complex cross feeding. Constraint-based modeling has been successfully applied to predicting microbe-microbe interactions, such as commensalism, mutualism, and competition. Here, we apply a constraint-based approach to model pairwise interactions between 11 representative gut microbes. Microbe-microbe interactions were computationally modeled in conjunction with human small intestinal enterocytes, and the microbe pairs were subjected to three diets with various levels of carbohydrate, fat, and protein in normoxic or anoxic environments. Each microbe engaged in species-specific commensal, parasitic, mutualistic, or competitive interactions. For instance, Streptococcus thermophilus efficiently outcompeted microbes with which it was paired, in agreement with the domination of streptococci in the small intestinal microbiota. Under anoxic conditions, the probiotic organism Lactobacillus plantarum displayed mutualistic behavior toward six other species, which, surprisingly, were almost entirely abolished under normoxic conditions. This finding suggests that the anoxic conditions in the large intestine drive mutualistic cross feeding, leading to the evolvement of an ecosystem more complex than that of the small intestinal microbiota. Moreover, we predict that the presence of the small intestinal enterocyte induces competition over host-derived nutrients. The presented framework can readily be expanded to a larger gut microbial community. This modeling approach will be of great value for subsequent studies aiming to predict conditions favoring desirable microbes or suppressing pathogens.
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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.