ArticleMolecular systems biology2021
Negative interactions determine Clostridioides difficile growth in synthetic human gut communities.
Article in Molecular systems biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
41 citing papers in PubMed.
- Optimization and application of probiotics complex for grouper based on dynamic model.World journal of microbiology & biotechnology · 2026Article
- Designing fiber-gut microbiome interactions with active learning.Nature chemical biology · 2026Article
- Ecological and dietary strategies to constrain Clostridioides difficile.Cell host & microbe · 2026Review
- From diet to function: using synthetic microbial communities to map gut microbial interactions.NPJ biofilms and microbiomes · 2026Review
- Ecology-microbiome engineering in Sauce-flavor Baijiu via Single-Cell Raman Spectroscopy.Biodesign research · 2026Review
- The network structure of cross-feeding impacts microbial community diversity under growth-inhibiting stresses.Nature communications · 2026Article
- Physics-constrained neural ordinary differential equation models to discover and predict microbial community dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Bile acid dependent attenuation of toxin mediated disease is independent of colonization resistance againstbioRxiv : the preprint server for biology · 2026Article
- Doblin: inferring dominant clonal lineages from high-resolution DNA barcoding time series.Bioinformatics (Oxford, England) · 2025Article
- Unravelling three-way interactions betweenJournal of medical microbiology · 2025Review
- 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
- Personalized Clostridioides difficile colonization risk prediction and probiotic therapy assessment in the human gut.Cell systems · 2025Article
- Article
- Quantifying the intra- and inter-species community interactions in microbiomes by dynamic covariance mapping.Nature communications · 2025Article
- Biotic resistance predictably shifts microbial invasion regimes.Nature communications · 2025Article
- Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile.Cell host & microbe · 2025Article
- A data-driven modeling framework for mapping genotypes to synthetic microbial community functions.bioRxiv : the preprint server for biology · 2025Article
- Function-based selection of synthetic communities enables mechanistic microbiome studies.The ISME journal · 2025Article
- Oral pathogens meet the gut microbiome: new mechanistic insights on systemic disease.Frontiers in cellular and infection microbiology · 2025Review
- Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes.Nature communications · 2024Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Understanding the principles of colonization resistance of the gut microbiome to the pathogen Clostridioides difficile will enable the design of defined bacterial therapeutics. We investigate the ecological principles of community resistance to C. difficile using a synthetic human gut microbiome. Using a dynamic computational model, we demonstrate that C. difficile receives the largest number and magnitude of incoming negative interactions. Our results show that C. difficile is in a unique class of species that display a strong negative dependence between growth and species richness. We identify molecular mechanisms of inhibition including acidification of the environment and competition over resources. We demonstrate that Clostridium hiranonis strongly inhibits C. difficile partially via resource competition. Increasing the initial density of C. difficile can increase its abundance in the assembled community, but community context determines the maximum achievable C. difficile abundance. Our work suggests that the C. difficile inhibitory potential of defined bacterial therapeutics can be optimized by designing communities featuring a combination of mechanisms including species richness, environment acidification, and resource competition.
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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.