ArticleNature microbiology2024
Resource competition predicts assembly of gut bacterial communities in vitro.
Article in Nature microbiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
46 citing papers in PubMed.
- Oligosaccharides With Defined Glycosidic Bonds Shape Gut Microbial Succession and Metabolism Via Bond-Specific Microbial Responders.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Anaerobic riboflavin degradation by human gutJournal of bacteriology · 2026Article
- Systematic profiling of growth interactions in human gut microbiome species.Nature communications · 2026Article
- Article
- Functional and ecological drivers of bacterial interactions in glacier-fed stream biofilms.mSystems · 2026Article
- Antibiotic-induced gut microbiome dysbiosis: risks and strategies for mitigation.The EMBO journal · 2026Review
- Interspecies interactions drive bacterial proteome reorganization and emergent metabolism.Nature ecology & evolution · 2026Article
- A bifidobacterial enzyme orchestrates ecology and function of infant gut bacterial community.bioRxiv : the preprint server for biology · 2026Article
- The network structure of cross-feeding impacts microbial community diversity under growth-inhibiting stresses.Nature communications · 2026Article
- mGem: Applying microbiome therapeutic learnings to next-generation agricultural bioproducts.mBio · 2026Review
- Mathematical Modelling and Intuition in Microbiology: A Perspective.Environmental microbiology · 2026Review
- Anaerobic riboflavin degradation by human gutbioRxiv : the preprint server for biology · 2026Article
- Host and microbial factors influence bacterial colonization of the honey bee gut.The ISME journal · 2026Article
- Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia.bioRxiv : the preprint server for biology · 2026Article
- Precision microbiome medicine and therapeutics: the enabling role of in vitro gut models.FEMS microbiology reviews · 2026Review
- Article
- Strain displacement in microbiomes via ecological competition.Nature microbiology · 2025Article
- Accuracy of the Lotka-Volterra model fails in strongly coupled microbial consumer-resource systems.PLoS computational biology · 2025Article
- Article
- The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals.Communications biology · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Microbial community dynamics arise through interspecies interactions, including resource competition, cross-feeding and pH modulation. The individual contributions of these mechanisms to community structure are challenging to untangle. Here we develop a framework to estimate multispecies niche overlaps by combining metabolomics data of individual species, growth measurements in spent media and mathematical models. We applied our framework to an in vitro model system comprising 15 human gut commensals in complex media and showed that a simple model of resource competition accounted for most pairwise interactions. Next, we built a coarse-grained consumer-resource model by grouping metabolomic features depleted by the same set of species and showed that this model predicted the composition of 2-member to 15-member communities with reasonable accuracy. Furthermore, we found that incorporation of cross-feeding and pH-mediated interactions improved model predictions of species coexistence. Our theoretical model and experimental framework can be applied to characterize interspecies interactions in bacterial communities in vitro.
Indexed as
Identifiers
38486074What OpenQuestion holds
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.