ArticleCell systems2025
Personalized Clostridioides difficile colonization risk prediction and probiotic therapy assessment in the human gut.
Article in Cell systems, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- Microbiome compositional changes and clonal engraftment in a phase 3 trial of fecal microbiota, live-jslm for recurrentGut microbes · 2025Trial
- Metagenome-scale modeling to assess microbiome metabolic complementarity for precision microbiota transplantation therapies.Gut microbes · 2026Article
- Microbiome-based therapeutics forGut microbes · 2026Review
- Systems engineering of engineered live biotherapeutics: A discovery-to-translation framework for streamlining microbiome therapeutic development.Journal of controlled release : official journal of the Controlled Release Society · 2026Review
- A regulator of amino acid catabolism controls Acinetobacter baumannii gut colonization.Nature communications · 2026Article
- Next-generation probiotics: an outlook into current applications and future developments.Nature reviews. Microbiology · 2026Review
- Mechanisms of Gut Microbiota-Derived Metabolites in Treating Hyperuricemia: Natural Products as Interventions.Molecules (Basel, Switzerland) · 2026Review
- Metagenome-scale Modeling to Assess Microbiome Metabolic Complementarity for Precision Microbiota Transplantation Therapies.bioRxiv : the preprint server for biology · 2026Article
- Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials.PLoS biology · 2026Article
- A regulator of amino acid catabolism controlsbioRxiv : the preprint server for biology · 2025Article
- Amino acid competition shapes Acinetobacter baumannii gut carriage.Cell host & microbe · 2025Article
- Moving from genome-scale to community-scale metabolic models for the human gut microbiome.Nature microbiology · 2025Review
- Metabolic modeling of host-microbe interactions.Computational and structural biotechnology journal · 2025Review
- Metabolic modelling uncovers the complex interplay between fungal probiotics, poultry microbiomes, and diet.Microbiome · 2024Article
Corrections and comments
- Commented on by
- Update ofPersonalized2024
Authors and funding
4 authors.
Funding
Abstract
Clostridioides difficile (C. difficile) colonizes up to 40% of community-dwelling adults without causing disease but can eventually lead to infection (C. difficile infection [CDI]). There has been a lack of focus on how to prevent colonization and facilitate the successful clearance of C. difficile prior to the emergence of CDI. We show that microbial community-scale metabolic models (MCMMs) accurately predict C. difficile colonization susceptibility in vitro and in vivo, offering mechanistic insights into microbiota-specific interactions involving metabolites like succinate, trehalose, and ornithine. MCMMs reveal distinct C. difficile metabolic niches-two growth-associated and one non-growth-associated-observed across 15,204 individuals from five cohorts. We further demonstrate that MCMMs can predict personalized C. difficile growth suppression by a probiotic cocktail designed to replace fecal microbiota transplants (FMTs) for the treatment of recurrent CDI, and we identify new probiotic targets for future validation. MCMMs represent a powerful framework for predicting pathogen colonization and assessing probiotic efficacy across diverse microbiota contexts. A record of this paper's transparent peer review process is included in the supplemental information.
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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.