ArticleThe ISME journal2025
Function-based selection of synthetic communities enables mechanistic microbiome studies.
Article in The ISME journal, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 8 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
8 citing papers in PubMed.
- Harnessing synthetic microbial communities for desert vegetation restoration.Synthetic and systems biotechnology · 2027Review
- Plasticity of the infant immune system during the perinatal period.Nature reviews. Immunology · 2026Review
- It takes a village: how plant-associated bacterial communities socialise to shape plant growth and health.Essays in biochemistry · 2026Review
- Plant-Microbiome Interactions in Medicinal Plants: A Synergistic Partnership for Biomass Production and Secondary Metabolite Accumulation.Microorganisms · 2026Review
- From diet to function: using synthetic microbial communities to map gut microbial interactions.NPJ biofilms and microbiomes · 2026Review
- Ecological drift simulations reveal key factors influencing minimal microbiome engineering and community assembly.ISME communications · 2026Article
- Synthetic microbial consortia based on quorum-sensing for disease therapy.Bioresources and bioprocessing · 2025Review
- Metabolic modeling of host-microbe interactions.Computational and structural biotechnology journal · 2025Review
Corrections and comments
- Erratum issued
Authors and funding
10 authors.
Funding
Abstract
Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynComs). We developed a functionally directed approach to generate SynComs by selecting strains that encode key functions identified in metagenomes. This approach enables the rapid construction of SynComs tailored to any ecosystem. To optimize community design, we implemented genome-scale metabolic models, providing in silico evidence for cooperative strain coexistence prior to experimental validation. Using this strategy, we designed multiple host-specific SynComs, including those for the rumen, mouse, and human microbiomes. By weighting functions differentially enriched in diseased versus healthy individuals, we constructed SynComs that capture complex host-microbe interactions. We designed an inflammatory bowel disease SynCom of 10 members that successfully induced colitis in gnotobiotic IL10-/- mice, demonstrating the potential of this method to model disease-associated microbiomes. Our study establishes a framework for designing functionally representative SynComs of any microbial ecosystem, facilitating mechanistic study.
Indexed as
Identifiers
What 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.