ArticleCell systems2023
Control points for design of taxonomic composition in synthetic human gut communities.
Article in Cell systems, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Designing fiber-gut microbiome interactions with active learning.Nature chemical biology · 2026Article
- 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
- Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome.PLoS computational biology · 2025Article
- Enabling next-generation anaerobic cultivation through biotechnology to advance functional microbiome research.Nature biotechnology · 2025Review
- 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
- Proteomic study ofFrontiers in microbiology · 2025Article
- Human gut microbiota interactions shape the long-term growth dynamics and evolutionary adaptations ofbioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Microbial communities offer vast potential across numerous sectors but remain challenging to systematically control. We develop a two-stage approach to guide the taxonomic composition of synthetic microbiomes by precisely manipulating media components and initial species abundances. By combining high-throughput experiments and computational modeling, we demonstrate the ability to predict and design the diversity of a 10-member synthetic human gut community. We reveal that critical environmental factors governing monoculture growth can be leveraged to steer microbial communities to desired states. Furthermore, systematically varied initial abundances drive variation in community assembly and enable inference of pairwise inter-species interactions via a dynamic ecological model. These interactions are overall consistent with conditioned media experiments, demonstrating that specific perturbations to a high-richness community can provide rich information for building dynamic ecological models. This model is subsequently used to design low-richness communities that display low or high temporal taxonomic variability over an extended period. A record of this paper's transparent peer review process is included in the supplemental information.
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Registered trials
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