ArticleNPJ systems biology and applications2024
Designing function-specific minimal microbiomes from large microbial communities.
Article in NPJ systems biology and applications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Article
- MOFA: microbial optimization without forced altruism.BMC bioinformatics · 2026Article
- Metabolic modeling unveils potential probiotic roles ofISME communications · 2026Article
- Enabling next-generation anaerobic cultivation through biotechnology to advance functional microbiome research.Nature biotechnology · 2025Review
- Operationalizing Team Science at the Academic Cancer Center Network to Unveil the Structure and Function of the Gut Microbiome.Journal of clinical medicine · 2025Review
- Function-based selection of synthetic communities enables mechanistic microbiome studies.The ISME journal · 2025Article
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Authors and funding
3 authors.
Funding
Abstract
Microorganisms exist in large communities of diverse species, exhibiting various functionalities. The mammalian gut microbiome, for instance, has the functionality of digesting dietary fibre and producing different short-chain fatty acids. Not all microbes present in a community contribute to a given functionality; it is possible to find a minimal microbiome, which is a subset of the large microbiome, that is capable of performing the functionality while maintaining other community properties such as growth rate and metabolite production. Such a minimal microbiome will also contain keystone species for SCFA production in that community. In this work, we present a systematic constraint-based approach to identify a minimal microbiome from a large community for a user-proposed function. We employ a top-down approach with sequential deletion followed by solving a mixed-integer linear programming problem with the objective of minimising the L
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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.