ArticleNature communications2019
A theoretical framework for controlling complex microbial communities.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Keystone concept revisited: insights into microbial community dynamics and control.Nature reviews. Microbiology · 2026Review
- Alleviation of heat stress-induced microbial dysbiosis in pigs through dietary supplementation with vitamins and trace elements.Animal microbiome · 2026Article
- Metal-induced changes in the early-life gut microbial composition and life-history traits in three insectivorous passerines.Environmental science and pollution research international · 2025Article
- A computational framework for inferring species dynamics and interactions with applications in microbiota ecology.NPJ systems biology and applications · 2025Article
- Bioenergetically constrained dynamical microbial interactions govern the performance and stability of methane-producing bioreactors.NPJ biofilms and microbiomes · 2025Article
- Meta-omics reveals subgingival plaque reconstruction dynamics.Journal of oral microbiology · 2025Article
- mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data.Briefings in bioinformatics · 2024Article
- Progress on network modeling and analysis of gut microecology: a review.Applied and environmental microbiology · 2024Review
- Article
- Sparse species interactions reproduce abundance correlation patterns in microbial communities.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The Diverse Mycorrizal Morphology ofJournal of fungi (Basel, Switzerland) · 2024Article
- Healthy gut microbiomes are host-controllable microbiomes.Frontiers in microbiology · 2024Article
- Microbiome modeling: a beginner's guide.Frontiers in microbiology · 2024Review
- Autoencoder neural networks enable low dimensional structure analyses of microbial growth dynamics.Nature communications · 2023Article
- Article
- A computational method to dissect colonization resistance of the gut microbiota against pathogens.Cell reports methods · 2023Article
- Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities.Bioinformatics (Oxford, England) · 2023Article
- Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics.Nature communications · 2023Article
- Structural Identifiability and Observability of Microbial Community Models.Bioengineering (Basel, Switzerland) · 2023Article
- Controlling the human microbiome.Cell systems · 2023Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbes form complex communities that perform critical roles for the integrity of their environment or the well-being of their hosts. Controlling these microbial communities can help us restore natural ecosystems and maintain healthy human microbiota. However, the lack of an efficient and systematic control framework has limited our ability to manipulate these microbial communities. Here we fill this gap by developing a control framework based on the new notion of structural accessibility. Our framework uses the ecological network of the community to identify minimum sets of its driver species, manipulation of which allows controlling the whole community. We numerically validate our control framework on large communities, and then we demonstrate its application for controlling the gut microbiota of gnotobiotic mice infected with Clostridium difficile and the core microbiota of the sea sponge Ircinia oros. Our results provide a systematic pipeline to efficiently drive complex microbial communities towards desired states.
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