ArticleNature communications2024
Data-driven prediction of colonization outcomes for complex microbial communities.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
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- Cerebrospinal Fluid Over Plasma Links Analytes to Cognitive Decline in Older Adults at Risk for Alzheimer's Disease.Annals of clinical and translational neurology · 2026Article
- Foundation Models for Microbiome Research: From Sequence Semantics to Community Dynamics and Multimodal World Models.Advanced genetics (Hoboken, N.J.) · 2026Review
- Review
- Next-generation probiotics: an outlook into current applications and future developments.Nature reviews. Microbiology · 2026Review
- Synthetic Microbial Community Biosensors: From Engineered Ecosystems to Modular Detection Platforms with AI-Driven Intelligence.Biosensors · 2026Review
- Advances and future directions in identifying specific taxa from microbial meta-omics data: from pipeline to deep learning.mSystems · 2026Review
- Artificial Intelligence for Microbial Isolation and Cultivation: Progress and Challenges.Microorganisms · 2026Review
- DynaBiome: interpretable unsupervised learning of gut microbiome dysbiosis via temporal deep models.BMC bioinformatics · 2026Article
- Dietary intake of enrofloxacin promotes the spread of antibiotic resistance from food to simulated human gut.The ISME journal · 2026Article
- Precision microbiome medicine and therapeutics: the enabling role of in vitro gut models.FEMS microbiology reviews · 2026Review
- Synthetic microbiomes in bioengineered rhizospheres: new frontiers for climate-resilient agriculture.Frontiers in microbiology · 2026Review
- Article
- CRISPR-engineered microbiome: living therapeutics revolutionize blood cancer immunotherapy.NPJ biofilms and microbiomes · 2025Review
- Probiotic Engraftment of Akkermansia muciniphila in an In Vitro Synthetic Microbial Community.Microbial ecology · 2025Article
- Multidrug-ResistantVeterinary sciences · 2025Article
- Arbuscular Mycorrhizal Fungi as Core Engineers in Synthetic Microbial Communities: Boosting Plant Growth and Soil Health for Sustainable Agriculture.Journal of fungi (Basel, Switzerland) · 2025Review
- Targeted Intervention Strategies for Maternal-Offspring Transmission of Christensenellaceae in Pigs via a Deep Learning Model.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Antibacterial microcins are ubiquitous and functionally diverse across bacterial communities.Nature communications · 2025Article
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8 authors.
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Abstract
Microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse mechanisms governing microbial dynamics. Here, we propose a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validate this approach using synthetic data, finding that machine learning models can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conduct colonization experiments for commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approaches can predict the colonization outcomes in experiments. Furthermore, we find that while most resident species are predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., Enterococcus faecalis inhibits the invasion of E. faecium invasion. The presented results suggest that the data-driven approaches are powerful tools to inform the ecology and management of microbial communities.
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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.