ArticleMicrobiome2023
Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics.
Article in Microbiome, 2023. 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, 75 citations in OpenAlex.
- From gut dysbiosis to eubiosis: understanding microbiome recovery as an ecological process.Gut microbes · 2026Review
- Advances in causal discovery methods for ecological time series.Biological reviews of the Cambridge Philosophical Society · 2026Review
- Growth characteristics of natural microbial populations are skewed toward bacteria with low specific growth rates.Microbiology spectrum · 2026Article
- Reconstructing community dynamics from limited observations.Microbiome · 2026Article
- Stochastic Forces in Microbial Community Assembly: Founding Community Size Governs Divergent Ecological Trajectories.Ecology letters · 2026Article
- MicrobTiSDA: A flexible R package for inferring interspecies interactions and abundance dynamics in microbiome time-series data.iMetaOmics · 2026Article
- Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials.PLoS biology · 2026Article
- Microbiome assembly statistics toward ecosystem-scale insights, forecasting, and management.The ISME journal · 2026Review
- Sugar ABC transporter repertoires predict ecological dynamics in gut microbiome communities.Research square · 2026Article
- Preoperative gut microbiota combined with machine learning for predicting post-hepatectomy liver failure in HBV-related hepatocellular carcinoma: a pilot study.Frontiers in cellular and infection microbiology · 2026Article
- Psychological distress among Japanese high school students during the COVID-19 pandemic: An energy landscape analysis.PLoS medicine · 2026Article
- A foundation model for microbial growth dynamics.bioRxiv : the preprint server for biology · 2025Article
- Systematic metaproteomics mapping reveals functional and ecological landscapes of Ex vivo human gut microbiota responses to therapeutic drugs.Nature communications · 2025Article
- Mixed Evidence for Species Diversity Affecting Ecological Forecasts in Constant Versus Declining Light.Global change biology · 2025Article
- Controlling metabolic stability of food microbiome for stable indigenous liquor fermentation.NPJ biofilms and microbiomes · 2025Article
- Linear scaling reveals low-dimensional structure in observable microbial dynamics.bioRxiv : the preprint server for biology · 2025Article
- parafac4microbiome: exploratory analysis of longitudinal microbiome data using parallel factor analysis.mSystems · 2025Article
- Revealing unseen dynamical regimes of ecosystems from population time-series data.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Advancements in Algal Microbiome Research: A Game-Changer for Climate Resilience and Invasion Success?Microbial ecology · 2025Review
- Probiotic colonization ofInfection and immunity · 2025Article
Corrections and comments
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Authors and funding
12 authors at 9 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicrobiome dynamics are both crucial indicators and potential drivers of human health, agricultural output, and industrial bio-applications. However, predicting microbiome dynamics is notoriously difficult because communities often show abrupt structural changes, such as "dysbiosis" in human microbiomes.
methodsWe integrated theoretical frameworks and empirical analyses with the aim of anticipating drastic shifts of microbial communities. We monitored 48 experimental microbiomes for 110 days and observed that various community-level events, including collapse and gradual compositional changes, occurred according to a defined set of environmental conditions. We analyzed the time-series data based on statistical physics and non-linear mechanics to describe the characteristics of the microbiome dynamics and to examine the predictability of major shifts in microbial community structure.
resultsWe confirmed that the abrupt community changes observed through the time-series could be described as shifts between "alternative stable states" or dynamics around complex attractors. Furthermore, collapses of microbiome structure were successfully anticipated by means of the diagnostic threshold defined with the "energy landscape" analysis of statistical physics or that of a stability index of nonlinear mechanics.
conclusionsThe results indicate that abrupt microbiome events in complex microbial communities can be forecasted by extending classic ecological concepts to the scale of species-rich microbial systems. Video Abstract.
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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.