ArticlemBio2023
Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome.
Article in mBio, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Article
- Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Article
- Uniform bacterial genetic diversity along the gut.Nature communications · 2026Article
- Priority effects drive strain-level community composition of honeybee gut microbiota.The ISME journal · 2026Article
- Importance of human microbiome: an update.Frontiers in microbiomes · 2026Review
- Community coalescence reveals strong selection and coexistence within species in complex microbial communities.bioRxiv : the preprint server for biology · 2025Article
- Macroecological Laws Can Naturally Arise from Chaotic Internal Species Dynamics.bioRxiv : the preprint server for biology · 2025Article
- Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli.Cell reports · 2025Article
- Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics.Cell genomics · 2025Article
- Multi-omics analysis of gut-organ axes reveals the high-altitude adaptation in Tibetan chicken.iMetaOmics · 2025Article
- Experimental systems are essential for strengthening ecological modeling of microbiomes beyond observational data.mSystems · 2025Review
- Linear scaling reveals low-dimensional structure in observable microbial dynamics.bioRxiv : the preprint server for biology · 2025Article
- Resilience of a stochastic generalized Lotka-Volterra model for microbiome studies.Mathematical biosciences and engineering : MBE · 2025Article
- Macroecological patterns in experimental microbial communities.PLoS computational biology · 2025Article
- Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices.Biological reviews of the Cambridge Philosophical Society · 2025Review
- Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission.Microbiome · 2025Article
- Timescale of environmental change modulates metabolic guild cohesion in microbial communities.The ISME journal · 2025Article
- Two decades of bacterial ecology and evolution in a freshwater lake.Nature microbiology · 2025Article
- Characterization ofFrontiers in microbiology · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The human gut microbiome harbors substantial ecological diversity at the species level as well as at the strain level within species. In healthy hosts, species abundance fluctuations in the microbiome are thought to be stable, and these fluctuations can be described by macroecological laws. However, it is less clear how strain abundances change over time. An open question is whether individual strains behave like species themselves, exhibiting stability and following the macroecological relationships known to hold at the species level, or whether strains have different dynamics, perhaps due to the relatively close phylogenetic relatedness of cocolonizing lineages. Here, we analyze the daily dynamics of intraspecific genetic variation in the gut microbiomes of four healthy, densely longitudinally sampled hosts. First, we find that the overall genetic diversity of a large majority of species is stationary over time despite short-term fluctuations. Next, we show that fluctuations in abundances in approximately 80% of strains analyzed can be predicted with a stochastic logistic model (SLM), an ecological model of a population experiencing environmental fluctuations around a fixed carrying capacity, which has previously been shown to capture statistical properties of species abundance fluctuations. The success of this model indicates that strain abundances typically fluctuate around a fixed carrying capacity, suggesting that most strains are dynamically stable. Finally, we find that the strain abundances follow several empirical macroecological laws known to hold at the species level. Together, our results suggest that macroecological properties of the human gut microbiome, including its stability, emerge at the level of strains.
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