ArticlePLoS biology2021
Ecological rules for the assembly of microbiome communities.
Article in PLoS biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
69 citing papers in PubMed, 1 synthesis or guideline pooled it, 140 citations in OpenAlex.
- Gut protozoa of wild rodents - a meta-analysis.Parasitology · 2024Pooled it
- Orchestrating life's first community: molecular assembly by human milk oligosaccharides.Gut microbes · 2026Review
- Effects of Timing of Microbial Exposure on Microbiome Assembly and Amphibian Immune Development.Ecology and evolution · 2026Article
- Species-Specific Bacterial Associations Emerge From Stochastically Assembled Microbiomes in Northeastern American Fireflies.Molecular ecology · 2026Article
- The island biology of the host microbiome.Trends in microbiology · 2026Review
- The uropygial gland of the European hoopoe as a symbiotic organ.Animal microbiome · 2026Article
- The eco-evolutionary assembly of complex communities with multiple interaction types.Nature communications · 2026Article
- Emergent coexistence and the limits of reductionism in ecological communities.PLoS computational biology · 2026Article
- Microbiome assembly statistics toward ecosystem-scale insights, forecasting, and management.The ISME journal · 2026Review
- Probability, parameters, and duration of immigration and extinction in microbial communities.The ISME journal · 2026Article
- Article
- Long-term heating differently impacts diversity and seasonal dynamics of prokaryotes and micro-eukaryotes in Baltic Sea coastal biofilm communities.ISME communications · 2026Article
- Bacterial immune systems as causes and consequences of microbiome structure.PLoS biology · 2025Article
- Scarce data, noisy inferences and overfitting: the hidden flaws in ecological dynamics modelling.Journal of the Royal Society, Interface · 2025Article
- Mutualism provides a basis for biodiversity in eco-evolutionary community assembly.PLoS computational biology · 2025Article
- Experimental systems are essential for strengthening ecological modeling of microbiomes beyond observational data.mSystems · 2025Review
- Community living causes changes in metabolic behavior and is permitted by specific growth conditions in two bacterial co-culture systems.Journal of bacteriology · 2025Article
- Metabolic ecology of microbiomes: Nutrient competition, host benefits, and community engineering.Cell host & microbe · 2025Review
- Alternative stable states of microbiome structure and soil ecosystem functions.Environmental microbiome · 2025Article
- Population-level analyses identify host and environmental variables influencing the vaginal microbiome.Signal transduction and targeted therapy · 2025Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Humans and many other hosts establish a diverse community of beneficial microbes anew each generation. The order and identity of incoming symbionts is critical for health, but what determines the success of the assembly process remains poorly understood. Here we develop ecological theory to identify factors important for microbial community assembly. Our method maps out all feasible pathways for the assembly of a given microbiome-with analogies to the mutational maps underlying fitness landscapes in evolutionary biology. Building these "assembly maps" reveals a tradeoff at the heart of the assembly process. Ecological dependencies between members of the microbiota make assembly predictable-and can provide metabolic benefits to the host-but these dependencies may also create barriers to assembly. This effect occurs because interdependent species can fail to establish when each relies on the other to colonize first. We support our predictions with published data from the assembly of the preterm infant microbiota, where we find that ecological dependence is associated with a predictable order of arrival. Our models also suggest that hosts can overcome barriers to assembly via mechanisms that either promote the uptake of multiple symbiont species in one step or feed early colonizers. This predicted importance of host feeding is supported by published data on the impacts of breast milk in the assembly of the human microbiome. We conclude that both microbe to microbe and host to microbe interactions are important for the trajectory of microbiome assembly.
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What OpenQuestion holds
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.