ArticlePLoS computational biology2015
Neutral Models of Microbiome Evolution.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
36 citing papers in PubMed.
- Linking complex microbial interactions and dysbiosis through a disordered Lotka-Volterra model.eLife · 2026Article
- Applying evolutionary theory to understand host-microbiome evolution.Nature ecology & evolution · 2025Review
- Within-host microbial selection and multiple microbial generations buffer the loss of host fitness under environmental change.FEMS microbiology ecology · 2025Article
- Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices.Biological reviews of the Cambridge Philosophical Society · 2025Review
- Models of microbiome evolution incorporating host resource provisioning.ISME communications · 2025Article
- Maternal transmission as a microbial symbiont sieve, and the absence of lactation in male mammals.Nature communications · 2024Article
- A computational framework for resolving the microbiome diversity conundrum.Nature communications · 2023Article
- Gut microbes predominantly act as living beneficial partners rather than raw nutrients.Scientific reports · 2023Article
- Host-mediated gene engineering and microbiome-based technology optimization for sustainable agriculture and environment.Functional & integrative genomics · 2023Review
- Gut microbiota plasticity in insular lizards under reversed island syndrome.Scientific reports · 2022Article
- Host genomic influence on bacterial composition in the switchgrass rhizosphere.Molecular ecology · 2022Article
- On the effect of inheritance of microbes in commensal microbiomes.BMC ecology and evolution · 2022Article
- Species Identity Dominates over Environment in Driving Bacterial Community Assembly in Wild Invasive Leaf Miners.Microbiology spectrum · 2022Article
- Cross-Scale Analyses of Animal and Human Gut Microbiome Assemblies from Metacommunity to Global Landscape.mSystems · 2021Article
- Towards an ecosystem model of infectious disease.Nature ecology & evolution · 2021Review
- Agent Based Models of Polymicrobial Biofilms and the Microbiome-A Review.Microorganisms · 2021Review
- The yellow perch (Perca flavescens) microbiome revealed resistance to colonisation mostly associated with neutralism driven by rare taxa under cadmium disturbance.Animal microbiome · 2021Article
- Stochastic colonization of hosts with a finite lifespan can drive individual host microbes out of equilibrium.PLoS computational biology · 2020Article
- A theoretic approach to the mode of gut microbiome translocation in SIV-infected Asian macaques.FEMS microbiology ecology · 2020Article
- Influences of a Prolific Gut Fungus (Applied and environmental microbiology · 2020Article
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.
Funding
Abstract
There has been an explosion of research on host-associated microbial communities (i.e.,microbiomes). Much of this research has focused on surveys of microbial diversities across a variety of host species, including humans, with a view to understanding how these microbiomes are distributed across space and time, and how they correlate with host health, disease, phenotype, physiology and ecology. Fewer studies have focused on how these microbiomes may have evolved. In this paper, we develop an agent-based framework to study the dynamics of microbiome evolution. Our framework incorporates neutral models of how hosts acquire their microbiomes, and how the environmental microbial community that is available to the hosts is assembled. Most importantly, our framework also incorporates a Wright-Fisher genealogical model of hosts, so that the dynamics of microbiome evolution is studied on an evolutionary timescale. Our results indicate that the extent of parental contribution to microbial availability from one generation to the next significantly impacts the diversity of microbiomes: the greater the parental contribution, the less diverse the microbiomes. In contrast, even when there is only a very small contribution from a constant environmental pool, microbial communities can remain highly diverse. Finally, we show that our models may be used to construct hypotheses about the types of processes that operate to assemble microbiomes over evolutionary time.
Indexed as
Identifiers
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.