ReviewmBio2016
Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts.
Review in mBio, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 144 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
144 citing papers in PubMed, 345 citations in OpenAlex.
- A genomic catalog of Earth's bacterial and archaeal symbionts.Nature biotechnology · 2026Article
- Holobiontic Intercellular Relationships Between the Oral Cavity and the Rest of the Human Organism: A Narrative Review.Medicina (Kaunas, Lithuania) · 2026Review
- The uropygial gland of the European hoopoe as a symbiotic organ.Animal microbiome · 2026Article
- From Molecules to Metabolomes, Understanding Symbiosis through Small Molecules.Journal of natural products · 2026Review
- Bacteria-soil-plant linkages underlie the mosaic structure of the soil bacterial communities in near-natural stands of Białowieża Primeval Forest.Scientific reports · 2026Article
- Bacterial and Fungal Communities in Old Vines and Their Progeny: Insights into Microbial Inheritance Through Mass Selection.Microorganisms · 2026Article
- Two kinds of evolutionary individuals: the concept of common interest as an evolutionary foundation of dualism on biological individuality.History and philosophy of the life sciences · 2026Article
- The microbiota elicits compensatory adaptation in a seasonally-adapting animal host.bioRxiv : the preprint server for biology · 2025Article
- Applying evolutionary theory to understand host-microbiome evolution.Nature ecology & evolution · 2025Review
- Microbiome evolution plays a secondary role in host rapid adaptation.bioRxiv : the preprint server for biology · 2025Article
- ArtSymbioCyc, a metabolic network database collection dedicated to arthropod symbioses: a case study, the tripartite cooperation inmSystems · 2025Article
- Article
- Solitary Bees Acquire and Deposit Bacteria via Flowers: Testing the Environmental Transmission Hypothesis UsingEcology and evolution · 2025Article
- Microbial solutions to dietary stress: experimental evolution reveals host-microbiome interplay inProceedings. Biological sciences · 2025Article
- Rethinking Conservation in the Anthropocene-The Case of Holobionts.Disease biology, genetics, and socioecology · 2025Article
- Estimates of microbiome heritability across hosts.Nature microbiology · 2024Review
- Decoupling of strain- and intrastrain-level interactions of microbiomes in a sponge holobiont.Nature communications · 2024Article
- Community interactions among microbes give rise to host-microbiome mutualisms in an aquatic plant.mBio · 2024Article
- Describing endosymbiont-host interactions within the parasitism-mutualism continuum.Ecology and evolution · 2024Article
- Seed or soil: Tracing back the plant mycobiota primary sources.Environmental microbiology reports · 2024Article
84 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
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The advent of relatively inexpensive tools for characterizing microbial communities has led to an explosion of research exploring the diversity, ecology, and evolution of microbe-host systems. Some now question whether existing conceptual frameworks are adequate to explain microbe-host systems. One popular paradigm is the "holobiont-hologenome," which argues that a host and its microbiome evolve as a single cooperative unit of selection (i.e., a superorganism). We argue that the hologenome is based on overly restrictive assumptions which render it an approach of little research utility. A host plus its microbiome is more effectively viewed as an ecological community of organisms that encompasses a broad range of interactions (parasitic to mutualistic), patterns of transmission (horizontal to vertical), and levels of fidelity among partners. The hologenome requires high partner fidelity if it is to evolve as a unit. However, even when this is achieved by particular host-microbe pairs, it is unlikely to hold for the entire host microbiome, and therefore the community is unlikely to evolve as a hologenome. Both mutualistic and antagonistic (fitness conflict) evolution can occur among constituent members of the community, not just adaptations at the "hologenome" level, and there is abundant empirical evidence for such divergence of selective interests among members of host-microbiome communities. We believe that the concepts and methods of ecology, genetics, and evolutionary biology will continue to provide a well-grounded intellectual framework for researching host-microbiome communities, without recourse to the limiting assumption that selection acts predominantly at the holobiont level.
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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.