The DOI matches its Crossref record; 76 of the 76 references it cites were found in a registry or an index.
Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
Diet rapidly and reproducibly alters the human gut microbiome
David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100
A core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823
THE MAJOR TRANSITIONS OF EVOLUTION
Leigh, E. G. (1995) · Evolution · doi:10.1111/j.1558-5646.1995.tb04464.x · Cited by 3,410
Human Genetics Shape the Gut Microbiome
Goodrich, J. K., Waters, J. L., Poole, A. C., Sutter, J. L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., Bell, J. T., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.053 · Cited by 3,164 · cited 1×
“For example, the gut microbiota in genetically defined strains of laboratory mice and Drosophila melanogaster varies among laboratories, and also within one laboratory, over time (32–35); studies on the gut microbiota in human twins have revealed either no effect of host genotype or effects that are restricted to spec…”
BackgroundWolbachia: master manipulators of invertebrate biology
Werren, J. H., Baldo, L., & Clark, M. E. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1969 · Cited by 2,819
Self-citationThe ecology of the microbiome: Networks, competition, and stability
Coyte, K. Z., Schluter, J., & Foster, K. R. (2015) · Science · doi:10.1126/science.aad2602 · Cited by 2,748
The relation of recombination to mutational advance
Muller, H. J. (1964) · Mutation Research · doi:10.1016/0027-5107(64)90047-8 · Cited by 2,512
Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile
Buffie, C. G., Bucci, V., Stein, R. R., McKenney, P. T., Ling, L., Gobourne, A., No, D., Liu, H., Kinnebrew, M., Viale, A., et al. (2015) · Nature · doi:10.1038/nature13828 · Cited by 1,872
Ivanov, I. I., Frutos, R. D. L., Manel, N., Yoshinaga, K., Rifkin, D. B., Sartor, R. B., Finlay, B. B., & Littman, D. R. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.09.009 · Cited by 1,770
Research works printed but not linked: 5
- 10.3389/fcimb.2014.00134 · doi:10.3389/fcimb.2014.00134
- 10.1126/science.1251997 · doi:10.1126/science.1251997
- 10.1111/j.1600-0706.2012.19976.x · doi:10.1111/j.1600-0706.2012.19976.x
- 10.1086/597376 · doi:10.1086/597376
- Huigens ME, Stouthamer R. 2003. Parthenogenesis associated with Wolbachia. Insect Symbiosis 1:247–266.
Cited by
Interplay Between Innate Immunity and the Plant Microbiota
Hacquard, S., Spaepen, S., Garrido-Oter, R., & Schulze-Lefert, P. (2017) · Annual Review of Phytopathology · doi:10.1146/annurev-phyto-080516-035623 · Cited by 513
The human microbiome in evolution
Davenport, E. R., Sanders, J. G., Song, S. J., Amato, K. R., Clark, A. G., & Knight, R. (2017) · BMC Biology · doi:10.1186/s12915-017-0454-7 · Cited by 393
Microbiomes as sources of emergent host phenotypes
Lynch, J. B., & Hsiao, E. Y. (2019) · Science · doi:10.1126/science.aay0240 · Cited by 339
Cross talk: the microbiota and neurodevelopmental disorders
Kelly, J. R., Minuto, C., Cryan, J. F., Clarke, G., & Dinan, T. G. (2017) · Frontiers in Neuroscience · doi:10.3389/fnins.2017.00490 · Cited by 271
A psychology of the human brain-gut-microbiome axis
Allen, A. P., Dinan, T. G., Clarke, G., & Cryan, J. F. (2017) · Social and Personality Psychology Compass · doi:10.1111/spc3.12309 · Cited by 174
Metadata
- Authors
- Douglas, A. E., & Werren, J. H.
- Venue
- mBio
- Publisher
- American Society for Microbiology
- Published
- 2016-05-04
- Volume
- 7
- Issue
- 2
- Pages
- e02099-e02099
- ISSN
- 2150-7511 (ISSN-L)
- 2161-2129
- OpenAlex
- W2323772253
- Cited by
- 363
- References
- 76
- FWCI
- 34.74
- Type
- journal article
- Language
- en
- Open access
- gold
- Licence
- creativecommons.org/licenses/by-nc-sa/3.0/ (vor)
- journals.asm.org/non-commercial-tdm-license (tdm)
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts. https://app.cochat.ai/papers/10.1128/mbio.02099-15
- The paper
- Douglas, A. E., & Werren, J. H. (2016). Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts. mBio. https://doi.org/10.1128/mbio.02099-15
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
