ReviewNature microbiology2018
Defining microbiome function.
Review in Nature microbiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed.
- Proteomic study of evolvedmSystems · 2025Article
- Microbiome evolution plays a secondary role in host rapid adaptation.bioRxiv : the preprint server for biology · 2025Article
- Urbanization leads to asynchronous homogenization of soil microbial communities across biomes.Environmental science and ecotechnology · 2025Article
- Rational management of the plant microbiome for the Second Green Revolution.Plant communications · 2024Review
- Plant-Microbe Interactions under the Extreme Habitats and Their Potential Applications.Microorganisms · 2024Review
- Temporal variations in the gut microbial diversity in response to high-fat diet and exercise.Scientific reports · 2024Article
- Article
- microbioTA: an atlas of the microbiome in multiple disease tissues of Homo sapiens and Mus musculus.Nucleic acids research · 2023Article
- Host's genetic background determines the outcome of reciprocal faecal transplantation on life-history traits and microbiome composition.Animal microbiome · 2022Article
- The microbiome extends host evolutionary potential.Nature communications · 2021Review
- Insights into the taxonomic and functional characterization of agricultural crop core rhizobiomes and their potential microbial drivers.Scientific reports · 2021Article
- C. elegans: A biosensor for host-microbe interactions.Lab animal · 2021Review
- The use of fecal microbiota transplant in sepsis.Translational research : the journal of laboratory and clinical medicine · 2020Review
- MetaRibo-Seq measures translation in microbiomes.Nature communications · 2020Article
- Host-associated microbiomes are predicted by immune system complexity and climate.Genome biology · 2020Article
- The microbiome: an emerging key player in aging and longevity.Translational medicine of aging · 2020Article
- Review
- Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Why does a microorganism associate with a host? What function does it perform? Such questions are difficult to unequivocally address and remain hotly debated. This is partially because scientists often use different philosophical definitions of 'function' ambiguously and interchangeably, as exemplified by the controversy surrounding the Encyclopedia of DNA Elements (ENCODE) project. Here, I argue that research studying host-associated microbial communities and their genomes (that is, microbiomes) faces similar pitfalls and that unclear or misapplied conceptions of function underpin many controversies in this field. In particular, experiments that support phenomenological models of function can inappropriately be used to support functional models that instead require specific measurements of evolutionary selection. Microbiome research also requires uniquely clear definitions of 'who the function is for', in contrast to most single-organism systems where this is implicit. I illustrate how obscuring either of these issues can lead to substantial confusion and misinterpretation of microbiome function, using the varied conceptions of the holobiont as a current and cogent example. Using clear functional definitions and appropriate types of evidence are essential to effectively communicate microbiome research and foster host health.
Indexed as
Identifiers
30046174What 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.