The Healthy Microbiome—What Is the Definition of a Healthy Gut Microbiome?
Abstract
Use of microbiome-based biomarkers in diagnosis, prognosis, risk profiling, and precision therapy requires definition of a healthy microbiome in different populations. To determine features of the intestinal microbiota associated with health, however, we need improved microbiome profiling technologies, with strain-level resolution. We must also learn more about how the microbiome varies among apparently healthy people, how it changes with age, and the effects of diet, medications, ethnicity, geography, and lifestyle. Furthermore, many intestinal microbes, including viruses, phage, fungi, and archaea, have not been characterized, and little is known about their contributions to health and disease.Whether a healthy microbiome can be defined is an important and seemingly simple question, but with a complex answer in continual need of refinement.
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Healthy individuals display highly divergent gut microbiomes while retaining similar functional capacities.
“This is necessary because healthy individuals display highly divergent gut microbiomes while retaining similar functional capacities [149], hence further work is needed to understand functional changes in the gut-microbiome, interactions between microbes, and hot-microbiome interactions [150].”
From The gut–brain axis in early Parkinson’s disease: from prodrome to prevention (2025) · cites this paper as [149]
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References 81 · Cited by 383
- Authors
- Shanahan, F., Ghosh, T. S., & O’Toole, P. W.
- Affiliations
- National University of Ireland (IE)
- Corresponding author
- Shanahan, Fergus
- Venue
- Gastroenterology
- Publisher
- Elsevier BV
- Published
- 2021-01
- Volume
- 160
- Issue
- 2
- Pages
- 483-494
- ISSN
- 0016-5085 (ISSN-L)
- OpenAlex
- W3108994080
- Cited by
- 383
- References
- 81
- Citations by year
- 2026: 56 · 2025: 76 · 2024: 81 · 2023: 66 · 2022: 75 · 2021: 26 · 2020: 1 · 2017: 2
- FWCI
- 4.05
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Gastroenterology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Science Foundation Ireland
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- gut microbiota, microbiome biomarkers, strain-level resolution, interindividual variability, age-related changes, diet, medication effects, ethnicity, microbiome diversity, viruses, bacteriophages, fungi, archaea
- MeSH terms
- Gastrointestinal Microbiome, Host Microbial Interactions, Environment, Health, Health Status, Humans, Life Style, Reference Standards, Risk, Microbiota, Dysbiosis
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