The healthy human microbiome
Open accessAbstract
Humans are virtually identical in their genetic makeup, yet the small differences in our DNA give rise to tremendous phenotypic diversity across the human population. By contrast, the metagenome of the human microbiome-the total DNA content of microbes inhabiting our bodies-is quite a bit more variable, with only a third of its constituent genes found in a majority of healthy individuals. Understanding this variability in the "healthy microbiome" has thus been a major challenge in microbiome research, dating back at least to the 1960s, continuing through the Human Microbiome Project and beyond. Cataloguing the necessary and sufficient sets of microbiome features that support health, and the normal ranges of these features in healthy populations, is an essential first step to identifying and correcting microbial configurations that are implicated in disease. Toward this goal, several population-scale studies have documented the ranges and diversity of both taxonomic compositions and functional potentials normally observed in the microbiomes of healthy populations, along with possible driving factors such as geography, diet, and lifestyle. Here, we review several definitions of a 'healthy microbiome' that have emerged, the current understanding of the ranges of healthy microbial diversity, and gaps such as the characterization of molecular function and the development of ecological therapies to be addressed in the future.
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Disruption in human-microbiome symbiosis is associated with, and may contribute to, the increasing prevalence of chronic diseases including IBD, obesity, RA and asthma.
“Disruption in human–microbiome symbiosis is associated with, and may contribute to, the increasing prevalence of numerous chronic diseases including inflammatory bowel disease (IBD), obesity, rheumatoid arthritis (RA) and asthma (Lloyd-Price et al., 2016).”
From Viral Infections, the Microbiome, and Probiotics (2021) · cites this paper as Lloyd-Price et al., 2016
Under healthy conditions, the microbiota influences numerous physiological processes within the host, including protection against pathogens, nutrient digestion and absorption, development, and education of multiple host organs and the immune system.
“Under healthy conditions, the microbiota influences numerous physiological processes within the host, such as protection against pathogens, nutrient digestion and absorption, development, and education of multiple host organs and the immune system (3–6).”
From The gut-brain axis: how microbiota and host inflammasome influence brain physiology and pathology (2020) · cites this paper as [3]
We still do not know what a 'healthy microbiome' is.
“A significant limitation in any FMT study is the fact that although research on the gut microbiome has been prolific, we still do not know what a ‘healthy microbiome’ is.”
From Effect of fecal microbiota transplant on symptoms of psychiatric disorders: a systematic review (2020) · cites this paper as [63]
Even among individuals considered healthy, the variation in taxonomic composition is great.
“Some researchers refer to a healthy microbiome as one of an individual with no overt diseases and others, however, even among those who are considered healthy, the variation in taxonomic composition is great [63–65].”
From Effect of fecal microbiota transplant on symptoms of psychiatric disorders: a systematic review (2020) · cites this paper as [63]
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References 136 · Cited by 1,891
- Authors
- Lloyd-Price, J., Abu-Ali, G., & Huttenhower, C.
- Affiliations
- Harvard University (US)
- Broad Institute (US)
- Corresponding author
- Huttenhower, Curtis
- Venue
- Genome Medicine
- Published
- 2016-04-27
- Volume
- 8
- Issue
- 1
- Pages
- 51-51
- ISSN
- 1756-994X (ISSN-L)
- PMC
- PMC4848870
- OpenAlex
- W2343175653
- Cited by
- 1,891
- References
- 136
- Citations by year
- 2026: 150 · 2025: 215 · 2024: 212 · 2023: 216 · 2022: 230 · 2021: 226 · 2020: 218 · 2019: 183 · 2018: 150 · 2017: 75 · 2016: 14 · 2015: 1
- FWCI
- 12.73
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Genome Medicine (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- human microbiome, microbial diversity, metagenome, Human Microbiome Project, microbial functional potential, regional variation, diet and lifestyle
- MeSH terms
- Bacteria, Humans, Phylogeny, Genetic Variation, Metagenome, Phylogeography, Microbiota, Healthy Volunteers
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