The impact of the gut microbiota on human health: an integrative view
Open accessAbstract
The human gut harbors diverse microbes that play a fundamental role in the well-being of their host. The constituents of the microbiota—bacteria, viruses, and eukaryotes—have been shown to interact with one another and with the host immune system in ways that influence the development of disease. We review these interactions and suggest that a holistic approach to studying the microbiota that goes beyond characterization of community composition and encompasses dynamic interactions between all components of the microbiota and host tissue over time will be crucial for building predictive models for diagnosis and treatment of diseases linked to imbalances in our microbiota.
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The therapeutic effectiveness of ICIs depends on a healthy gut microbiota, which requires microbial diversity and dynamic equilibrium with the immune system.
“The therapeutic effectiveness of ICIs depends on a healthy gut microbiota, which requires microbial diversity and dynamic equilibrium with the immune system135,136.”
From Microbiome meets immunotherapy: unlocking the hidden predictors of immune checkpoint inhibitors (2025) · cites this paper as [136]
The Introduction and ‘Interactions between the Host Immune System and the Microbiota’ sections describe the gut microbiota’s role in normal immune function; the paper also discusses microbial diversity, dynamic interactions, and dysbiosis. It does not address immune checkpoint inhibitors (ICIs) or establish that their therapeutic effectiveness depends on a healthy gut microbiota. Page numbers are unavailable in our copy. (LLM, conf=0.87)
Experimental — accuracy not yet measuredBifidobacterium and Lactobacillus spp. are more abundant in healthy states than in disease states.
“Specific bacteria shown to be more abundant in health compared with disease states include Bifidobacterium and Lactobacillus spp.(2,7,14)”
From Dietary fiber intervention on gut microbiota composition in healthy adults: a systematic review and meta-analysis (2018) · cites this paper as [7]
Specific nutrients, especially protein and insoluble fiber, have profound effects on gut microbiota structure, function, and secretion of metabolites that modulate immune function and multiple metabolic and inflammatory pathways.
“Accumulating metagenomic data show that specific nutrients, especially protein and insoluble fiber, have profound effects on gut microbiota structure, function, and secretion of metabolites that modulate immune function and multiple metabolic and inflammatory pathways (86–88).”
From Health Benefits of the Mediterranean Diet: Metabolic and Molecular Mechanisms (2018) · cites this paper as [86]
Altered composition and function of gut microbiota have been linked to a number of chronic diseases, including colon cancer, irritated bowel syndrome, colitis, obesity, and diabetes mellitus.
“Altered composition and function of gut microbiota have been linked to a number of chronic diseases, including colon cancer, irritated bowel syndrome, colitis, obesity, and diabetes mellitus.3”
The gut bacteria of urban-industrialized populations often have high abundances of Bacteroides, while the gut bacteria from traditional hunter-gatherer or agropastoral societies have higher abundances of Prevotella.
“The gut bacteria of urban-industrialized populations often have high abundances of Bacteroides, while the gut bacteria from traditional hunter-gatherer or agropastoral societies have higher abundances of Prevotella [22–28].”
From Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana (2019) · cites this paper as [26]
Bacteroides has been used to distinguish between developing (low Bacteroides abundance) and industrialized (high Bacteroides abundance) populations.
“Bacteroides has been used to distinguish between developing (low Bacteroides abundance) and industrialized (high Bacteroides abundance) populations [22–28, 30]”
From Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana (2019) · cites this paper as [26]
The Hadza have the highest abundance of Prevotellaceae and Spirochetaceae among populations in this cohort.
“they have the highest abundance of Prevotellaceae and Spirochetaceae [24–27, 30]”
From Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana (2019) · cites this paper as [26]
Treponema within family Spirochetaceae is a common constituent of hunter-gatherer gut microbiomes and a catabolizer of fibrous plant materials (cellulose and xylans) that form a large component of Hadza diets.
“in particular, the genus Treponema within family Spirochetaceae, which is a common constituent of hunter-gatherer gut microbiomes [24–27, 30] and a catabolizer of fibrous plant materials (cellulose and xylans) that form a large component of Hadza diets [24]”
From Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana (2019) · cites this paper as [26]
Dietary interventions might influence the gut-brain axis by altering microbiota composition and therefore altering Parkinson's disease pathogenesis, or by affecting neuronal functioning in both the enteric nervous system and the central nervous system.
“Dietary interventions might influence the gut-brain axis by altering microbiota composition (and therefore altering PD pathogenesis) (Clemente et al., 2012;Cryan and Dinan, 2012;Maslowski and Mackay, 2011) or by affecting neuronal functioning in both the ENS and the CNS (Fig. 2).”
From The Gut-Brain Axis in Parkinson’s Disease: Possibilities for Food-Based Therapies (2017) · cites this paper as Clemente et al., 2012
Prebiotic fibers added to the diet might explain its better effects on gastrointestinal function and motor function via beneficial effects on immune function, bowel motility, and microbiota composition that can alter the enteric immune and nervous system and subsequently the central nervous system.
“Prebiotic fibers added to the diet might explain its better effects on GI-function since GOS and FOS have shown to have beneficial effects on immune function (de Kivit et al., 2011), bowel motility (Meksawan et al., 2014;Scholtens et al., 2014), but they might also contribute to its better efficacy on motor-function since the prebiotic fibers might positively affect microbiota composition that in”
From The Gut-Brain Axis in Parkinson’s Disease: Possibilities for Food-Based Therapies (2017) · cites this paper as Clemente et al., 2012
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- Authors
- Clemente, J. C., Ursell, L. K., Parfrey, L. W., & Knight, R.
- Affiliations
- University of Colorado Boulder (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Knight, Rob
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2012-03
- Volume
- 148
- Issue
- 6
- Pages
- 1258-1270
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC5050011
- OpenAlex
- W2033829415
- Semantic Scholar
- 370ed2c725f14753fefc20f41257eea80383a74a
- Cited by
- 3,710
- References
- 123
- Citations by year
- 2026: 156 · 2025: 243 · 2024: 308 · 2023: 283 · 2022: 365 · 2021: 407 · 2020: 372 · 2019: 309 · 2018: 311 · 2017: 284 · 2016: 191 · 2015: 172 · 2014: 146 · 2013: 121 · 2012: 37
- FWCI
- 13.88
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- National Human Genome Research Institute (R01HG004872)
- National Institute of General Medical Sciences (T32-GM08759, T32GM008759, T32GM142607)
- National Institute of Diabetes and Digestive and Kidney Diseases (P01DK078669)
- National Institute on Minority Health and Health Disparities (R01MD011389)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
- Keywords
- gut microbiota, human health, host-microbe interactions, immune system, microbial communities, disease development, microbiota imbalance, prediction model, diagnosis and treatment
- MeSH terms
- Animals, Bacteria, Humans, Parasites, Gastrointestinal Tract, Metagenome, Microbial Interactions
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