The gut microbiome and health: Insights from current research

Ever since the 17th century, the origins of disease have been traced to microorganisms. While the study of pathogens such as bacteria and viruses led to widespread improvements in sanitation and public health safety, it also led to the discovery of an amazing ecosystem called the “human microbiome.” Vigorous research over the past twenty years has identified how trillions of microbes, both helpful and potentially harmful, interact with different body systems.^1,2 While they are found throughout the body (such as on the skin and in the mouth), the most abundant number of microbes live in the intestinal tract or gut.^2-4 

Links between a disordered gut microbiome and disease are real and growing, but most remain associations rather than proven cause-and-effect relationships. Reproducing results across different populations, measuring outcomes, and developing guidelines continues to be a work in progress.¹⁰ Despite these limitations,the market for products and services that promote gastrointestinal health is thriving, along with misinformation and confusion. It is estimated that 3.9 million American adults use some form of probiotics or prebiotics, and enthusiasm for such products has led to a global multibillion-dollar industry.¹¹

Because pre- and probiotics are not considered drugs in the United States or Europe, they are largely unregulated. The marketing of a “gut-enhancing” product is often geared directly at consumers without providing direct and consistent proof of effectiveness.¹¹ Sometimes a probiotic supplement contains lower than the stated dose of bacterial strains or may even contain different types of strains than are listed. It is up to the manufacturer to ensure potency (listed in colony-forming units [CFUs]), purity, and identity of specific bacteria strains.^12,13 Live probiotics are susceptible to dying during storage, and responsible manufacturers will include the dose expected at the use-by date. 

What the clinical evidence supports

Proven therapies are narrow.

A small set of microbiome-based treatments are well supported. Three conditions are indicated by the American Gastroenterological Association (AGA) for certain probiotics: 1) preventing C. difficile infection among adults and children taking antibiotics, 2) preventing necrotizing enterocolitis among preterm, low birthweight infants, and 3) managing pouchitis (inflammation in the pouch made during surgery after colon removal).^11,13 Beyond this, the evidence is thin.¹¹

Broad probiotic use is not supported.

The AGA advises against routine use for most digestive disorders with added caution in infants, the elderly, and immunocompromised patients. In general, probiotics are not recommended for most GI disorders, including IBS.^11,13 Individual use of probiotics should be discussed with a gastroenterologist and Registered Dietitian Nutritionist (RDN). 

Routine microbiome testing is not yet ready.

A 2025 international consensus concluded there is not enough evidence to recommend microbiome testing in everyday practice; it remains investigational.¹⁴

Diet is still the best-supported approach.

Fiber-rich, plant-forward eating has the most consistent evidence for a healthy microbiome.^3,4,6,13 A diet that includes a diversity of whole plant and fermented foods contains an abundance of natural “biotics.” Conversely, an intake high in red meats, fat, sugar, and highly processed foods can negatively disrupt the gut microbiome.¹⁵

Helping patients maintain a healthy gut

Guidance on eating to heal and sustain health is the professional domain of RDNs. Through Clinicia™, Sodexo’s clinical and patient nutrition service offer, RDNs translate emerging microbiome science into individualized, evidence-based nutrition care. Rather than relying on one-size-fits-all recommendations, RDNs assess each patient’s diagnosis, nutrition status, symptoms, treatment plan, food preferences and goals to determine how fiber-rich foods, fermented foods, prebiotics, probiotics or supplements may fit safely and appropriately into the patient’s overall nutrition plan.²

The Clinicia Patient Menu, developed through collaboration between chefs and RDNs, supports this individualized approach by offering therapeutic, satisfying meals rich in fiber from whole grains, fruits, vegetables and legumes. These foods help nourish the gut microbiome while providing practical options that align with patients’ clinical needs and preferences.

Together, Sodexo RDNs and the Clinicia Patient Menu help translate the evolving science of the gut microbiome into practical, personalized nutrition strategies that support healing, recovery, and long-term health.

1. NIH Human Microbiome Portfolio Analysis Team. A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016. Microbiome. 2019;7(1):31. Published 2019 Feb 26. doi:10.1186/s40168-019-0620-y
2. Holscher HD. Diet Affects the Gastrointestinal Microbiota and Health. J Acad Nutr Diet. 2020;120(4):495-499. doi:10.1016/j.jand.2019.12.016  
3. The Microbiome. The Nutrition Source. Harvard T.H. Chan School of Public Health. Accessed August 27, 2026. https://nutritionsource.hsph.harvard.edu/microbiome/
4. Gut Microbiome. Cleveland Clinic. Updated August 18, 2023. Accessed August 27, 2026. https://m.clevelandclinic.org/health/body/25201-gut-microbiome  
5. Afzaal M,Saeed F, Shah YA, et al. Human gut microbiota in health and disease: Unveilng the relationship. Front Microbiol. 2022;13:999001. Published 2022 Sep 26. doi:10.389/fmicb.2022.999001  
6. Bulsiewicz W. Fiber Fueled. Penguin Random House; 2020.  
7. Marco ML, Sanders ME, Gänzle M, et al. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nat Rev Gastroenterol Hepatol. 2021;18(3):196-208. doi:10.1038/s41575-020-00390-5
8. Key Topics: Prebiotics, Probiotics, Synbiotics, Postbiotics, Fermented Foods, Live Dietary Microbes, Gut Health, Microbiome. International Scientific Association for Probiotics and Prebiotics (ISAPP). Accessed August 31, 2026. https://isappscience.org/
9. 10 Ways to Strengthen Your Microbiome. Canadian Digestive Health Foundation (CDHF). Updated June 11, 2026. Accessed August 27, 2026. https://cdhf.ca/en/10-ways-to-strengthen-your-microbiome
10. Marco ML, Cunningham M, Bischoff SC, et al. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of gut health. Nat Rev Gastroenterol Hepatol. 2026;23(5):432-448. doi:10.1038/s41575-026-01176-x
11. Su GL, Ko CW, Bercik P, et al. AGA Clinical Practice Guidelines on the Role of Probiotics in the Management of Gastrointestinal Disorders. Gastroenterology. 2020;159(2):697-705. doi:10.1053/j.gastro.2020.05.059
12. Probiotics for Gut Health. The Nutrition Source. Harvard T.H. Chan School of Public Health. Accessed August 27, 2026. https://nutritionsource.hsph.harvard.edu/probiotics/
13. Thakur R, Craven M, Keefer L, Hass DJ. A Primer for Discussing Complementary and Integrative Medicine in Gastroenterology Settings. Neurogastroenterol Motil. 2026;38(4):e70313. doi:10.1111/nmo.70313
14. Porcari S, Mullish BH, Asnicar F, et al. International consensus statement on microbiome testing in clinical practice. Lancet Gastroenterol Hepatol. 2025;10(2):154-167. doi:10.1016/S2468-1253(24)00311-X
15. Malesza IJ, Malesza M, Walkowiak J, et al. High-Fat, Western-Style Diet, Systemic Inflammation, and Gut Microbiota: A Narrative Review. Cells. 2021;10(11):3164. Published 2021 Nov 14. doi:10.3390/cells10113164