Health, Nutrition, & the Role of the Microbiome

The human gastrointestinal microbiome is, in and of itself, a complex ecosystem;1 it is a “microbial organ” within the gastrointestinal tract.2 The intestinal microbiome is dominated by anaerobic bacteria and includes approximately 500-1,000 species, whose collective genomes are estimated to contain 100 times more genes than our own human genome.3

When the intestinal ecology is altered, so too is the health of the host; studies show that the maintenance of a healthy microbiome is inseparable from host health.1 These microbes influence physiological function (particularly metabolism), local mucosal homeostasis, inflammation, and immunity.1,4 Supporting a healthy microbiome is an important cornerstone for immune health and response to infections,5 as well as overall resilience.

In the following video, IFM educator Michael Stone, MD, MS, shares his assessment and treatment techniques for dysbiosis, including:

  • Physical cues found in the mouth indicating dysbiosis
  • Antecedents and triggers to consider for dysbiosis
  • Using the IFM Timeline to evaluate dysbiosis and personalize treatment
  • Conditions under which he uses stool testing
  • The role of prebiotics

How to Support the Microbiome

The microbiome is plastic, not static. Alterations to the gut microbiota may start at the earliest stages of life; disruption of the developing microbiota in infancy can contribute to the risk of immune and metabolic disease as an adult.1 At the other end of the age spectrum, in a large study of the elderly, reduction of microbial diversity is associated with a shift toward a monotonous diet; the loss of diversity was also linked with increased markers of inflammation and frailty.8

Throughout life, a range of healthy lifestyle factors, including a diversified diet, limited use of processed foods, avoidance of prolonged restricted diets, and consumption of adequate dietary fiber, all promote a healthy microbiome.1 In a 2020 systematic review of the literature, researchers found that consumption of whole grains/fiber may modify the intestinal microbiota and promote the growth of Bifidobacteria and Lactobacilli.6 Studies have shown that seafood, including marine seaweeds and invertebrates, are rich in dietary fibers and can help maintain symbiosis in the gut.7 Other research suggests that gut microbiota alterations due to unhealthy lifestyle factors and inadequate nutrition may contribute to the pathogenesis of a broad spectrum of diseases such as obesity, diabetes mellitus, non-alcoholic fatty liver disease,3 colorectal cancer, cardiovascular disease, Parkinson’s disease, and Alzheimer’s disease.7

Mediterranean Diet Benefits

The good news is that the intestinal microbiome may be modified by long-term dietary interventions, according to a 2015 study with patients with obesity.9 The study observed changes in the microbiota after one year of consumption of either a Mediterranean diet or a low-fat, high complex carbohydrate diet in an obese population. Results suggest that long-term consumption of both diets exerts a protective effect on the development of type 2 diabetes, due to an increasing abundance of Roseburia genus and F. prausnitzii, respectively.9

Although the exact mechanisms of action are not yet fully understood, a variety of recent hypotheses have been explored in the medical literature to explain the potential benefits of the Mediterranean diet on the gut microbiota.10 A 2020 study of 612 elderly people suggests that adherence to a Mediterranean diet led to a higher abundance of different taxa that are positively associated with markers of lower frailty and better cognitive function.11 This was mainly due to the ingestion of fiber, certain vitamins (C, B6, B9), and various minerals.11


As a clinician, you can help your patients restore a healthy, diverse microbiome at any stage of their life through modifiable lifestyle factors like diet. In Functional Medicine, nutrition interventions are key components of personalized therapeutic strategies that address gastrointestinal imbalances and a patient’s overall wellness. Implementing practical lifestyle approaches for a healthy intestinal microbiome and supporting immune health will help lead to patient engagement and improved outcomes.

Learn more about the microbiome, nutrition, and human health by following these links:

Learn More About Functional Medicine

Emerging Concept: Optimizing the pediatric microbiome

The role of the microbiome in immune-related diseases

The connection between leaky gut and arthritis


  1. Shanahan F, van Sinderen D, O’Toole PW, Stanton C. Feeding the microbiota: transducer of nutrient signals for the host. Gut. 2017;66(9):1709-1717. doi:1136/gutjnl-2017-313872
  2. Okubo H, Nakatsu Y, Kushiyama A, et al. Gut microbiota as a therapeutic target for metabolic disorders. Curr Med Chem. 2018;25(9):984-1001. doi:2174/0929867324666171009121702
  3. Bäckhed F, Ding H, Wang T, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A. 2004;101(44):15718-15723. doi:1073/pnas.0407076101
  4. Cammarota G, Ianiro G. Gut microbiota and cancer patients: a broad-ranging relationship. Mayo Clin Proc. 2017;92(11):1605-1607. doi:1016/j.mayocp.2017.09.009
  5. Thaiss CA, Zmora N, Levy M, Elinav E. The microbiome and innate immunity. Nature. 2016;535(7610):65-74. doi:1038/nature18847
  6. Tangestani H, Emamat H, Ghalandari H, Shab-Bidar S. Whole grains, dietary fibers and the human gut microbiota: a systematic review of existing literature. Recent Pat Food Nutr Agric. Published online March 16, 2020. doi:2174/2212798411666200316152252
  7. Shang Q, Jiang H, Cai C, Hao J, Li G, Yu G. Gut microbiota fermentation of marine polysaccharides and its effects on intestinal ecology: an overview. Carbohydr Polym. 2018;179:173-185. doi:1016/j.carbpol.2017.09.059
  8. Claesson MJ, Jeffery IB, Conde S, et al. Gut microbiota composition correlates with diet and health in the elderly. Nature. 2012;488(7410):178-184. doi:1038/nature11319
  9. Haro C, Montes-Borrego M, Rangel-Zúñiga OA, et al. Two healthy diets modulate gut microbial community improving insulin sensitivity in a human obese population. J Clin Endocrinol Metab. 2016;101(1):233-242. doi:1210/jc.2015-3351
  10. Cani PD, Van Hul M. Mediterranean diet, gut microbiota and health: when age and calories do not add up! Gut. Published online March 13, 2020. doi:1136/gutjnl-2020-320781
  11. Meslier V, Laiola M, Roager HM, et al. Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake. Gut. Published online February 19, 2020. doi:1136/gutjnl-2019-320438

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