May 18, 2022

Wellness Read: Gut Microbiome – The Basics

by Rachel Klomstad, MS, RD

Advances in human genomics have spurred a new interest in and attention to the critical role of the gut microbiome in human health. The Human Microbiome Project, initiated in the fall of 2007, set the stage to uncover much of what we know today regarding the complexity of our microbiome and how it can affect overall health.1 Still, while much has been discovered over the past 15 years, the role of the microbiome in health and disease is still not fully understood. In this month’s Wellness Read, we explain the basics of the gut microbiome, the benefits of microbiota to the body, and the effect of diet on the microbiome.


The human microbiome refers to the collection of trillions of microorganisms (also called microbiota or microbes) of thousands of different species located on and within the human body.2 These include mostly bacteria, but also parasites, viruses, protozoa, and fungi. These microorganisms co-exist peacefully in healthy individuals and are largely concentrated in the intestines, although can also be found in other areas throughout the body.3 The microbiome is now considered a supporting organ due to the many key roles it plays in promoting routine functions of the human body.

Each person’s microbiome is completely unique and is established at birth through contact with either the delivery canal, the mother’s skin, and/or the mother’s breast milk. Exactly which microbes the infant is exposed to depends solely on the mother’s microbiota. As infants grow, environmental exposures and expanded diets change their microbiomes. By the age of two, the gut microbiome stabilizes and appears to have similar complexity to that of an adult.1 Throughout one’s life, however, diet, drugs, and body composition changes (e.g., BMI and waist circumference) can significantly alter microbiota composition and serve to either promote health or increase disease risk.4

The balance of specific microbes within the body dictates the role the microbiome plays in health and disease. Of the trillions of microorganisms that make up the microbiome, most are symbiotic (benefiting both the organism and the human body), but a small number are pathogenic (disease-promoting). Symbiotic and pathogenic organisms coexist harmoniously in a healthy body, but if there is a disturbance in their balance – brought on by infectious disease, low-quality diets, certain diets, or prolonged use of antibiotics – dysbiosis (altered functional composition and distribution of microbiota) occurs. This causes microbiota to be more susceptible to disease.5 Much new research is being conducted to understand the specific mechanisms by which this happens.


While the effects of the gut microbiome were once thought to be limited to the digestive tract, new research verifies effects extending to immune status, metabolism, organ development and beyond.6

For example, microbiota produce the enzymes necessary for the fermentation of non-digestible dietary fiber (found in whole grains, legumes, vegetables, and fruits). This process produces short chain fatty acids (SCFAs) (such as acetate, butyrate, and propionate)2 as byproducts, which modulate a variety of bodily functions and disease states. Butyrate, for instance, activates pathways affecting glucose and energy balance, stabilizes gut pH and prevents microbiota dysbiosis. Butyrate and propionate play a role in gut hormone and satiety signaling.7 Acetate, the most abundant SCFA, contributes to cholesterol metabolism, appetite regulation, and the growth of other bacteria. Experimental studies correlate higher production of SCFAs with lower incidence of diet-induced obesity,8 as well as reduced insulin resistance.9

In addition to SCFAs, other components of microbiota enact beneficial effects, including the breakdown of toxic food compounds, such as oxalate (a compound found in many foods that inhibits the absorption of various nutrients in the gut such as calcium, zinc, and magnesium)10, and the synthesis of certain vitamins and amino acids, including B vitamins and vitamin K.11

Independent of their byproducts, certain strains of bacteria are linked to beneficial functions in the body. Despite the existence of hundreds of bacteria strains, most may be grouped within a few large families, including Prevotella, Ruminococcus, Bacteroides, and Firmicutes. The colon, due to its low oxygen environment, hosts anaerobic bacteria (bacteria that can live without oxygen), such as Peptostreptococcus, Bifidobacterium, Lactobacillus, and Clostridium.12 These specific species are believed to prevent the overgrowth of harmful bacteria by competing for nutrients and attachment sites in the mucus membranes of the gut, a main area for immune activity.13

Lower bacterial diversity has been observed in those with inflammatory bowel disease, type 2 diabetes, celiac disease, and obesity compared to healthy controls. This indicates an association between reduced microbiome diversity and disease, providing the basis for recommendations around fueling for gut health.2


Specific foods and dietary patterns can alter both the abundance and variety of bacteria in the gut, which in turn can affect health. For example, a low FODMAP (a prescribed diet restricting foods containing specific poorly absorbed carbohydrates) is shown to reduce symptoms for those with IBS and is associated with a reduced proportion of Bifidobacterium. Alternatively, artificial sweetener consumption has been linked to dysbiosis of Bacteroides, resulting in glucose intolerance.2

High fiber intake, however, seems to be the largest driver of microbiota concentration and diversity in the intestines. The breakdown and fermentation of indigestible fiber in the gut results in the creation of beneficial SCFAs (as mentioned earlier). Specific foods with gut-feeding fiber are called prebiotics. Raw versions of foods such as garlic, onion, leek, asparagus, banana as well as most other fruits, vegetables, beans, and whole grains (e.g., wheat, oats, and barley) provide good sources of prebiotic fiber.3

Probiotic foods contain beneficial live bacterial cultures and can also alter the gut microbiome. Fermented foods, such as kefir, Greek yogurt, pickled vegetables, tempeh, kombucha, kimchi, miso, and sauerkraut contain probiotics and, when eaten, can contribute to healthy microbial diversity. Probiotics can also be found in the form of supplements. In fact, probiotic supplement sales are projected to exceed $65 billion by 2024.3 While supplementing probiotics may be helpful for some people, specifically those finishing antibiotic treatment or recovering from C. Difficile (an infection in the colon), no significant benefit of probiotic supplements has been established when compared to probiotic foods in a healthy population.14


The amount and diversity of short chain fatty acids (SCFAs) and other specific products produced by gut microbiota play an important role in human health and influence the development of chronic disease. Dietary and environmental factors have a profound impact on the composition of one’s microbiome, and the concentrations of microbial byproducts. Increased intake of fiber and probiotic foods contribute to microbiota diversity and is correlated with decreased chronic disease risk. Consider the following recommendations for improving the diversity and health of your gut microbiome:

  1. Incorporate whole, fiber-rich foods (fruits, vegetables, whole grains, and legumes) regularly. Remember to start gradually to prevent increased gas and bloating. Start by adding 1-2 new foods a week to allow time for the gut to adjust.
  2. Aim for variety. The greater the variety of fiber-rich prebiotic foods consumed, the greater the diversity of bacterial strains fermented and available to contribute to metabolism, immune support, and optimal digestion.
  3. Add probiotic foods. For example, experiment with pickled onion on your poke bowl or tempeh with your stir fry to add helpful bacteria to your microflora.

If you have further questions about the gut microbiome or how to incorporate gut-feeding foods into your diet, reach out to your Registered Dietitian for a more individualized approach.

In Real Health,

Rachel & Lauren

SHIFT Registered Dietitians


  1. Institute of Medicine (US) Food Forum. The Human Microbiome, Diet, and Health: Workshop Summary. Washington (DC): National Academies Press (US); 2013. 2, Study of the Human Microbiome. Available from:
  2. Valdes AM, Walter J, Segal E, Spector TD. Role of the gut microbiota in nutrition and health. BMJ. 2018;361:k2179. Published 2018 Jun 13. doi:10.1136/bmj.k2179
  3. The microbiome. The Nutrition Source. Published May 1, 2020. Accessed May 4, 2022.
  4. Goodrich JK, Waters JL, Poole AC, et al. Human genetics shape the gut microbiome. Cell. 2014;159(4):789-799. doi:10.1016/j.cell.2014.09.053
  5. Hills RD Jr, Pontefract BA, Mishcon HR, Black CA, Sutton SC, Theberge CR. Gut Microbiome: Profound Implications for Diet and Disease. Nutrients. 2019;11(7):1613. Published 2019 Jul 16. doi:10.3390/nu11071613
  6. Sommer F, Bäckhed F. The gut microbiota–masters of host development and physiology. Nat Rev Microbiol. 2013;11(4):227-238. doi:10.1038/nrmicro2974
  7. De Vadder F, Kovatcheva-Datchary P, Goncalves D, et al. Microbiota-generated metabolites promote metabolic benefits via gut-brain neural circuits. Cell. 2014;156(1-2):84-96. doi:10.1016/j.cell.2013.12.016
  8. Lin HV, Frassetto A, Kowalik EJ Jr, et al. Butyrate and propionate protect against diet-induced obesity and regulate gut hormones via free fatty acid receptor 3-independent mechanisms. PLoS One. 2012;7(4):e35240. doi:10.1371/journal.pone.0035240
  9. Zhao L, Zhang F, Ding X, et al. Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes. Science. 2018;359(6380):1151-1156. doi:10.1126/science.aao5774
  10. Food Revolution Network. Are oxalates bad for you? and should you avoid foods that are high in oxalates? Food Revolution Network. Published August 4, 2021. Accessed May 17, 2022.
  11. den Besten G, van Eunen K, Groen AK, Venema K, Reijngoud DJ, Bakker BM. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res. 2013;54(9):2325-2340. doi:10.1194/jlr.R036012
  12. Arumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome [published correction appears in Nature. 2011 Jun 30;474(7353):666] [published correction appears in Nature. 2014 Feb 27;506(7489):516]. Nature. 2011;473(7346):174-180. doi:10.1038/nature09944
  13. Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Nageshwar Reddy D. Role of the normal gut microbiota. World J Gastroenterol. 2015;21(29):8787-8803. doi:10.3748/wjg.v21.i29.8787
  14. Homayoni Rad A, Vaghef Mehrabany E, Alipoor B, Vaghef Mehrabany L. The Comparison of Food and Supplement as Probiotic Delivery Vehicles. Crit Rev Food Sci Nutr. 2016;56(6):896-909. doi:10.180/10408398.2012.733894


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