“Healthy” and “gut” are two words we usually don’t put together. We usually associate “gut” with belly fat, but this is something totally different with fascinating emerging science. So, what do we mean by a “healthy gut”?

We’re actually talking about the trillions of invisible, microscopic organisms, mostly bacteria, that live in the human digestive tract, the greatest concentration being found in the large intestine. Until recently, not a lot of attention was given to these creatures because, 1) the technology wasn’t available to study them, and 2) come on, we’re talking about poop bugs; how important can they really be to human health?

Improvements in molecular technologies since 2006 have led to an explosion of scientific research indicating that the microorganisms living in our digestive tract actually play a central role in human health and biological processes, influencing our physiology, metabolism, nutrition, hormonal balance, brain health, immune function, even gene expression.

Furthermore, disruption or damage to these microorganisms, called “dysbiosis,” has been associated with the development of numerous diseases, including inflammatory bowel disease (ulcerative colitis, Crohn’s disease), diabetes, heart disease, colon and breast cancer, obesity, Alzheimer’s, autoimmune diseases, depression and more.^{1- 3}

Bottomline: the emerging science of the human gut microbiome is telling us that a healthy, thriving gut microbiota is necessary for a healthy, thriving human being. So profoundly important is the gut microbiota to human health it’s been called the “forgotten organ.”⁴

Let’s take a closer look at this exciting new area of research and learn what we can do to optimize our health by optimizing our gut microbiota. But first, it’s important we’re on the same page with a few basic terms.

Definition of four important terms

• Gut. While the gut can refer to the entire digestive tract, in this area of research it generally refers to the large intestine, or colon, because that’s where the majority of the microbes live, ~39 trillion. (That’s 12 zeros!) So, when we say gut we’re talking about the large intestine.
• Gut bacteria. The different types of organisms that live in the gut include bacteria, archaea, viruses, yeasts, protozoa and fungi. Since 90% of them are bacteria, the words ‘gut bacteria’ or ‘bacterial species’ are used to refer to all the different types of microorganisms living in our gut.
• Microbiota. Refers to all the living microorganisms in the gut.
• Microbiome. Refers to the collective genetic material of all the microbiota. Even though these two words do not mean the same thing, they are generally used interchangeably, which is what we will do in this article.

What constitutes a healthy gut microbiome?

Our gut bacteria can be divided into two broad categories:

1. Beneficial bacteria – health-promoting bacterial species (the good guys)
2. Pathogenic bacteria – disease-promoting bacterial species (the bad guys)

A healthy gut microbiome has balance and harmony defined by two essential characteristics:⁵

• The beneficial, health-promoting bacterial species predominate over the pathogenic ones. In other words, the good guys outnumber the bad guys.
• There is a great diversity of beneficial bacterial species.

How do we get a healthy gut microbiome?

Like humans, our gut bacteria are living organisms that need food to provide energy. Since they live in our digestive tract, they eat what we eat. So, if we want the beneficial gut bacteria to thrive, we need to feed them their preferred food—Fiber!

Dietary fiber is THE key nutrient for fueling beneficial bacterial species.⁶ They love to ferment fiber and can’t survive without it. So, in order to have the good gut bacteria outnumber the bad ones, we need to eat a high-fiber diet. Since dietary fiber is only found in plant foods, fruits, vegetables, beans, whole grains, nuts and seeds become the necessary foundation of the daily diet.

As noted above, diversity of beneficial bacterial species is also necessary for a healthy gut microbiome. The American Gut Project, the largest study to date connecting the human gut microbiome with dietary choices, has discovered an important key: the single most powerful predictor of a diverse gut microbiota is the diversity of plants in the diet. Another way to think of that is the diversity of whole, plant fiber foods in the diet, like apples, carrots, pinto beans and oats, for example.

The greater the diversity of fiber foods eaten, the greater the abundance and diversity of the beneficial bacterial species. In fact, their research has shown, no matter the type of diet, those participants who ate more than 30 different plant foods per week had gut microbiomes that were more diverse than those who ate 10 or fewer plants per week.⁷

What causes an unhealthy gut microbiome (dysbiosis)?

Many factors play a role in keeping our gut microbiome balanced: diet, sleep habits, exercise, stress management, alcohol and cigarette use, toxins, diseases, drugs and medications, genetics.⁸ We will focus on 1) dietary habits that harm the gut bacteria, because diet is one of the main determinants of the composition of the gut microbiota, and 2) on prescription drugs and over-the-counter (OTC) medicines, because their use is so common in the US: 66% of US adults take prescription drugs, and nearly 9 out of every 10 Americans use OTC medications regularly.

Diet

According to the recent 9th edition of the Dietary Guidelines for Americans,⁹ more than 90% of adult women and 97% of adult men do not meet daily fiber recommendations of 25 and 38 grams.¹⁰ This is associated with the fact that more than 85% of adults under consume fruits, vegetables and whole grains, key sources of dietary fiber.⁹

Since health-promoting bacterial species thrive on dietary fiber and die out without it,¹¹ the Standard American Diet does not promote a healthy, thriving gut microbiome because it is a low-fiber diet. It is further characterized by a high intake of ultra-processed foods, sugar and refined grains, excess salt, food additives, artificial sweeteners, animal fat, especially saturated and trans fat, and animal protein, all of which cause an unhealthy gut microbiome by promoting the increase of pathogenic bacterial species, increasing inflammation and compromising the intestinal barrier by increasing gut permeability.^5,8 Simply put, it feeds the bad guys and harms the good guys.

Drugs and Medications

Outside of diet, prescription drugs and OTC medications can have a significant impact on our gut microbiome. Some, like life-saving antibiotics, have a direct role in not only destroying pathogenic bacteria, but also the beneficial bacterial species,⁸ throwing our gut microbiome out of balance. In this case, your doctor may ask you to eat fermented foods, like yogurt, and/or prescribe specific probiotic supplements.

Our gut microbiota can also dictate how our body responds to a drug or medication, affecting how much is digested, how potent it will be and what it will do.¹² The complex relationship between drugs, OTC medications and the microbiome is an area of active research which will yield important information for helping us understand how to maintain a healthy gut microbiome.

What about probiotics?

The word ‘probiotics’ refers to live microorganisms that are good for us. There are three main sources of probiotics:

1. The beneficial bacterial species already living in our large intestine
2. Probiotic supplements
3. Fermented foods: sauerkraut, kimchi, tempeh, miso, yogurt, kefir, kombucha

Let’s consider each of one these probiotic sources.

1. Beneficial bacteria already present in our gut.

   We’ve already discussed how to increase the beneficial bacterial species living in the gut—eat a plant-predominant diet of whole, unprocessed fiber foods, fruits, veggies, beans and legumes, whole grains, nuts and seeds, incorporating a diversity of different fiber foods each week.

2. Probiotic supplements.

   Probiotic supplements are highly concentrated amounts of live, beneficial bacterial strains. There is evidence that they can be helpful for many health conditions, including irritable bowel syndrome, antibiotic-associated diarrhea, allergies, inflammatory bowel disease and female urogenital problems.¹³ Since antibiotics destroy both good and bad bacterial species, it would seem like a good idea to take probiotic supplements after a course of antibiotics. However, researchers have shown that probiotics actually slow the recovery of the gut microbiota to normal after antibiotics.¹⁴ For this reason, and the fact that their health benefits are species specific, it is prudent to consult with your doctor or other appropriate healthcare professional before taking them.

   Probiotic supplements alone can not fully optimize beneficial bacterial diversity because 1) the supplements contain a limited number of species, and 2) all the different species in the supplements may not necessarily take up permanent residence in the gut.¹⁵ If you stop taking a probiotic supplement, research suggests it is possible that within two to five days, it can be like you never took it.¹⁶ That’s why eating a wide variety of whole fiber foods from day to day is the foundation of a healthy gut microbiome.

3. Fermented foods.

   Research studies have shown that eating fermented foods daily is one way to increase the amount and diversity of beneficial gut bacteria.^17-19

   Traditionally fermented foods are growing in popularity in the US. These fermented foods are made in brine, meaning the vegetables and/or fruits are covered with water, salt is added, and they are left at room temperature for several days or longer until they are bubbling with an abundance of beneficial bacteria. Some examples of traditionally fermented foods include sauerkraut, kimchi, beets, pickles.

   Choose vegetables and/or fruits fermented in brine rather than pickled in vinegar in order to maximize the number of beneficial bacterial species present.

   There are other types of fermented foods that contain probiotics:

   • Tempeh: soaked, cooked soybeans that are fermented by being inoculated with a mold
   • Miso paste: soybeans fermented in several steps involving mold, bacteria and yeast
   • Yogurt: made by adding beneficial bacterial cultures to milk. Two tips to keep it healthy: 1) use low-fat dairy yogurts or non-dairy yogurts without coconut milk or cream to avoid unnecessary saturated fat; 2) choose plain low-fat yogurts to avoid added sugar; sweeten with fresh fruit instead–berries, sliced banana or your favorite fruit.
   • Kefir: fermented cow, goat or sheep’s milk made by adding colonies of yeast and lactic acid bacteria for about 24 hours. The colonies are removed and the resulting sour milk is the kefir drink. Choose low-fat kefirs, avoiding those made from coconut milk. Choose unsweetened coconut water kefirs.
   • Kombucha: tea beverage fermented with bacteria and yeast. Kombucha is highly acidic, which can erode the enamel on your teeth. So, it’s prudent to dilute it with water and limit how much you drink daily. Water should always be your primary beverage.
   Note: while the lactobacillus starter for sourdough bread contains probiotics, the bread does not because the baking process destroys the bacteria.¹⁹

Three Steps to Positively Improve Your Gut Bugs

In order to optimize your gut microbiome to enhance your health, do these three things:

1. Aim to enjoy at least 30 different whole, unprocessed fiber foods each week – fruits, vegetables, beans, whole grains, nuts and seeds.
2. Include probiotic supplements when medically appropriate. Use the brand prescribed by your doctor.
3. Eat a serving of fermented foods most days of the week: sauerkraut, kimchi, beets, tempeh, miso, yogurt, kefir, kombucha.

Not sure how to add more fiber foods to your plate? The Full Plate Living Membership was created to help readers like you easily identify whole fiber foods and find delicious ways of adding them to meals at home or any favorite restaurant. Sign up for your free membership to access self-paced courses, practical recipes, healthy living workshops and more.

If you are under medical supervision for any reason, please consult with your doctor before following any of the dietary recommendations above. If you are taking any prescription drugs or regularly use OTC medications, it would be prudent to discuss with your doctor the nature of their impact on your gut microbiome.

 

 

 

 

 

 

 

 

 

References

1. 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
2. Guinane CM, Cotter PD. Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ. Therap Adv Gastroenterol. 2013;6(4):295‐308. doi:10.1177/1756283X13482996
3. Shen TD. Diet and Gut Microbiota in Health and Disease. Nestle Nutr Inst Workshop Ser. 2017;88:117‐126. doi:10.1159/000455220
4. Quigley EM. Gut bacteria in health and disease. Gastroenterol Hepatol (N Y). 2013;9(9):560-569.
5. Malesza IJ, Malesza M, Walkowiak J, Mussin N, Walkowiak D, Aringazina R, Bartkowiak-Wieczorek J, Mądry E. High-Fat, Western-Style Diet, Systemic Inflammation, and Gut Microbiota: A Narrative Review. Cells. 2021 Nov 14;10(11):3164. doi: 10.3390/cells10113164. PMID: 34831387; PMCID: PMC8619527.
6. Makki K, Deehan EC, Walter J, Bäckhed F. The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease. Cell Host Microbe. 2018 Jun 13;23(6):705-715. doi: 10.1016/j.chom.2018.05.012. PMID: 29902436.
7. https://www.sciencedaily.com/releases/2018/05/180515092931.htm
8. Cresci GA, Bawden E. Gut Microbiome: What We Do and Don't Know. Nutr Clin Pract. 2015 Dec;30(6):734-46. doi: 10.1177/0884533615609899. Epub 2015 Oct 8. PMID: 26449893; PMCID: PMC4838018.
9. https://www.dietaryguidelines.gov/sites/default/files/2020-12/Dietary_Guidelines_for_Americans_2020-2025.pdf
10. Institute of Medicine, Food and Nutrition Board. Dietary Reference Intakes: Energy, Carbohydrates, Fiber, Fat, Fatty Acids, Cholesterol, Protein and Amino Acids. Washington, DC: National Academies Press; 2005.
11. Tanes C, Bittinger K, Gao Y, Friedman ES, Nessel L, Paladhi UR, Chau L, Panfen E, Fischbach MA, Braun J, Xavier RJ, Clish CB, Li H, Bushman FD, Lewis JD, Wu GD. Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. Cell Host Microbe. 2021 Mar 10;29(3):394-407.e5. doi: 10.1016/j.chom.2020.12.012. Epub 2021 Jan 12. PMID: 33440171; PMCID: PMC8022197.
12. Weersma RK, Zhernakova A, Fu J. Interaction between drugs and the gut microbiome. Gut. 2020;69(8):1510-1519. doi:10.1136/gutjnl-2019-320204
13. https://www.health.harvard.edu/vitamins-and-supplements/health-benefits-of-taking-probiotics
14. Suez J, Zmora N, Zilberman-Schapira G, Mor U, Dori-Bachash M, Bashiardes S, Zur M, Regev-Lehavi D, Ben-Zeev Brik R, Federici S, Horn M, Cohen Y, Moor AE, Zeevi D, Korem T, Kotler E, Harmelin A, Itzkovitz S, Maharshak N, Shibolet O, Pevsner-Fischer M, Shapiro H, Sharon I, Halpern Z, Segal E, Elinav E. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell. 2018 Sep 6;174(6):1406-1423.e16. doi: 10.1016/j.cell.2018.08.047. PMID: 30193113.
15. Zmora N, Zilberman-Schapira G, Suez J, Mor U, Dori-Bachash M, Bashiardes S, Kotler E, Zur M, Regev-Lehavi D, Brik RB, Federici S, Cohen Y, Linevsky R, Rothschild D, Moor AE, Ben-Moshe S, Harmelin A, Itzkovitz S, Maharshak N, Shibolet O, Shapiro H, Pevsner-Fischer M, Sharon I, Halpern Z, Segal E, Elinav E. Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features. Cell. 2018 Sep 6;174(6):1388-1405.e21. doi: 10.1016/j.cell.2018.08.041. PMID: 30193112.
16. Ohland CL, Macnaughton WK. Probiotic bacteria and intestinal epithelial barrier function. Am J Physiol Gastrointest Liver Physiol. 2010 Jun;298(6):G807-19. doi: 10.1152/ajpgi.00243.2009. Epub 2010 Mar 18. PMID: 20299599.
17. Wastyk HC, Fragiadakis GK, Perelman D, et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021;184(16):4137-4153.e14. doi:10.1016/j.cell.2021.06.019
18. Stiemsma LT, Nakamura RE, Nguyen JG, Michels KB. Does Consumption of Fermented Foods Modify the Human Gut Microbiota? J Nutr. 2020 Jul 1;150(7):1680-1692. doi: 10.1093/jn/nxaa077. PMID: 32232406; PMCID: PMC7330458.
19. Dimidi E, Cox SR, Rossi M, Whelan K. Fermented Foods: Definitions and Characteristics, Impact on the Gut Microbiota and Effects on Gastrointestinal Health and Disease. Nutrients. 2019;11(8):1806. Published 2019 Aug 5. doi:10.3390/nu11081806