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Happy gut happy butt: how your microbiome runs the show.

Aside from coaching, I am a nurse practitioner in gastroenterology. In other words, I get to talk extensively about poop for a good portion of my day. How many times a day do you go? What does it look like? Is it formed, soft, pebble- like, watery? Is there blood? Is it painful when you go? What color is it? What does it smell like? These are just a few of the questions that patients will be asked when they come to visit my office. These questions will give many clues into someone's gut health, but theres more to it than just poop. There is a whole entire world of bacteria, viruses and fungi wandering around in our gut. We can't see them, but they are there. And they control much more than we have previously given them credit for. Our microbiota. Our second brain. Give me five minutes and I'll give you a crash course on the human microbiome!

The real scoop on poop

The human body is comprised of around ten trillion human cells. But there are around one hundred trillion microbial cells in our bodies (1). Plainly put- you are mostly not you. You are a combination of independent and interdependent ecosystems. Microbial systems with their own agendas all working cohesively to maintain the complex human body and all of its functions.

The collection of microscopic organisms (bacteria, viruses and fungi) within us is called the microbiota. The genes of these organisms collectively are called the microbiome. Microbiota stimulate the immune system, break down potentially toxic food compounds, and produce certain vitamins and amino acids, [2] including the B vitamins and vitamin K. For example, the key enzymes needed to form vitamin B12 are only found in bacteria, not in plants and animals. [3]

Sugars like table sugar (sucrose) and lactose (milk sugar) are quickly absorbed in the upper part of the small intestine, but more complex carbohydrates like starches and fibers are not as easily digested and may travel lower to the large intestine (this is why complex carbohydrates promote longer satiety).

There, the microbiota help to break down these compounds with their digestive enzymes. There are some fibers that are not able to be completely broken down by the gut (dietary fiber). These fibers will go on to be fermented and used to feed all the microscopic "bugs" in our digestive tract. The fermentation of these indigestible fibers causes the production of short chain fatty acids (SCFA) that can be used by the body as a nutrient source. SCFA's also play an important role in muscle function and possibly the prevention of chronic diseases, including certain cancers and bowel disorders.

Clinical studies have shown that SCFA's may be useful in the treatment of ulcerative colitis, Crohn’s disease, and antibiotic-associated diarrhea. [2]

The microbiota of a healthy person will also provide protection from pathogenic organisms that enter the body such as through drinking or eating contaminated water or food.

In the large intestine, a low oxygen environment, you will find the anaerobic bacteria like Peptostreptococcus, Bifidobacterium, Lactobacillus, and Clostridium. [4] These microbes are believed to prevent the overgrowth of harmful bacteria by competing for nutrients and attachment sites to the lining of the gut which is a major site of our immune systems' activity and production of antimicrobial proteins. [5,6]

Can diet affect one’s microbiota?

In addition to family genes, environment and medication use, diet plays a massive role in determining what kinds of bugs live in your colon. All of these factors create a unique microbiome from person to person; more unique than your fingerprint!

A high-fiber diet in particular affects the type and amount of microbiota in the intestines. Dietary fiber can only be broken down and fermented by enzymes from microbiota living in the large intestine. Short chain fatty acids (SCFA) are released as a result of this fermentation (as discussed above). This lowers the pH of the large intestine, which in turn determines the type of microbiota present that would survive in this acidic environment. The lower pH limits the growth of some harmful bacteria like Clostridium difficile. Growing research on SCFA's explores their wide-ranging effects on health, including stimulating immune activity and maintaining normal blood levels of glucose and cholesterol.

Are you completely nerded out yet? Good, lets keep going.

Foods that support all this fermentation are indigestible carbohydrates and fibers such as inulin, resistant starches, gums, pectins, and fructooligosaccharides (i.e REAL unprocessed foods) These fibers are sometimes called prebiotics because they feed our beneficial microbiota in our gut. Although there are supplements containing prebiotic fibers, there are many foods naturally containing prebiotics. The highest amounts are found in raw versions of the following: garlic, onions, leeks, asparagus, Jerusalem artichokes, dandelion greens, bananas, and seaweed. In general, fruits, vegetables, beans, and whole grains like wheat, oats, and barley are all good sources of prebiotic fibers.

Be aware that a high intake of prebiotic foods, especially if introduced suddenly, can increase gas production (flatulence) and bloating. Individuals with gastrointestinal sensitivities or irritable bowel syndrome (IBS) should introduce these foods in small amounts to first assess tolerance. With continued use, tolerance may improve with fewer side effects.

If you do not have food sensitivities, it is important to gradually implement a high-fiber diet because a low-fiber diet may not only reduce the amount of beneficial microbiota, but increase the growth of harmful bacteria that thrive in a lower acidic environment.

Probiotic foods contain beneficial live microbiota that may further alter one’s microbiome. These include fermented foods like kefir, yogurt with live active cultures, pickled vegetables, tempeh, kombucha tea, kimchi, miso, and sauerkraut.

So to put all this in simple terms: To protect our species we gotta respect our feces !



2. den Besten, Gijs., et al. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res. 2013 Sep; 54(9): 2325–2340.

3. Morowitz, M.J., Carlisle, E., Alverdy, J.C. Contributions of Intestinal Bacteria to Nutrition and Metabolism in the Critically Ill. Surg Clin North Am. 2011 Aug; 91(4): 771–785.

4. Arumugam, M., et al. Enterotypes of the human gut microbiome. Nature. 2011 May 12;473(7346):174-80.

5. Canny, G.O., McCormick, B.A. Bacteria in the Intestine, Helpful Residents or Enemies from Within. Infect and Immun. August 2008 vol. 76 no. 8, 3360-3373.

6. Jandhyala, S.M. Role of the normal gut microbiota. World J Gastroenterol. 2015 Aug 7; 21(29): 8787–8803.

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1 Comment

José F
José F
Jul 23, 2020

Great stuff! Thank you for sharing and not making me feel so alone anymore 😊

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