Eat POOP and Live!! The Human Microbiome

Microbial Minions

When you think of the most important organ in your body, what comes to your mind? Probably the brain, or maybe the heart and lungs. If damaged, these are, after all, the ultra-sensitive organs that allow us to survive not even a few moments without. But what if there was an organ that affected our body in an even more systemic capacity, from the moment you’re born, throughout your life. This organ can change the course of your future health, affect the way you develop acute or chronic diseases, and help or hinder the digestion of every morsel of food you ever eat. And perhaps the most amazing thing about this organ is that it isn’t even human. It is the human microbiome, and it’s made up of the more than 30 trillion bacterial cells living in and on every surface of your body. Your excrement is a by-product of your microbiome and pretty much every time we take a breath or put anything else into our body, we are inserting more bacteria into it. An American’s greatest challenge is to eat healthy bacteria that can strengthen the microbiome.

Functions of the Microbiome

Germaphobic readers might be squirming in their seats right now, but the truth is, your microbiome or natural flora, is incredibly vital to the way your body works. Not only do they synthesize vitamins and break down complex carbohydrates in your gut, they also help train your immune system to recognize pathogens. They take up prime real estate in mucous membranes like your mouth, airways, and even your eyes to help prevent pathogenic bacteria from gaining a foothold and causing infection. A lot of research is now being done to look at the effects that the microbiome can have on our genetics. Increasing evidence is demonstrating that different populations of bacteria can toggle the genes and metabolic pathways that can raise or lower your risk for different diseases such as obesity, diabetes, cardiovascular disease, cancer, and even more mundane conditions like allergies and heartburn.

One of the things that makes the study of the microbiome very difficult is how individual each person’s microbiome is. The variances in populations and amount of the different species of bacteria from person to person are immense, and beyond the individual variances, the diversity in species varies greatly based on anatomy. This would be expected if you were looking at, say skin vs gut microbes, but studies have shown that even the difference between the microbes colonizing the forearm and elbow is significant. All of this complexity can make setting up experiments and studies extremely difficult. Fortunately, the recent advent of big data processing is helping scientists keep things straight and even the most nascent results of this work are revolutionizing our approach to managing health.

So What is Poop Anyway?

Poop, also known as stool, feces, defecate, manure, muck, poo, kaka and many more colorful names, has a vital role in your body’s function. It is produced primarily from the microbiome of the lower intestinal tract. When normal and healthy it is about 90%+ bacteria with the remainder being partially digested food suspended by water and soluble fibers.* It is an excellent marker of overall health and there are entire professions dedicated to the study of it. Understanding the Bristol Stool Scale can help you keep an eye on your stool health. Problems with defecation can lead to significant discomfort, pain, and even death. Simply stated, the flow of your poop is directly proportional to your very ability to stay alive and healthy, so don’t be too shy to take a look at it every time you go.

Microbiome from Birth

Research is being done, and although we’re only scratching the surface, what has been discovered so far about the effect that the microbiome has on our health and the health of our children, is nothing short of incredible. Starting with our mother’s microbiome this non-human organ has a huge impact on our health. Studies have shown that mothers with a healthier, more robust gut microbiome will pass some of this diversity on to their baby in utero. These children tend to have activation of metabolic pathways in the gut that lead to a healthier life with a lower risk of diabetes, obesity, and other metabolic diseases – this is of course ignoring any future lifestyle choices. Even the method of delivery of a child (C-section vs vaginal) can also have a tremendous impact on this.

A study conducted in Venezuela looked at the microbial populations of newborn babies who were born vaginally vs those born via C-section. The naturally born babies had larger proportions of microbes commonly found in the gut, which they had acquired while moving through their mother’s vaginal tract. The C-section babies were found to have mostly skin associated bacteria on them, since they were removed directly from the uterus and did not get to pass through their mothers’ microbial population. A later study followed children to adulthood and found that the babies born via C-section were more likely to suffer from childhood obesity, Celiac disease (gluten sensitivity), asthma, and allergies. While there are certainly many factors that contribute to this, the study was controlled enough that researchers believe the initial colonization of microbes is a significant part. A great TED talk by Robert Knight elaborates further on this and can be found here.

The Microbiome and Immunity

Not only does the microbiome play a role in chronic illnesses, it’s also essential during acute periods of infection as well. Clostridium difficile (C. diff) has become one of news television’s superstars in recent years. It is a particularly nasty bacteria that are resistant to most antibiotics and take up residence in the gut. When the normal microbiome has been disrupted enough (by antibiotics), they have a huge party in the gut overtaking a chunk of of it and eventually growing out of control. These infections are particularly difficult to eradicate, causing severe diarrhea, fever, nausea, and in severe cases kidney failure and even death. Even after the infection has been treated, it has a high recurrence rate (1 out of every 5 infected patients). For decades, standard treatment for C. diff infection has been antibiotics, however, fecal transplant is becoming increasingly common in the treatment of particularly stubborn infections. Yes, this is pretty much what it sounds like: fecal material is collected from a healthy patient (often a relative of the patient since microbiomes of those who live together tend to share more similarities) and transplanted to the affected patients GI tract by one of several methods (don’t ask). These treatments have had much more dramatic results than standard antibiotic treatment in many patients, relieving months of almost constant diarrhea in days or even hours. This relief is due to the reestablishment of a healthier microbiome, which can bring the out of control C. diff back in check. You should never underestimate the value of poop.

Steps for Good Poop Health

There are tons of articles on the web supporting this topic, but here is our “quick list” of recommendations:

  1. Water- stay hydrated
  2. Fiber- eat whole foods, stay away from processed foods
  3. Activity- ideally exercise, but even simply walking 40 minutes a day and moving around during your routine activities is better than being dormant
  4. Probiotics- are actually good bacteria: yogurt, kefir, fermented vegetables
  5. Prebiotics- support the growth of bacteria: kimchi, raw garlic, raw onions, green tea
  6. Organic – eat organic food sources as much as possible and avoid all GMO (genetically modified organisms) products, hormones, and antibiotic-laden food
  7. Magnesium- promotes muscle activity
  8. Take your time- don’t be hasty when defecating, give your body a chance to do it’s business
  9. Position- squatting turns out to be the best position for defecation. Check out the Squatty Potty.
  10. Anxiety and other emotional stress can reduce the nervous function of your gastrointestinal tract
  11. When necessary, use natural laxatives and not chemicals- flaxseeds, whole foods, prunes, psyllium husk, aloe vera, and many, many, many others. Most of which are significantly cheaper than the over-the-counter aisle in the grocery store.
  12. AVOID ANTIBIOTICS!!! Both from your doctor and in the food that you eat (see #6)
How to Help Your Microbes

So since it is apparent that having a healthy microbiome is so incredibly important, what are some of the things we can do to help support it? Good nutrition certainly seems to be a large piece of the puzzle. You’ve probably seen products in the store such as yogurts labeled “probiotic”. These foods contain either cultures of gut microbes, or compounds that help those microbes to grow and flourish in the gut, and are commonly found in fermented foods, like sauerkraut, kimchi, or increasingly popular kombucha and other fermented drinks. The biggest enemy of the microbiome is antibiotics. This is NOT to say that if you have a bacterial infection you should not take antibiotics that are prescribed to you. However, inappropriate use of antibiotics is impacting our microbiomes as a whole. Even in a non-medical sense, livestock are often fed antibiotics, not only to treat illnesses that crop up in populations, but also at very low levels to help fatten them up. Since the antibiotics keep the populations of microbes in the animals guts low, they are competing with less organisms for the nutrients they eat and are able to grow fatter more quickly. Despite guidelines from the FDA about the amount of antibiotics allowed in our food by the time it gets to us, the meat and dairy products we buy in the supermarket often have more than the allowable amounts, exposing us to more antibiotics without our even realizing. Yes antibiotics have been linked to increased obesity in humans too!!

Being cognizant of the effects that the foods we eat have on our microbiome is essential to preserving its function. The bacteria of the microbiome are far more than just a group of hitchhikers, they are an essential component of our body, without which we literally could not survive. We are already beginning to see the effects of the stresses being put on the microbiome in the form of rapidly elevating numbers of people with diabetes, obesity, allergies, asthma, and autoimmune diseases. As physicians, we often focus on the human factors that contribute to disease, but we have to make sure we don’t ignore the 50 trillion non-human factors as well. Help your doctor remember the importance of the microbiome in your care.

Only 1% of all the DNA in your body is actually yours. So the next time you’re standing at the mirror, take a really close look realize that you may not be who you always thought you were…

* Incidentally, insoluble fibers are not easily digested and often show up whole in your stool.


  1. Avril, Tom. “Hospitals Struggling against ‘C. Diff’ Bacteria.” N.p., 07 Oct. 2016. Web.
  2. Blaser, Martin J. Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues. New York City: Henry Holt & LLC, 2014. Print.
  3. Burling, Stacey. “Treatment of Last Resort for C. Difficile Infection.” Philly-archives. N.p., 07 Apr. 2014. Web.
  4. Enriquez, Juan, and Steve Gullans. Evolving Ourselves: How Unnatural Selection and Nonrandom Mutation Are Changing Life on Earth. London: Oneworld Publications, 2016. Print.
  5. Turnbaugh, Peter J., Ruth E. Ley, Michael A. Mahowald, Vincent Magrini, Elaine R. Mardis, and Jeffrey I. Gordon. “An Obesity-associated Gut Microbiome with Increased Capacity for Energy Harvest.” Nature Publishing Group, 21 Dec. 2006. Web.

One thought on “Eat POOP and Live!! The Human Microbiome”

  1. The title caught my interest; very funny! But the article was extremely interesting and informative and I really enjoyed.

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