You are what you eat: The organisms living inside you

Kyrie Wilson
February 14, 2022
Cartoon schematic of a probiotic combating pathogenic bacteria.
Licensed from

At some point in our lives, we’ve all had to take a medication that seemed unbearable at the time. Maybe it was a giant pill following a surgery, or that foul tasting cough medicine you took as a child. But have you ever considered needing to take a Poop Pill? Perhaps “crapsule” is better name? Either sounds better to me than the highly scientific “Fecal Transplant Pill,” or “Fecal Microbiota Transplant,” but neither sound like something I would willingly ingest.

Yet for some people, these pills offer a lifesaving treatment by restoring the host of microscopic organisms in their bodies, which are collectively known as the microbiome.

What is the microbiome?

From the time we are born, our bodies become host to hundreds of microorganisms, including bacteria, viruses and fungi (yeast). Collectively, these organisms are known as our microbiome, or microbiota. Unlike the pathogenic (disease causing) microorganisms we usually think of, these tiny organisms work with our bodies to keep us healthy. In fact, there are more bacteria living in/on our bodies than our own cells, and there are tens of thousands of different types of microbes living in different areas of our bodies. The most well-known part of the human microbiome is the gut microbiota, which can contain 3-5lbs of microorganisms.

What does the microbiome do?

The microorganisms in our gut help us digest food, produce several vital vitamins, and help protect us from pathogenic organisms by interacting with our immune systems and directly killing the invaders. Our microbiomes typically regulate themselves, with each organism growing and competing with its neighbors, so that all the essential roles are filled but no one species becomes dominant.

By coexisting with us, these microbes can affect more than just how we digest food and fight diseases. They are known to secrete molecules that can affect our mood and directly impact our mental health. The microbiome might also play a role in aging; its composition drastically changes with aging and disease.

"Healthy, happy microbiomes have been linked to healthy, happy people with a reduced risk of disease."

-- Kyrie Wilson

What can go wrong with the microbiome and what happens when it does?

There are many examples of situations that disrupt the composition of our normal microbiota, such as poor diet, or prolonged or heavy antibiotic treatment as well as some diseases. This situation, known as “dysbiosis,” can lead to the loss of beneficial microorganisms, overpopulation of normally harmless organisms, or general lack of microbiota diversity. In less severe cases of microbial dysbiosis, certain molecules aren’t produced enough, which can lead to general poor health. In fact, mild microbial dysbiosis is being investigated as a key driver in the aging process and age-related diseases, as well as playing a role in mental disorders, such as depression.

In more extreme cases of dysbiosis, one organism overgrows to the point of killing other beneficial organisms and produces toxic levels of byproducts, causing a serious medical emergency. One example of such an emergency is the overgrowth of the bacterium Clostridium difficile, which is usually present in small numbers in the large intestine and colon and its population is controlled by the surrounding microbes. Sometimes, following antibiotic treatments (which can kill off other good bacteria) or exposure to contaminated objects, C. difficile can grow out of control and produce a toxin, which can lead to colon inflammation (colitis) and diarrhea. Usually, good bacteria are able to grow back on their own, but in some cases, they are so depleted they need an outside boost to replenish their numbers.

How is homeostasis restored/maintained in the gut microbiome?

Extreme dysbiosis, requiring medical intervention, can be treated with the aforementioned “crapsule,” or Fecal Transplant. These pills are created by harvesting the flora from a very healthy gut, processing it so only the desired microorganisms remain, and then safely packaged for delivery to patients, such as those with C. difficile infection. In 90% of cases, fecal transplant is successful at restoring a healthy gut microbiome, leading to ongoing clinical trials to normalize use of such treatment for severe infections, and even other cases of dysbiosis (while being handed a poop pill may not seem like something nice to do for a patient with depression, early results suggest it may be beneficial).

Fortunately, this is rarely necessary, as the microbiome is largely capable of maintaining a healthy balance on its own. There are things we can do to improve the diversity of organisms in our gut, which maintains thriving colonies of good flora and helps our physical and mental wellbeing. The simplest method is to consume probiotics and prebiotics.

Probiotics are foods that contain cultures of microorganisms that stick around and live in our guts after we eat them. These include fermented foods, like yogurt, pickles, miso, buttermilk and even some cheeses and wines.

Prebiotics are foods that are “eaten by” our resident microbiota, and include most fruits, vegetables and whole grains. These foods encourage the healthy flora to grow, and as they grow they produce necessary molecules our bodies need (like some vitamins).

With moderation, there are very few downsides to eating foods high in probiotics, although some people may experience mild side effects such as thirst, bloating, gas or constipation. To prevent these side effects, it’s recommended to consume high quality probiotics, such as plain yogurt (my favorite is Greek, added to scrambled eggs or as a substitute for sour cream on baked potatoes or tacos).

Healthy, happy microbiomes have been linked to healthy, happy people with a reduced risk of disease. Maintaining a healthy microbiome by eating a balanced diet containing plenty of probiotics and prebiotics helps your microbiome stay healthy, so hopefully you don’t have to be on the receiving end of a crapsule.