Exploring the Impact of the Microbiome on Human Health and Wellbeing

First things first, have you heard of the microbiome? 

Hopefully so, as it is 2025. If not, the microbiome refers to the host of bacteria that live in our gastrointestinal systems, that are responsible for digesting the food we eat, and extracting and making available for absorption, the nutrients we need to survive.  If these populations of bacteria in our system are not balanced appropriately, there is a lot of evidence that disease (movement away from health) occurs, with known links to cardiovascular disease, cancers, immune dysfunction/auto-immune diseases, and poor mental health.

First, just a brief review of digestion, or how our gastrointestinal system functions.  The process starts in our mouths, where our food is broken apart with our teeth, and saliva is added to help start making nutrients more available, which continues in our stomachs where acids are mixed in, and then into the beginning of our small intestines (duodenum) where bile salts are added.  Once we reach the far end (pylorus) of the stomach, and are past the acidic environment, we have a population of billions of different bacteria (the microbiome) that digest what remains of our food.  These bacteria differ in type and function, and for a healthy microbiome, we need for variety/diversity to be present.  To feed these various bacteria, they need different sources of nutrients, which we can get from the diversity of whole food that we eat. 

Our current measures of gut health have largely been based on how our system is functioning, and an “if it’s not broken, don’t fix it” mentality, meaning, if we aren’t having symptoms or recognizing those symptoms, we don’t change what we are doing.  If we are having symptoms, or dysfunction, the approach of conventional medicine has been to treat the symptoms or dysfunction with medication, rather than focusing on the behavior that led to the dysfunction.  

Relatively recently, a new chemical has become apparent as a commonly found chemical in patients with heart disease.  This chemical, TMAO (tri-methylamine n-oxide), can be measured with a blood test.  Evidence has shown that high levels of TMAO are significantly associated with promotion of atherosclerosis, and linked to cardiovascular and cerebrovascular disease.  TMAO is produced in our bodies in the breakdown process of certain foods: fish, eggs, meat, and dairy…womp, womp.

Don’t worry, we’ll get back to the microbiome, just a few more things that are known to damage the gastrointestinal system… Next up, heme iron.  Heme iron, which is present in meat, is said to be more bioavailable than non-heme iron, present in plants, but this increased bioavailability hasn’t resulted in any health-related benefits, and in fact, has been linked to inflammatory disorders and bowel cancer, through increased oxidative stress.  Avoiding heme iron can help improve the health of our gastrointestinal system. 

Next are artificial sweeteners/chemicals/engineered food.  Artificial sweeteners are zero calorie, but the sugar-like chemicals in them still cause the release of insulin in our bodies, and high levels of insulin in our blood is known to be linked to obesity, diabetes, and heart disease.  In fact, artificial sweeteners in your diet are a bigger dietary risk factor than sugar for diabetes!  As is meat (animal protein)!

A last solidly known irritant/danger to our gastrointestinal systems are NSAIDs (non-steroidal anti-inflammatory drugs, like ibuprofen, celecoxib, naproxen, and diclofenac).  These drugs are linked to potentially fatal GI bleeding, from erosions, perforations and longitudinal ulcers, and also are known to increase intestinal permeability (leaky gut).  Taking these medications every once in awhile to treat certain aches and pains can be ok, but taking these medications on a chronic basis is risky, and often just leads to the need for additional medications (PPIs, H2blockers, and antacids) to “protect your stomach” or to treat the symptoms of the dysfunction caused by the NSAIDs.  These medications are not more effective at treating symptoms/protecting your stomach than avoiding the behavior would be. It would more worthwhile to look at the root cause of the pain or inflammation.

More of a “if it hurts when I do ________, perhaps I should just stop doing _______” mentality.  If something is knowingly damaging your GI system, the best medical advice should be to avoid those things, right? 

The next, in line of what we are consuming that is harming our GI systems, are pesticides.  Pesticides are chemicals used to help deter pests away from eating the food we eat, and are present on food that is not organically grown.  Probably the most commonly used pesticide that you have heard of is Round-Up (glyphosate), which was originally patented as an antibiotic.  This chemical also unfortunately kills the healthy bacteria living in our guts. Pesticides have also been linked to gut dysbiosis and metabolic disorders.  Also just a note that almost all dairy consumed comes from animals treated with antibiotics, which also filter down to our microbiomes, and can have a detrimental effect.   One way to reduce the pesticide burden you consume is to soak your produce in a mixture of 1 tbsp baking soda: 4L or 4Qts. water for about 10 min, then thoroughly rinse before consuming. This can reduce up to 95% of surface pesticides.

Let’s move to the positive and talk about things that improve the health of our gut microbiome! 

What is a healthy gut microbiome? 

Studies from the 1950s showed that rates of auto-immune diseases and inflammatory disorders such as eczema, were noted to be lower in children with lots of siblings, and children living with extended families, where they were exposed to a greater variety of childhood illnesses, as well as children from less affluent/hygienic households.  Evidence also shows lower rates of immune dysfunction in children raised on farms, and children with household pets.  It was concluded that the more microbes a child is exposed to early in life, the healthier their immune system.

A diet high in fiber rich foods has been shown to lead to more metabolites present in our body that are health promoting, with less inflammation, and improved insulin sensitivity. 

Our microbiome needs variety in the microbes it encounters, which comes from the food we eat and our environment.  Variety in what we consume correlates to variety in the bacteria that live in our guts, and microbiome research has shown that a healthy gut microbiome is diverse in composition. 

In 2018, a research study (The American Gut Project) collected stool studies and information about the livestock and diets of more than 12,000 volunteers from the US, UK, Europe and Australia.  With 1600 of the volunteers, they did a deeper dive into their diets and did laboratory analysis of their gut microbes.  The data showed that individuals consuming more than 30 different plants/week had a more diverse microbiome, including having some bacteria that those consuming less than 10 plants/week didn’t even have.

This diversity has also been shown to allow more resilience, because the gut is exposed to different things, gut bacteria develop to respond to different challenges, which leads to improved immunity and improved mental health.

Fiber, also known as prebiotics, is the food our microbiomes need to survive, and is only present in plants.  There are 2 forms of fiber: soluble and insoluble.  Soluble fiber helps support bacterial growth, feeds the bacteria in the microbiome, and helps support the gut barrier and bowel regulation. Soluble fiber is found in things like oats, apples, and chia seeds.. Insoluble fiber adds bulk to the stool, and helps remove toxins and maintain bowel regularity. Insoluble fiber is found in whole grains, nuts/seeds, and many vegetables. Your bowels need to be moved every day (or very close to it) to function well, to basically remove toxins and other sh*t from your body.

What about probiotics?  Probiotics are "good bacteria" (or bacteria that are known to be beneficial to our guts), taken in a pill form. Probiotics have a massive global market ($60B in the US!), but studies have never shown any health benefit, except in 3 different clinical scenarios (certain people with ulcerative colitis, pouchitis, and some recurrent Clostridium difficile infections).  Your money would be better spent in the produce aisle of your local grocery store, or in the development of your garden. 

An largely underutilized source of probiotics is fermented foods.  They have prebiotics (fiber), probiotics (Stanford research showed 1tbsp kimchi, miso or sauerkraut can contain up to 1B live bacteria), and post-biotics, which are short chain fatty acids that are produced during the fermentation process, that help produce ATP (which is energy for our cells).   During fermentation, the micro-organisms (bacteria and yeast) break down sugars and starches, creating probiotics, vitamins, and organic acids that support gut health.  This process can also boost nutrient absorption by making nutrients more bioavailable.

Another way to improve your microbiome:  gardening! Gardening improves your microbiome by having your hands in the soil, where they are exposed to millions of microbes, which translates into an increase in the diversity of bacteria in your microbiome.  Studies have shown that even small amounts of soil exposure can help strengthen your immune system. 

Physical activity is also known to improve gut health.  Studies of healthy athletes have shown that regardless of their diet, athletes have been shown to have more healthy, fiber-loving bacteria present in their guts. Even better if this activity is done outdoors, where again, you are exposed to more diverse micro-organims.

Also helpful for our microbiome, staying hydrated. Our bodies need water to help extract and absorb nutrients from our food, and to help things that are not absorbed keep moving through our systems, and help us from feeling bloated.

In summary, a healthy microbiome can improve overall health, support immunity, reduce inflammation, aid digestion, and enhance mental health. A healthy microbiome needs diversity in the fiber-rich foods it is presented with, and an adequate amount of water to keep the system functioning properly. It is important to go slowly, especially if you develop symptoms, when adding more fiber to your diet, but equally as important to stick with it. Symptoms are a little like DOMS (delayed-onset muscle soreness) from lifting weights, just your gut adjusting to the new normal. Drinking more water can help with symptoms, timing meals and caffeine consumption can help, soaking beans overnight and rinsing can help, regular movement can help. I was taught in medical school that your bowels are linked to your feet, so if you are able to move your feet (walk), that will help stimulate your bowels to move as well...this is why we encourage all post-surgical patients to get out of bed the day after any surgery near the gut, to help prevent an ileus (gut paralysis) from happening.

Listen to your body, it's always giving you feedback in the form of symptoms...reflux, bloating, constipation. This feedback is for our survival, and letting us know that what we are doing isn't working.

Bottom Line:

1. Eat a variety of whole, fiber rich foods.

2. Incorporate fermented foods.

3. Stay hydrated.

4. Cut back on UPF, sugar and artificial additives to reduce strain on the microbiome

5. Connect to nature- which helps lower stress and exposes you to more microbes.

Hope you learned a little something :-)