How Lifestyle Affects Gut Health

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The gut microbiome is a vast community of microbes that line the entire intestinal tract and are responsible for many specialized functions in the body. It not only affects digestion and elimination of waste, but also can have an effect on your mood, stress response, immune system, musculoskeletal system, and even sleep! 

The gut microbiome is mainly composed of bacteria and yeast species, but also contains viruses, protozoa, and other non-infectious microorganisms. It’s been reported that the gut microbiome contains 10 times more microbes than there are cells in your body, with a whopping 100 trillion microbes living in your gut! 

Why Is the Microbiome So Important?

As more research is done to study the microbiome, we are learning that this community of microbes is very important for overall health. It has many functions in the body including:

  • Synthesis of vitamin K, vitamin B12, and folate
  • Modulation of the immune system and promotion of a healthy immune response
  • Digestion and assimilation of food and nutrients
  • Protection against pathogenic bacteria and other “bad” bugs
  • Support of the mucosal layer lining the gut
  • Assistance in the metabolism of medications
  • Communication with the brain via the gut-brain axis
  • Fermentation of certain carbohydrates into short chain fatty acids (SCFAs)

Most of us have been raised believing that bacteria and other micro-organisms are “bad” and cause more problems than good. We’ve been taught to wash our hands with anti-bacterial soap if we come into contact with anything dirty and to slather anti-bacterial ointment on every scrape or cut. In fact, we’ve tried to control microbes with all our might, but in doing so may have disrupted the fine balance that nature has created from the beginning. 

The fact of the matter is, we co-evolved with microbes for a reason, and we need to learn to live in harmony with them as they play an integral role in our health. From an evolutionary perspective, microbes have inhabited this planet a lot longer than humans and know how to survive. 

There are many lifestyle factors that either support your microbiome or hurt it.  Some of these factors you don’t have any control over (like your birth), but many of them you do. In fact, certain exposures before birth can dramatically decrease the chances that a baby will grow up with asthma, allergies, eczema, and even some autoimmune conditions like type I diabetes, as I describe in the next section. 

The Connection Between Pregnancy, Birth, and Gut Health

The gut microbiome begins to develop around the time of birth. When the mother’s water breaks, the soon-to-be-born baby is bathed in a wave of mom’s microbes. In addition, if the baby travels through the birth canal, the baby is exposed to even more microbes. These initial exposures to the mother’s bugs are critical moments in the development of the baby’s microbiome and immune system. 

There is fascinating research showing that the development of a baby’s microbiome may begin even earlier than birth. Pregnant women living on a farm with exposure to animals give birth to children with lower rates of asthma, allergies, and atopic conditions (eczema). In fact, the more farm animals the mother is exposed to on a regular basis during pregnancy, the greater the protection her children will possess against these allergic conditions. The rationale behind this finding is that, during pregnancy, increased regular exposure to different microorganisms via these animals allows the developing fetus’s immune system to react accordingly to environmental allergens. This supports a healthy immune response. 


The next phase in the development of the microbiome is breastfeeding. As soon as the baby latches onto mom’s breast, there is transfer of microbes from mom’s skin into baby’s mouth. Then the breast milk itself is rich with 700+ species of bacteria that will “seed” the lining of the baby’s digestive tract. Research has showed that 30% of a baby’s gut microbiome comes directly from mom’s breast milk.  

Dirt, Animals, Environment and the Microbiome

Generally, as Americans, we fear dirt. We’ve become accustomed to being too clean and, unfortunately, we are missing out on nature’s free source of healthy microbes. Instead of stopping our children from playing in the mud, we should actually encourage them to take their shoes off and run around in the grass and dirt.  

Here are some other tips for supporting a healthy microbiome via environmental exposures:

  • If a baby’s pacifier drops on the kitchen floor, it’s okay to brush off any dust and give back to baby. Of course, if the baby drops a pacifier into the toilet, then you’ll want to thoroughly clean it.
  • Don’t panic if a dog comes up and licks your baby or child. A quick exposure like this helps build microbial diversity.
  • Allow your child to take off his or her shoes and play in the grass or mud. Besides exposure to microbes, walking barefoot is a form of “grounding” or “earthing,” which is a way to connect with the Earth’s energy.
  • Eliminate the use of antibacterial soaps. Simply washing hands with soap and water is enough to clean hands.
  • If you buy produce from trusted local farmers who grow their food organically without chemicals, it’s okay to eat some produce without washing it (unless it’s really muddy).

The overall message here is regular exposure to small amounts of dirt can help build and support a healthy microbiome, and thus, a healthy immune system. 

The Best Diet for Gut Health

The foods you eat have a tremendous impact on your gut microbiome. In fact, I believe that diet is probably the most important lifestyle modification that you can make to improve the microbiome. You can basically look at foods as either supportive or detrimental. 

Supportive foods

  • Fiber rich foods (i.e., fruits and veggies)
  • Probiotic rich foods (i.e., kefir, sauerkraut, kimchi, miso, pickled veggies, etc.)
  • Prebiotic rich foods (i.e., artichokes, leeks, onions, garlic, asparagus, etc.)
  • Organic foods (fewer pesticides and chemicals including glyphosate)

Detrimental foods

  • Sugar containing foods (i.e., candies, pastries, ketchup, etc.)
  • Processed foods (i.e., chips, cereals, bars, etc.)
  • Fried foods

Think of it this way: you can eat something that will feed and support the growth of good bugs or eat something that will feed the bag bugs. For example, a high sugar and processed food diet (which is VERY common these days) will encourage the growth of candida, and candida overgrowth can cause all sorts of problems for people.   

The same concept applies to drinks:

Supportive drinks

  • Water
  • Tea
  • Coffee
  • Smoothies high in fiber
  • Probiotic beverages (i.e., kombucha, beet kvass, kefir, sauerkraut juice)

Detrimental drinks

  • Sweetened beverages with processed sugar or high fructose corn syrup
  • Alcohol

I also recommend using a water purifier to remove chlorine and other chemicals.   

Chemicals/Toxins and the Microbiome

Some chemical and toxins can wreak havoc on our microbiome. For example, glyphosate, the main chemical used in Round Up Ready and other herbicides, is sprayed on many crops and is now ubiquitous in our environment (and our bodies!). Glyphosate was originally patented as an antibiotic, so it does affect the composition of the microbiome. Not to mention that the World Health Organization recently declared glyphosate a “probable carcinogen,” but don’t let me get started on this one J . . .

Other chemicals you may want to reduce:

  • Chlorine (use a water filter)
  • Antibacterial soaps and other home care products (use chemical-free soaps and cleaning solutions, or better yet, make you own)
  • Pesticides, herbicides, and other chemicals from foods (choose organic when possible)
  • Conventional meats treated with antibiotics or hormones (choose organic grass fed or pasture raised when available)

Medications and their Hostile Effects on the Microbiome

Medications like antibiotics can be lifesavers. When my son developed a nasty tooth abscess, I didn’t hesitate to prescribe him amoxicillin as I knew the bad bags could cause significant damage and needed to be eliminated. I made sure I gave him probiotics in between antibiotic doses and continue to give him probiotics to support his microbiome. 

There are situations when antibiotics are not necessary and may cause more harm than good. For example, it’s easy to reach for antibiotics when your child has an ear infection, but research shows that giving an antibiotic for ear infections—which are generally viral in origin—doesn’t offer much benefit compared to no treatment. Unfortunately, antibiotics are non-discriminate and destroy the bad and the good bacteria, which can lead to condition like dysbiosis (an imbalance in the microbiome).

Here is a list of medications that adversely affect the gut microbiome:

  • Antibiotics
  • Acid-blocking medications (PPIs, H2 Blockers)
  • Birth control pills
  • Corticosteroids
  • Antipsychotics

According to a recent German study, there are many more medications that can disrupt the equilibrium of the microbiome. In fact, out of the 1,000 commonly prescribed medications that were tested, 24% of them had an effect on the bacteria that normally colonize the gut. That’s essentially 1 in 4 medications!

The Gut/Brain Axis: How Stress Impacts the Microbiome

Ah, stress. Who isn’t under a lot of stress these days? Suffice it to say that we all suffer, on some level, from chronic stress and it can negatively impact the microbiome.

Things you can do to reduce stress:

  • Exercise
  • Meditate
  • Yoga, tai chi, qi gong, etc.
  • Belly breathing or slow breathing exercises
  • Visualization
  • Spending as much time as possible in nature
  • Talk therapy (discussing with a trusted ear what’s on your mind)

And don’t forget to take a probiotic to support the gut-brain axis, which can help modulate the stress response. One study showed that students administered fermented milk (which contains probiotics) maintained more diverse and healthier populations of gut bacteria compared to the control group. These students also reported less stress and anxiety. 

Better Sleep, Healthier Gut

We all know the importance of a good night’s sleep on how we feel the following morning. We also know that consistent high-quality sleep improves overall health, including the cardiovascular system, immune system, brain health, and metabolism. 

Sound sleep can positively impact the gut microbiome as well. The better one sleeps, the more melatonin is released, which leads to less leaky gut. 

My tips on getting a good night’s sleep:

  • Make sure the bedroom is completely dark and cool if possible.
  • Avoid adrenaline/dopamine-promoting activities before bed like TV watching, scary movies, or video games.
  • Avoid screens in general before bed including iPads, iPhones, TVs, and computers as these devices emit blue light which can suppress melatonin production.
  • Look into downloading F.lux onto your computer or iPhone or tablet if you are going to use the Internet before bed. F.lux minimizes the amount of blue light coming from screens.
  • Dim the lights at home in the hours before you go to sleep.
  • Try to go to sleep before 10 pm each night.
  • Aim for 7–9 hours of sleep per night.

Your Microbiome Needs Nature

I’ve already discussed the importance of regularly exposing yourself to dirt, whether this is through eating farmers market fruits/veggies, or walking barefoot on the Earth.  There is a now a movement that is encouraging “Forest Bathing,” which literally means “taking in the forest atmosphere,” or quite simply spending time in nature

All of us can appreciate the tranquil feeling of being in a forest, but science is actually proving that taking a walk in a forest actually improves energy, vigor, mood, and feelings of vitality. 

There are likely many mechanisms for the positive effects we see with time spent in nature, but one of them might be exposure to different types of bacteria. When you walk in a forest, you are exposed to all sorts of soil-based bacteria, which can enter your body through your lungs and pass through your GI tract, and have a transient effect on your immune system. 

 My recommendations are as follows:

  • Take a walk as often as you can through the woods.
  • Increase your outdoor activities including hiking, water sports, or camping.
  • Get your kids in nature as much as possible, but be vigilant and check for ticks afterward.

Exercise Can Improve the Microbiome

We don’t have much research looking at how exercise affects the microbiome, but what we do know is that exercise can indeed improve the diversity of the gut microbiome. One study looked at rugby players and found that with more exercise and protein consumption, there was a greater level of bacterial diversity. Since protein really doesn’t feed the microbiome, we can infer that exercise probably had a large role to play here. 

Most people feel good during and after exercise, so I suggest the following:

  • Move your body in a way that feels right and engage in an activity that you enjoy.
  • If you are stressed out, anxious, or depressed, exercise can really help with these conditions.
  • If you are new to exercise, go slow and work your way up to a frequency and intensity that feels good.

We now know that our lifestyle can positively or negatively dramatically influence the health of the trillions of bacteria and other microbes living in our gastrointestinal tract. Fortunately, activities recommended for overall health like healthy eating, exercise, and stress reduction can all positively impact the growth and diversity of the gut microbiome. It’s never too late to support the microbiome, so incorporate as many of the above recommendations into your life as you can and see what changes you notice over time. 

Additional Resource:

Ruscio, M.  Health Gut Healthy You. Las Vegas: The Ruscio Institute; 1998.

Dr. Drew Sinatra

Meet Dr. Drew Sinatra

Dr. Drew Sinatra is a board-certified naturopathic doctor and self-described “health detective” with a passion for promoting natural healing, wellness, and improving quality of life by addressing the root cause of illness in patients of all ages. His vibrant practice focuses on treating the whole person (mind, body, and spirit) and finding missed connections between symptoms and health issues that are often overlooked by conventional medicine.

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