What to Know About the Gut Microbiome

By, Fiona McMahon PT, DPT, Beyond Basics Physical Therapy


What we eat can directly affect the bacterial and fungal makeup of the gut, also known as the human gut microbiome. The gut requires a certain level of good bacteria to help us digest what we eat and establish a healthy microbiome. 

Over time a poor gut microbiome can affect how efficiently the gut works. The function of the gut goes beyond just digesting food, but also is vitally important for the production of neurotransmitters, which help to spread messages within the brain and throughout the whole body. A healthy gut microbiome also plays an important role in our hormones and immune system. When the microbiome of the gut is not balanced, it is called dysbiosis.

Let’s explore dysbiosis further, including the symptoms that can result from too much bad gut bacteria and tips for improvement. 

What Can Cause Bad Gut Bacteria to Occur?

One of the most common culprits in gut microbiota dysbiosis is candida, (Yeast!). Candida is a naturally occurring inhabitant of the body and when it’s at appropriate levels, it doesn’t tend to be noticed or affect the stomach microbiome. However, anyone who has experienced a yeast infection knows that if this little guy is allowed to go unchecked, it can do a lot to make you miserable. Besides plaguing women with itching, burning vulvas, a yeast overgrowth may cause many other ailments.

Science has pointed to the role candida can play in microbiome gut health in contributing to chronic and inflammatory conditions. In one study by Kumamoto in 2011, candida overgrowth was associated with delayed healing of inflammatory lesions and was associated with pro-inflammatory cytokines (chemicals) and increased incidence of inflammatory bowel disease like ulcerative colitis and Crohn’s disease.

Yeast overgrowth can also affect the bladder along with over colonization of Saccharomyces (another form of fungus). In fact, yeast and Saccharomyces were found to be higher in women during a flare of interstitial cystitis than when their symptoms were low.

Yeast is not the only bad gut bacteria that can get out of balance and affect our bodies in harmful ways. There are many other players that can get out of balance. Some signs of an altered human gut microbiome is a history of allergies, eczema, or repeated fungal infection.

Tips for Better Microbiome Gut Health

Here are a few simple steps you can start with to help maintain balance and promote a healthy microbiome in your gut:

Avoid Antibiotics, Unless Your Doctor Thinks You Need Them

The medical community has become a lot more aware of the dangers of over-prescribing antibiotics from their perspective and how it affects gut flora, but it is important to keep in mind that a powerful antibiotic can wipe out good bacteria and bad bacteria in one fell swoop. If the good guys in your gut are reduced, the bad gut bacteria have a better chance of taking over. Take antibiotics only when recommended. Keep in mind that antibiotics will not help treat viruses like the flu; they can only treat bacterial infections.

Modify Your Diet


Increase your consumption of good fats (omega 3’s) to help reduce inflammation.

Food high in omega 3’s includes flax and hemp seed/oils, and fish. The fishier the fish usually means more omega 3’s. For example, herring is higher in omega 3 than a milder fish like snapper. Also, reduce your consumption of processed foods – which can increase inflammation levels – and eliminate simple sugars and fried foods. If this is only minimally successful as you try to achieve a healthy gut microbiome, try a gluten and dairy free diet.  

Exercise Every Day 

Research shows that exercising at a high intensity to improve cardiorespiratory fitness increases gut microbota and diversity, and therefore is correlated with better health. In fact, such exercise accounted for about a quarter of the variance in gut species and their evenness. In order to keep up with an intense level of activity, it’s important to take care of the aches and pains that are likely to occur. This is where physical therapy can help. Seeing a PT to ease discomfort and provide an effective treatment plan can ensure you continue to exercise at a high intensity and see the benefits when it comes to you gut microbiome. 

If Simple Changes Are Not Helping, Consider Seeing A Professional

Find a naturopath, functional or integrated MD, or nutritionist who can investigate more fully whether or not you have SIBO (Small intestinal bacterial overgrowth), candida overgrowth, or other gut microbiome disorder. Or perhaps you are lacking certain ingredients, vitamins or mineral.  These professionals can tailor a diet and medication regimen to help return your gut microbiome to tip-top shape. 


When a Healthy Microbiome Matters Most

 As you recover from injury, you need your body to be in sync from the inside out. In order for you to recover as quickly and fully as possible, your gut microbiome needs to be balanced in order for your muscle and bone health to thrive. Along with seeking out a physical therapist to assist with your injury, be sure to also consult with one of the specialists listed above (e.g. a naturopath or nutritionist) for a holistic approach to recovery. 

To find a physical therapist near you or your gut microbiome specialist, use the BetterPT website or app to find Beyond Basics Physical Therapy or other clinics in your area. With the right medical professionals on your side, you can reduce discomfort and ensure your body is in balance – from your gut to your muscles. 


Fiona McMahon’s clinical studies included training in inpatient rehabilitation orthopedic rehabilitation at NYU Hospital for joint diseases, as well as three other outpatient orthopedic rotations, including at Beyond Basics Physical Therapy! Fiona expands on her passion for pelvic floor health by promoting awareness of various pelvic floor and health topics as the head of the blog at BBPT.

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