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What is the Gut Microbiome?

Hello friends! Pre- and pro-biotics are all the rage recently thanks to recent scientific findings about the gut microbiome. But, what is the gut microbiome?

The gut microbiome describes the different bacteria, sometimes called “good bacteria,” living in our digestive systems. It was previously thought that these bacteria simply lived in our digestive systems; however, scientists are now learning that these organisms are important to help keep us healthy. In fact, studies show promising results that testing the gut microbiome may be able to detect gut-related diseases before traditional diagnostic tests can (Marchesi, 2016).

There are changes to the gut microbiome in individuals with conditions like functional constipation and irritable bowel disease (Zhang, 2021; Marchesi, 2016). These changes can include less of this “good” bacteria or an unequal balance. Multiple species of bacteria are important to maintain the gut microbiome, but sometimes one species becomes dominant.

Certain medications, including antibiotics or proton pump inhibitors (like Prilosec), are known to impact the gut microbiome (Zhang, 2021).

You might be asking yourself why myPFM, pelvic health organization, is talking about the gut microbiome. Individuals with constipation often strain to have a bowel movement which increases stress on the pelvic floor muscles and can lead to dysfunction and incontinence as well as prolapse, hemorrhoids, chronic pelvic pain, and even a vasovagal response (which can actually make you pass out!) (Irion, 2010). Solid waste filling the rectum can also put pressure on the bladder making you feel a stronger urge to pee (Irion, 2010). Constipation is often a cause of nocturnal enuresis (bed wetting) especially in children. The good news is, most children with constipation respond to education, toilet training, and laxatives (Lu, 2018).

What can we do to promote a healthy and balance gut microbiome?

It has been well known that a healthy diet with plenty of water and fiber along with regular exercise are important for optimal digestive function. Newer research has supported the use of pre- and pro-biotics.

Typically, you should have bowel movements anywhere from three times per week to three times per day (Irion, 2010; Binford, 2013). 21% of women and 8% of men have bowel movements less frequently than this and are diagnosed with having chronic constipation. (Irion, 2010). 30% of individuals over the age of 60 suffer from constipation (Irion, 2010; Hayat 2017).

It is important to speak with a healthcare provider about your constipation, especially if you are experiencing symptoms such as unintentional weight loss, bleeding, severe abdominal pain or rectal pain (Irion, 2010; Hayat 2017). These symptoms can be signs of more serious conditions like infection, bowel obstruction, or malignancies.

Probiotics are foods/supplements that contain the actual strains of “good” bacteria in attempt to replenish your digestive tract. On the other hand, prebiotics are “food” that we are unable to digest but that the bacteria use. This helps to regulate the bacteria of the gut in both number and diversity (Zhang, 2021).

Probiotics with multiple species of bacteria have been shown to improve stool consistency and bloating (Zhang, 2021). Both prebiotics and probiotics and can improve the movement of stool in the digestive system and in turn improve how often you are pooping (Zhang, 2021).

Some common foods that have probiotics include yogurt, sauerkraut, kombucha, sourdough bread, pickles, and some cheeses. Some examples of prebiotics are inulin, lactitol, aloe vera gel (Zhang, 2021).

Here are some great resources to help you learn more about your pelvic floor:

For providers, check our online courses to help your clients. Consider joining our Ambassador Program and most of our courses are included with your membership!

Written by Emily Reul, PT, DPT


  1. Binford J. Physical therapy management of outlet dysfunction constipation and pelvic pain. J Womens Health Phys Therap. 2013 May;37(2):59-69. doi: 10.1097/jwh.0b013e31829df717.

  2. Hayat U, Dugum M, Garg S. Chronic constipation: update on management. Cleve Clin J Med. 2017 May;84(5):397-408. doi: 10.3949/ccjm.84a.15141.

  3. Irion JM, Irion GL. Women’s health in physical therapy.

  4. Lu PL, Mouse HM. Constipation: beyond the old paradigms. Gastroenterol Clin North Am. 2018 Dec;47(4):845-862. doi: 10.1016/j.gtc.2018.07.009.

  5. Marchesi JR et al. The gut microbiota and host health: a new clinical frontier. Gut.2016;65(2):330-9.

  6. Zhang S, Wand R, Li D, Zhao L, Zhu L. Role of gut microbiota in functional constipation. Gastroenterol Rep (Oxf). 2021;6(9):392-401.

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