The Brain Below: The Role Your Gut May Play in Pelvic Pain

In Female Interstitial Cystitis / Painful Bladder Syndrome, Male Interstitial Cystitis / Nonbacterial Chronic Prostatitis / Chronic Pelvic Pain Syndrome by Elizabeth Akincilar5 Comments


By Elizabeth Akincilar-Rummer, MSPT, Cofounder, PHRC Los Angeles


When is the last time you heard a little voice inside you that tried to give you advice or warn you of danger? Some describe it as ‘butterflies,’ others a ‘gut feeling.’ That feeling can be attributed to the extremely extensive network of over 100 million neurons that make up our gut. That’s more neurons that are in our spinal cord or peripheral nervous system! Our gut is so complex it has often been referred to as our “second brain.” In fact, Michael Gershon, MD, a prominent researcher of the gastrointestinal system, entitled his book, The Second Brain. Since that book was published nearly 20 years ago, our gut has received a lot of attention. Unless you’ve been living under a rock the last few years, you’ve likely heard the somewhat disturbing, yet strangely interesting phrase, ‘fecal transplant’, which is a very successful treatment for the widely feared intestinal bacterial infection, Clostridium difficile, or, C. diff. A quick google search of the word ‘gut’ yields more than 500 million results, whereas a search for ‘low back pain’ only turns up a little more than 11 million results. Terms like ‘leaky gut’, ‘microbiota’, ‘bacteria,’ and ‘probiotics’ dominate the first page of a google search for ‘gut’. It turns out, A LOT of people are interested in their guts.


Our guts do much more than just handle digestion or raise the occasional red flag. It can alter our mood as well as play a key role in many diseases and disorders. Our “second brain” is technically known as the enteric nervous system, which measures almost 30 feet from esophagus to anus. It has its own senses and reflexes, which makes it capable of controlling our gut behavior independently of our brain. You read that correctly. Our bellies literally have a mind of their own.


If you’ve ever spent a day praying to the porcelain god because you ate a bad oyster, or if you just had an upset stomach, it’s probably safe to say that it soured your mood. However, more recent research is suggesting that our everyday mood could be relying on messages from the brain below to the brain above.


In fact, some treatment strategies for depression are identical to those for some gastrointestinal disorders. This suggests that the connection between our gut and our psychological state may be more significant than we previously thought.


The enteric nervous system, as in the brain, has more than 30 neurotransmitters. Two commonly recognized neurotransmitters are serotonin and norepinephrine because of the role they play in depression and anxiety. You’ll probably be surprised to learn that 95% of the body’s serotonin is in fact, found in the gut. More than two million people in the United States suffer from irritable bowel syndrome, which in part is a result of too much serotonin in their bowels. It could be considered a “mental illness” of the gut. Regulation of serotonin by the gut has also been linked to osteoporosis and autism.


This complicated communication is often called the brain-gut axis, which refers to the bidirectional signaling between the brain and the gut microbiota or microbiome. Joshua Lederberg coined the term microbiota as “the ecological community of commensal, symbiotic and pathogenic microorganisms that literally share our body space.”  Alterations in the brain-gut microbiota have been implicated in several brain disorders such as autism and Parkinson’s, mood disorders, and chronic pain.


The adult gut microbiota is composed of trillions of microorganisms and contains 100 times as many genes as the whole genome.1 From the moment of birth, our guts are being colonized by bacteria. Many things can affect the amount and type of bacteria that set up shop in our intestines, including the way we came into this world, either through the vaginal canal or via Cesarean section. Whether we were breastfed or fed with formula will alter our microbiota. Rat studies suggest that experiencing stressors very early in life alters the types and abundance of bacteria in our intestines. In fact, these changes may be associated with exaggerated visceral (organ) pain responses, or visceral hypersensitivity, that persist into adulthood.2  Visceral hypersensitivity refers to a decreased pain threshold after a painful stimulus or an exaggerated response to a painful stimulus. There are various ways that visceral hypersensitivity can occur, one of which may include alterations in the gut microbiome. In fact, alterations in the gut microbiota are associated with changes in a variety of pain-related pathways.


So, you’re probably wondering, what impact does our gut microbiota have on pelvic pain? Good question!


In unsurprising news, there has been very little research to explore the connection between pelvic pain and our guts. It wasn’t until 2016 that any research was published on the possible connection between intestinal microbiota and pelvic pain! To date, there are two studies that specifically examined pelvic pain and the gut.


The first study looked at the role the gut microbiota may play in interstitial cystitis/painful bladder syndrome (IC/PBS). Published in Nature in 2016, they compared the DNA from stool and vaginal samples from healthy females to females with IC/PBS. They found differences that suggest that the IC microbiome may be functionally distinct from the normal adult fecal microbiome. This offers two possible exciting opportunities with further research. First, it could aid in correctly diagnosing IC/PBS, a notoriously difficult syndrome to correctly diagnose, and it suggests probiotic/prebiotic therapeutic opportunities for people suffering from IC/PBS.3


The second study studied the gut microbiome in men with chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) versus healthy men. Most men with CP/CPPS have been treated with multiple and usually unnecessary prolonged courses of antibiotics which can have an effect on the gut microbiome. It has been shown that prolonged courses of antibiotics can alter the intestinal flora, and these changes often do not return to baseline even after the antibiotics have been discontinued.4 They compared patients with CP/CPPS who were not currently taking antibiotics to healthy men. They revealed significant differences in the gut microbiomes between the two groups. Although this was the first study of its kind, this research is exciting as it could aid in better understanding the etiology of CP/CPPS as well as improve treatment strategies.


This emerging research suggesting our gut plays a key role in health and disease is extremely exciting, but before we can bust out the champagne, much more research needs to happen. However, after reviewing the current research, there are a few very interesting possible connections between the gut and chronic pelvic pain that I think are worth repeating.


  • People who suffer from pelvic pain as well as other chronic pain syndromes often experience hyperalgesia (an abnormally heightened sensitivity to pain) and altered pain thresholds. Alterations in the gut are also associated with changes in pain perception in other organs.
  • Patients with chronic pelvic pain often also suffer from autoimmune disorders, whether they are a contributor to pelvic pain, or a co-morbidity is unclear. The gut microbiota is involved in the development of our immune systems.
  • Patients suffering from chronic pelvic pain often have depression, emotional stress, and/or catastrophizing thoughts. Stress can have an effect on the gut microbiome and the gut microbiome can have an effect on our mood and behavior.


Not only could your gut be warning you to stay away from Creeper McCreepster who was staring at you on the bus this morning, but it could also be a large part of a long-awaited solution to many other chronic health issues. Listen to your gut, because you can count on it listening to you.    




  1. Gill SR, Pop M, Deboy RT, et al. Metagenomic analysis of the human distal gut microbiome. Science 2006;312:1355-1359.
  2. Barouei J, Moussavi M, Hodgson DM. Effect of maternal probiotic intervention of HPA axis, immunity and gut microbiota in a rat model of irritable bowel syndrome. PLoS One 2012;7:e46051.
  3. Braundmeier-Fleming A et al. Stool-based biomarkers of interstitial cystitis/bladder pain syndrome. Nature. Scientific Reports. May 2016.
  4. Dethlefsen L and Relman DA: Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci USA 2011;108:4554.


  1. Very interesting!

    The Chinese have used fecal transplants for centuries. More research needs to be done on the effects that this could have on more than Cdiff. The FDA regulations are too restrictive.

    I can attest as someone who has Crohns, that gut pain causes guarding too. My worst pelvic floor muscles are the ones controlling the rectal area. I would much rather have had a fecal transplant or series of fecal transplants than to have had an interstim implanted to help with fecal incontinence.

  2. So what do we do now while we are waiting for more research. What should we eat? Take Probiotics? Any amount/special kind?

    1. Author Liz Akincilar says:

      Hi Lana,

      There isn’t any conclusive evidence about exactly what to eat or if probiotics are actually helpful. However, there are some recommendations based upon some evidence. It is recommended that you completely eliminate any foods/drinks that you have an allergy or sensitivity to. If you don’t know if you do you can get allergy testing or you can go through an elimination diet. There are various ways to do that which I would consult with a nutritionist and/or a naturopath to discuss. It has also been suggested to limit red meat intake and incorporate fermented foods into your diet such as sauerkraut, yogurt or kimchi. Don’t eat anything that’s not a whole food, so no processed food. Take antibiotics ONLY when absolutely necessary. And, when eating meats, eat meats that have not been given antibiotics. It could potentially be better for you and your gut. Lastly, probiotics are generally suggested even though there isn’t data proving their effectiveness. Again, I would consult a nutritionist and/or a naturopath to discuss what probiotics are best.

      Hope this helps.



    1. Hi Joan,

      That is an extremely difficult question to answer because it is a very complex system that is affected by everything, literally. I’ll try to summarize. Eat healthy: whole foods, no processed foods, minimize red meats, incorporate fermented foods, and do not eat anything you are allergic or sensitive to. Maintain emotional health, minimize stress, maximize happiness. Exercise. Drink lots of water. Keep the rest of your body healthy. I know that is a very general answer, but that’s about as specific as I can get in this forum. I would recommend contacting other health providers to help you with these things, such as a mental health specialist, a nutritionist, a naturopath, and/or your general practitioner.

      Hope this helps.



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