The Gut Biome Vagina Connection: How Bacteria Can Help Us Heal (Episode 149)

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The Gut Biome Vagina Connection: How Bacteria Can Help Us Heal (Episode 149)

The risk of HPV is associated with imbalances in the gut biome and vaginal biome. Addressing this imbalanced gut bacteria and inflammation caused by food sensitivities can result in an improvement in the ability of the body to fight the HPV virus and an improvement in fertility.
Dr. Doni discusses the connection between the gut biome and the vaginal biome – the risk of HPV, the effects of stress and trauma, and other things that cause our bacteria to be out of balance.

In today’s episode I am going to be diving in deep on the gut biome vagina connection. That’s right, there is an interconnection between the gut health and vaginal health. 

As a naturopathic doctor and midwife, specializing in women’s health as well as a naturopathic doctor specializing in gut health, I’ve been observing this relationship between the gut and the vagina for many years.

It wasn’t until recently, in 2019, that studies starting to come out that demonstrate the relationship between the gut and the vagina. So, I want to help you to understand why there is an interconnection between them and how understanding this connection will help you heal. 

A lot of times, if you are having female reproductive issues or vaginal health issues you would normally go see a gynecologist, but they don’t deal with digestion issues. Or if you would have digestive issues, you would go see a gastroenterologist and they don’t deal with the vaginal area. So, when you’re seeing different specialists, they might not understand or address the connection between these two areas of your body.

The other thing is that the way to address it is not with medications. The way to heal and optimize the gut-vagina connection is through diet, herbs, probiotics, and natural substances. And this requires for you to be evaluated by a functional practitioner that evaluates your body as a whole and use an approach that is outside the standard medical approach.

Gut Biome, Vaginal Biome, and the Risk of HPV

One of the key health issues related to this connection is the predominance of HPV. HPV is the most common sexually transmitted disease so most of us are exposed to this virus. Now, most people will clear the virus within a couple of years so we know the human body can fend off the virus by itself and it doesn’t always cause cancer. But for some women this virus does cause abnormal cells on the cervix or vagina. So, the question is why are these women susceptible to this virus? Why is HPV not being cleared by their bodies? 

This risk of HPV is associated with imbalances in the gut biome and vaginal biome (microbiome or commensal bacteria), as well as inflammation in both the gut and cervicovaginal area. Also, I have witnessed that fertility is related with this biome too. 

When we focus on healing leaky gut, imbalanced gut bacteria and inflammation caused by food sensitivities, we will see an improvement in the ability of the body to fight the HPV virus and an improvement in fertility. This is why women who follow my protocol for healing HPV – which involves addressing gut health – see an improvement in their ovulation and ability to get pregnant.

Other health issues related to the gut and vaginal biome are Polycystic Ovary Syndrome or PCOS, irregular menstrual cycles, menstrual cramps, dysmenorrhea, endometriosis, vaginal infections, urinary tract (bladder) infections, and autoimmunity. This is why it’s so important to pay attention to your gut health. 

The Effect of Stress and Trauma on Our Gut Biome

We have a sense about how this works: We eat, we digest our food, we get the nutrients out of our food and any food that we don’t absorb gets eliminated in the stool. But sometimes we are racing through our days, and we don’t pay attention to our body’s digestive needs. In fact, when we are very stressed, our digestion gets turned off and therefore, we are not able to absorb the nutrients in our food and we could develop a condition called leaky gut which is when the intestinal cells are not as healthy as they should be.

Also, stress and trauma exposure affect the balance of bacteria. And we have bacteria living throughout our whole bodies, in our gut, intestines, vagina, uterus, ovaries, skin, etc. All these bacteria influence our health in many ways starting with our immune system. So, the gut biome really affects our ability to fend off infections. Also, when we have an imbalanced gut biome, we are more susceptible to autoimmunity illnesses like celiac disease, Crohn’s disease, and rheumatoid arthritis.

If you have any of these health issues you should immediately pay attention to your gut biome. Additionally, you should pay attention to your stress and trauma exposure. Not trying to ignore it, but help your body recover from it. For example, if stress and trauma are causing leaky gut and an imbalance in the gut biome then we can focus on healing the leaky gut and gut biome in order to recover from stress.

If you have leaky gut, then your gut lining, specifically the intestinal wall cells, are not healthy, so your food “leaks” through, triggering an immune response which causes inflammation that spreads everywhere, including in your reproductive system. 

Other Things that Affect Our Gut Biome and Vaginal Biome

The foods we eat determine the bacteria living in our gut. If we are eating too much food and not digesting it correctly it ends up overfeeding the bacteria and then we have too much of certain bacteria and that also causes inflammation and more disruption in our bodies.

The gut biome and vaginal biome are also affected by other things like if you were born by vaginal birth (this is how babies get the bacteria to seed their digestion and intestines) so people who are born through a C-section are not getting all the bacteria they need for their gut biome to work correctly. 

Your age, where you live, occupation, diet, stress and trauma exposure are also factors that affect your gut biome. Also exposure to antibiotics, because they kill bad and good bacteria disrupting your healthy gut biome. The use of laxatives and other medications like contraceptives, toxins, chemicals, and pesticides can all affect the gut biome.

So if you have been suffering from recurring vaginal infections or even HPV for a while now it could be that you haven’t addressed your gut health and may have leaky gut and/or an imbalance in your gut biome.

How to Get a Healthy Gut Biome

If you want to know if you have a healthy gut biome there is a specialty test that you can do through my office. It’s a stool panel that is a DNA analysis to show which bacteria are predominant in your intestines. This really helps to see if there is overgrowing or undergrowing bacteria, if there’s yeast, leaky gut, inflammatory reactions to gluten and the overall health of your gut biome. 

So, if you’re having a lot of digestive issues like bloating, gas, irregular bowel movements, constipation, or diarrhea or even autoimmunity and HPV that is not going away, then this panel will show what is out of balance and then I can help you rebalance your gut biome. You can schedule your test here.

One of the first things I recommend is to do a leaky gut test. To me, the best way to check for leaky gut is with a high-quality food sensitivity panel that you can do at home. This test will show you which foods are leaking through your intestines and triggering an inflammation response in your body. You can order this test here. Remember that healing leaky gut is the first step to rebalance your gut biome. If you want to start right away you can order my leaky gut pro package here and begin creating the foundation for rebalancing your gut biome.

Taking probiotics also helps promoting a healthy gut biome but it’s not about just swallowing a lot of probiotics. This will not solve the problem if you haven’t addressed leaky gut and inflammation first.

Another important thing to consider is your diet. If we always eat the same foods we are only feeding and promoting the growth of certain types of bacteria. It’s important to have a healthy diverse diet eating vegetables, fruits, nuts and seeds, fiber, different sources of protein and healthy fats. This way we are feeding a diverse population of bacteria.

Taking time when you’re eating is important too. Chewing your food well, taking deep breaths, feeling relaxed, telling your parasympathetic nervous system and your vagus nerve that you want to digest and absorb your nutrients and feed your healthy gut biome. If we are racing through our meals, we are not going to be able to feed our gut biome correctly.

Having a healthy gut biome will help with the health of your intestinal cells and therefore reduce inflammation in your body which will translate into having healthy bacteria living everywhere in your body including the vaginal area so you are going to be preventing HPV and cervical cancer. So the strategy specifically for HPV needs to be to reduce inflammation vaginally and rebalance the healthy bacteria living there. And this also applies for preventing BV and yeast or improving fertility even.

If you want to learn more about this be sure to check out my Leaky Gut Masterclass here. You can also download my Leaky Gut Guide for FREE.

I will also be hosting a FREE Online Workshop: 5 Days to Heal HPV so make sure to sign up here. And here you can find my FREE HPV Recovery Guide.

If you are interested in a detoxification, I will soon be hosting a FREE Online Detox Masterclass: Detox Yourself! How to do it Right, where we will cover everything you need to know about how to do an effective detox.

If you want to learn more about my approach on how you can overcome trauma and stress and apply my SelfC.A.R.E. approach so you get back to feeling your best, you may want to start by reading my book Master Your Stress Reset Your Health

In the book, I share the quiz I developed to help you identify how stress has affected you specifically by knowing your Stress Type. You can also take the Stress Type Quiz online.

For the most comprehensive support, even with the most difficult health issues (physical or mental), it is best to meet with me one-on-one, which is available to you no matter where you are in the world (via phone or zoom). You can set up a one-on-one appointment with me here.

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Disclaimer: This specific article and all other Content, Products, and Services of this Website are NOT intended as, and must not be understood or construed as, medical care or advice, naturopathic medical care or advice, the practice of medicine, or the practice of counseling care, nor can it be understood or construed as providing any form of medical diagnosis, treatment, cure, or prevention of any disease.


  1. Amabebe E, Anumba DOC. Female Gut and Genital Tract Microbiota-Induced Crosstalk and Differential Effects of Short-Chain Fatty Acids on Immune Sequelae. Front Immunol. 2020 Sep 10;11:2184. doi: 10.3389/fimmu.2020.02184. PMID: 33013918; PMCID: PMC7511578.
  2. Łaniewski P, Cui H, Roe DJ, Barnes D, Goulder A, Monk BJ, et al. Features of the cervicovaginal microenvironment drive cancer biomarker signatures in patients across cervical carcinogenesis. Sci Rep. (2019) 9:7333. doi: 10.1038/s41598-019-43849-5
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