How to Improve Gut Health During Pregnancy (+Why It Matters)

Imagine this: You just found out you're pregnant. You saw the two lines on the test, or maybe the fertility clinic called and told you after that long haul process—SUCCESS! You take a deep breath, and then immediately your mind starts creating a to-do list that is eight miles long.

Maybe it includes things like starting to eat better, researching car seats, and booking a prenatal appointment. I'm guessing getting your gut health in check may not have been the first thing that came to mind. You may not even know why gut health during pregnancy is so important and how your microbiome affects not only you but your growing baby, too.

Wait—my baby, too? Yep, that's right. I'll go over all the ways your gut health—and whole-body microbiome health for that matter—impacts your pregnant body, your developing baby, and how it even affects your optimal recovery postpartum.

photo credit: Matilda Wormwood

I'm new to all this—what even is the microbiome?

The microbiome is the collection of bacteria and other microscopic organisms called microbes that live in and on our body, along with their associated genes. There are distinct microbiome communities throughout the body, including the skin, gut, vagina, and oral cavities. Your gut microbiome is the largest and most impactful, but especially during pregnancy, your other microbiomes are an important focus area, too. The start of the microbiome is seeded at birth, with birth type, skin-to-skin contact, feeding type, and diet impacting how it develops.

Why should I care about my microbiome?

There are at least as many microbial cells as our own cells in our bodies and over 100 times as many genes! That is to say we are actually mostly microbial. They contribute to the health of almost every major system in our body.

Our microbiome plays a role in:

  • Protecting and maintaining the gut lining integrity- our first line of defense!

  • Helping optimal digestion and nutrient absorption

  • Breaking down food/fiber and creating beneficial byproducts

  • Calibrating and maintaining proper function of the immune system

  • Controlling inflammation

  • Synthesizing vitamins

  • Impacting mood through neurotransmitter production

  • Processing hormones and cholesterol in the body

In the case of pregnancy, it also impacts how the baby develops, too.

Specifically for pregnancy, your microbiome informs your risk of developing gestational diabetes, hypertension, and preterm birth, all of which can increase health risks in your baby in adulthood.

Related: top 5 tips for optimal gut health

How do I know if my microbiome needs support?

It can be hard to tell where normal pregnancy symptoms end and gut health issues begin—so many look the same. Lowered immune system function and hormonal fluctuations definitely play a role, but if the following have been really dampening the joy of your pregnancy, you may need to give your microbiome a bit more focus:

  • Pregnancy constipation or indigestion is plaguing you

  • You've been frequently getting sick

  • You're getting more vaginal infections than normal

  • You're struggling with anxiety or depressive moods

  • You've received a diagnosis of gestational diabetes or hypertension

It's very early research, but even melasma has been shown to be associated with changes in the gut microbiome.

Read on to learn about the main microbiome impacts on pregnancy and baby, and how best to support your microbiome health for you and your growing baby.

Whole-Body Microbiome Impacts on Pregnancy

We have many different microbiomes within our body, each having its own impact. For pregnancy, the most influential microbiome sites are the gut, vagina, and oral microbiomes. Let's see how each can impact your pregnancy and your future baby's health:

Gut Microbiome

Actually, our gut microbiome starts having impacts before we even start trying to have a baby. Our fertility and menstrual cycle are influenced by the health of our gut, as our gut microbiome plays a huge role in cycling hormones—namely estrogen—in our bodies. The microbes and their genes that affect estrogen cycling are referred to as the Estrobolome. If your gut microbes are out of balance, it can lead to insufficient removal of estrogen and, ultimately, estrogen dominance, which can lead to symptoms like bloating, heavy periods, and fertility challenges.

As pregnancy progresses, the microbiome of the mother changes due to myriad reasons, including hormonal fluctuations. Increasing progesterone is associated with an increase in beneficial Bifidobacterium, which is the main colonizer of the healthy, breast-fed infant microbiome.

A low microbial diversity and relative abundance of Bifidobacterium in a pregnant woman's gut microbiome are associated with a higher risk of preterm labor and gestational diabetes among other complications.

Another reason to focus on gut health during pregnancy: It appears that bifidobacteria are going missing in the Western world. Bifidobacteria, and in particular the subspecies Bifidobacterium longum subsp. infantis (B. infantis), are considered to be the hallmark of a healthy breastfed infant microbiome and are shown to be critical for proper immune development. In fact, it's hypothesized that the increase in immune-related issues like asthma, allergies, and eczema is due to improper calibration of the immune system from a lack of Bifidobacteria in early infancy. B. infantis thrives on human milk oligosaccharides (HMOs), which is why it can be outcompeted and go missing if breastfeeding is not prioritized.

A 2022 study showed that in Bangladesh and Gambia, where historical breastfeeding is considered high, B. infantis was found in four out of five infants. However, in the U.S., some communities had ZERO detectable B. infantis.

Is that as alarming to you as it is to me?


This gut species, which has been shown to calibrate the immune system and prove critical for optimal development, has gone extinct in some communities. But all is not lost—keep reading below to find out ways you can help improve your—and in turn your child's— gut microbiome and include this critical component, especially if you aren't able to breastfeed.

photo credit: Jonathan Borba

The gut microbiome also impacts our mood and mental health as well. The gut and the mind are incredibly linked by something called the gut-brain axis, and gut dysbiosis has been implicated in depression, including postpartum depression (PPD). Those with PPD have been shown to have significantly different microbial populations compared to healthy controls.

Vaginal Microbiome

Low levels of Lactobacillus in the vaginal microbiome have been associated with an increased risk for preterm labor. Women without abnormalities of the vaginal flora in the first trimester had a 75% lower risk of delivery before 35 weeks compared with women with abnormal vaginal flora.

Due to changes in hormones during pregnancy, bacterial vaginosis (BV) can become more prevalent, and it is estimated that up to 32% of pregnant women will develop BV during the course of their pregnancy.

Like gut dysbiosis, BV does appear to be associated with increased stress, so managing your stress levels through mindful practices throughout your day will benefit your whole-body microbiome health.

Oral Microbiome

Would you be surprised to hear that the health of your mouth, in particular your oral microbiome, impacts your risk of preterm birth? Research has shown that an imbalance in the oral microbiome can lead to systemic inflammation, which may trigger premature labor. The bacteria in the mouth can enter the bloodstream and affect overall health, highlighting the importance of oral hygiene not just for dental health but also for pregnancy outcomes. This connection underscores the need for expecting mothers to be mindful of their oral health during this critical time.

woman smiling with good oral health for pregnancy

photo credit: Guilherme Almeida

How to Improve Your Gut Health and Whole-Body Microbiome for a Healthier Pregnancy Today

OK, now you may realize this matters and are wondering, "But how can I improve my gut health during pregnancy?" Read on to hear the top tips for how to improve your gut health and whole-body microbiome starting today.

  1. Food first!

Focus on fermented foods and beverages, as well as abundant fiber, to increase the healthy bacteria in your body. Most traditionally fermented foods, while extemely beneficial for the microbiome in general, do not typically contain live bifidobacteria. An exception is yogurt; many yogurt manufacturers nowadays do include bifidobacteria in their starter cultures.

Still, eating adequate fiber is the best way to support healthy bifidobacterial levels. The best fibers to support bifidobacteria are prebiotic oligosaccharide fibers such as those found in beans, whole grains, onions, and Jerusalem artichokes (sunchokes), and resistant starches found in green bananas and cooked-then-cooled potatoes.

A prospective study of nearly 35,000 women showed that weekly to daily intake of fermented dairy significantly decreased preeclampsia risk. This could be because fermented foods have been shown to increase gut bacterial diversity.

Related: the #1 tip for better gut health

2.Eliminate inflammatory foods

In order to heal your gut you need to reduce inflammatory foods as much as possible. Foods that can trigger inflammation include added sugars, industrial seed oils, and any other specific food triggers you may have. These items contribute to systemic inflammation, which can lead to a compromised intestinal barrier, also known as leaky gut. Excess sugar can also promote the growth of harmful bacteria and yeast, disrupting the balance of our microbiome. To mitigate this, try to limit sweets to whole food options like fruit, and opt for less inflammatory cooking oils such as olive or coconut oil and grass-fed ghee. Observe how certain foods affect you and remove or reduce those that cause negative reactions such as grains or dairy, as this can help lower overall inflammation. Keep in mind that symptoms may not be limited to digestive issues; skin problems and chronic congestion can also indicate food sensitivities.

3. Consider probiotics

Probiotics have been shown to help with constipation, BV, immunity, and even postpartum mood disorders. They are also a great way to introduce human bifidobacterial species to the gut to ensure they are there to be passed down to your baby. Supplementation with a high-quality probiotic is especially suggested if you cannot eat adequate fiber due to pregnancy-related nausea or digestive distress, as fiber is the main way to increase beneficial bifidobacteria.

Probiotics containing B. infantis in particular—like the ones linked below— should be prioritized and can be very beneficial to ensure you have it in your system to pass down to your baby.

Be sure to read my entire guide on how to choose the right probiotic for pregnancy.

4. Practice proper oral and vaginal care

Ways to ensure proper oral care include:

  • Brush your teeth at least twice daily, ideally after every meal.

  • Floss every night, too

  • be sure to get your dental cleaning—ideally twice during pregnancy

  • consider oil pulling

Some tips for proper vaginal care include:

  • No douching

  • get rid of artificially fragranced and antimicrobial soaps

  • Wear cotton, breathable underwear

5. Lower stress

Notice I didn't say stressors. Pregnancy can be so full of stressors with so many unknowns, medical appointments, and your changing body causing what can be almost daily discomforts. How we show up and react to these stressors may be the only thing we can control, but that is more than enough.

It is more our response to stressors that impacts our microbiomes. Taking time throughout the day to check in with your feelings, acknowledge them, and take five minutes to breathe, meditate, or dance to your favorite song can help. I am a huge fan of emotional freedom technique, or tapping, and it has done wonders for my ability to move through stressful or highly emotional circumstances.

My go to is Tap with Brad aka everyone’s favorite internet Dad. But basically just type “tapping + [your issue]” into YouTube and you’ll find tons of options.

Benefits of Supporting Your Baby's Microbiome and Gut Health From the Very Start

Don't forget your microbiome is passed on to the baby in the case of vaginal birth. For cesarean birth, it is typically skin and hospital microbes that first colonize a newborn. So if you do have a C-section, it is especially important to take steps after your baby is born to help set their microbiomes and gut health up for long-term success.

Some of the benefits of a healthy microbiome for your baby include:

Better immune function and reduced risk of eczema and allergies

Bifidobacteria, in particular, help to calibrate the immune system, and their presence modulates immune functioning through various metabolites. Depletion of bifidobacteria has been shown to be associated with impaired immune function and autoimmune disorders such as atopic dermatitis (eczema) and allergies.

Less digestive stress and colic

Infants who exhibit signs of colic are observed to have a dysbiotic gut microbiome lacking in Bifidobacteria and Lactobacilli, and higher in non-beneficial bacteria like E. coli.

Reduced risk of type II diabetes and other metabolic disorders

Dysbiosis in the maternal microbiome that is passed down to the baby during birth, along with diet and other environmental factors, has been shown to increase the risk of childhood metabolic disorders.

A note on vaginal seeding

Some advocate for swabbing the infant with vaginal bacteria after a C-section birth to help seed them with beneficial bacteria. This is still in the early stages of research, and caution should be taken to ensure you are not Group B Strep positive or have another vaginal infection. It is also unclear what potential benefit vaginal seeding would provide to the infant—it may not be the vaginal microbes that help the infant gut develop but could be the not-so-glamorous, yet very common part of birth: pooping during labor and delivery!

A less risky approach would be to provide infants born via cesarean with infant-type Bifidobacteria such as B. infantis via a probiotic and encourage breastfeeding. Some good options include the Jarro-Dophilus® Infant Probiotic drops and the Evivo® Infant Probiotic Powder.

pregnant woman preparing a healthy pregnancy diet of a salad

Photo credit: Matilda Wormwood

Final Thoughts

I hope this post helped to highlight just how important the microbiome and gut health during pregnancy can be. As you embark on this incredible journey of pregnancy, prioritizing your gut health and overall microbiome can significantly impact both your well-being and that of your growing baby. Understanding the connections between your microbiome and myriad aspects of pregnancy—from immune function to mood regulation—empowers you to make informed choices that nurture both you and your child.

By focusing on a balanced diet rich in fiber and fermented foods, considering probiotics, and maintaining proper oral and vaginal health, you can foster a thriving microbiome that supports optimal health throughout your pregnancy and beyond. Remember, every small step you take can lead to substantial benefits for you and your little one. Embrace this opportunity to nourish not just your body but also the foundations of your baby's health for years to come.


If you would like more support to get your gut health in tip-top shape and ensure proper pregnancy nutrition, consider booking a pregnancy nutrition package or book a complimentary consultation to see how I can best support you today!

Allison Gregg MS, CNC

Certified Nutrition Consultant specifically trained in nutrition for fertility, pregnancy, postpartum and baby’s first 1000 days.

I also hold a Masters degree in biology with an emphasis in microbiology and have expertise in the gut microbiome, probiotics and food safety.

I started Flora & Fauna Nutrition to provide critical gut health and nutrition information to give babies the absolute best foundation and to help mothers not only recover—but thrive—to be able to feel their best for themselves, their families and their community.

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