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Microbiome in Pregnancy

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Can I just take a second to introduce my AMAZING colleague, Sarah O’Hara, RD? She runs a private practice here in Calgary specializing in prenatal and PCOS nutrition. When she suggested writing a blog post on the microbiome and pregnancy – I was ALL over that. As a gut health dietitian – the microbiome, especially in infancy BLOWS my mind. So let’s get to it!

Microbiome 101

The human “microbiome” refers to the community of microorganisms living in/on our bodies. It outnumbers our own cells by a factor of 10. It contains upwards of 100 trillion cells and a collective 27 times more genes than the human genome. (That’s a LOT of microbes!) The species diversity and abundance vary depending upon the location in/on our bodies. Our skin, mouth, nasal cavity, gut, reproductive tract, and the placenta each harbour a unique microcommunity. These tiny stowaways are far from benign. Many scientists go so far as to refer to the microbiome as a human organ. Microbiome research is flourishing, and has only just begun to reveal the extent to which these microbes influence our health.

How does the microbiome impact our health?

We now know that our microbiome and its composition influences our health and wellbeing through a variety of complex processes. In the gut, for example, microbes help with food digestion/fermentation and liberating short chain fatty acids (SCFA) from indigestible dietary fibres. (SCFA are an important energy source for our intestinal mucosa and modulate immune responses in the gut). It is also believed microbes are constantly engaging in active two-way communication with the brain via a gut-microbe-brain axis.

Conditions related to chronic inflammation (such as heart disease, certain forms of cancer, and inflammatory bowel diseases) are associated with lower microbiome diversity and abundance of certain species of microbes. The human microbiome begins to establish itself as early as in utero. With the first 3 years of life being an extremely sensitive period for development of your baby’s microbiome.

Around age 3, your microbiome becomes established and relatively stable. About 60-70% of its composition remains stable throughout our lifetime. This leaves 30-40% of the microbiota susceptible to influence from diet, activity, lifestyle, hygiene, antibiotic use, etc. Because of this – we have an excellent opportunity to consider how we can shape our baby’s microbiome. Here’s what we know so far.

Learn how to take care of mom and baby's microbiome - and important part of immune development and health through their lives! | Calgary dietitian Sarah O'Hara guest posts on Ignite Nutrition Blog about gut health in pregnancy

Microbiome in Pregnancy + Early Infancy

The maternal microbiome plays a role in influencing certain pregnancy risk factors and infant health outcomes. Imbalance in mom’s microbiome has been associated with increased risk for preterm delivery. As well as preeclampsia, gestational diabetes, and excess weight gain in pregnancy.

Colonization occurs during the birthing process, feeding, and with skin-to-skin contact. Baby’s size and age at delivery also impact microbiome composition. Preterm infants lack two main groups of bacteria found in healthy term infants (Bifidobacterium and Lactobacillus).

During the first several weeks of life, infants begin to develop body site-specific microbiomes. How an infant feeds greatly influences the composition of gut colonies.

Breastfed infants have guts with greater abundance of Bifidobacteria, a key player in healthy immune system development. Breast milk naturally contains high numbers and variety of beneficial microbes, and baby also receives mom’s microbes from her skin while breastfeeding.

Skin-to-skin contact is known to be beneficial immediately after birth and beyond. Helping to regulate baby’s temperature, blood sugars, breathing rate, and promoting colonization of bacteria from mom’s skin (and of other caregivers who practice skin-to-skin).

The timing of introducing solid foods as a complement to infant milk also plays an important role in baby’s future health. If introduced too early (<4 months of age), baby is at increased risk for developing gastrointestinal infection and food allergies. Most infants are developmentally and physically ready for complementary foods around 6 months of age. With each developmental change in eating pattern that occurs, we know baby’s microbiome continues to develop and change.

It’s known that modifiable factors can either positively or negatively influence our microbiome composition and pregnancy outcomes. Here’s what you can do to promote a healthy microbiome for yourself and baby:

Eating for Two (+100 Trillion)

Is the western diet bad?

  • The typical Western diet, high in refined carbohydrates, fats, and animal protein sources, have been linked to gut microbiome imbalance and poor health outcomes. Choosing a Mediterranean style of dietary intake, rich in whole grains, pulses (such as beans and lentils), plenty of fruit and vegetables, and more modest amounts of lean protein (such as fish) and healthy oils (such as olive oil) will have a positive impact on your gut microbiota. Finding ways to boost your plant-based food intake not only helps to increase your body’s supply of many important nutrients for health and pregnancy, but also provides plenty of the dietary fibre that healthy gut microbes love.

Are probiotics good?

  • Foods containing probiotics (bacteria that have been proven to confer a benefit when consumed) have been shown to reduce risk of preterm birth and preeclampsia. Additionally probiotics may also help to reduce postpartum waist circumference. One double-blind, placebo controlled study found a reduced incidence of gestational diabetes amongst women who received probiotic supplements during pregnancy. Be sure to choose a probiotic that is evidence based – your dietitian can help you with that!

Are fermented foods good for the gut microbiome?

  • Fermented beverages and foods, such as kombucha, kimchi, sauerkraut, tempeh, and others, are popular amongst those seeking gut health benefits. However, evidence is lacking to provide a clear answer of which/how much fermented foods impact the microbiome and human health. Choosing some of these foods in moderation in the context of a healthy and balanced diet is fine. But don’t use them as an excuse to consume a lot of processed foods. (Note: if choosing kombucha in pregnancy, ensure you’re enjoying only the commercially produced non-alcoholic variety. There are increased food safety risks associated with homebrewed version you’re not likely wanting to take in pregnancy. Additionally, any quantity of alcohol is not recommended during pregnancy or for infants/children.)

Moving for Two (+100 Trillion)

There’s plenty of evidence to support the benefits of regular physical activity at all life ages and stages. Exercise helps to reduce inflammation and protects against chronic inflammatory diseases. It’s hypothesized that these particular benefits are related, at least in part, to positive effects of exercise on the microbiome. Studies are beginning to show that different forms of activity produce changes to microbiome characteristics. So, it’s plausible that in addition to the known benefits of moderate pregnancy-safe activity, a positive effect on your microbiome might be another reason to get moving while baby’s on board.

Oral Hygiene

Poor oral hygiene in pregnancy (such as smoking, and lack of regular brushing/flossing) is known to increase risk for preterm delivery. It’s hypothesized this is due to negative consequences on the oral microbiome that might also impact the gut microbiome – and overall health risks by extension. Avoid smoking or secondhand smoke, and practice healthy tooth brushing and flossing habits throughout pregnancy.

Stress Management

Chronic levels of physical or mental stress create an inflammatory response within the body. Which may increase risk of preterm delivery, high blood pressure in pregnancy, and diabetes. Gut microbes can also influence depression symptoms and mental responses to stress, which are also associated with preterm delivery. So it’s a two-way street. Focus on lifestyle and nutrition strategies for promoting a healthy microbiome and find meaningful ways to manage the stress in your life. (Such as physical activity, relaxation, meditation, working with a Registered Psychologist, and/or medical management in collaboration with your healthcare provider).

Early Infant Microbiome

The top 3 ways to promote healthy microbiome development and balance in your little one are skin-to-skin contact/Kangaroo care. As well as breastfeeding, and avoiding early introduction of solid foods.

Skin to Skin

Practice Kangaroo care (holding baby skin-to-skin, chest-to-chest) with baby as soon as safely possible following birth, and for as many hours as possible per day with your newborn.


While I am certainly a believer that a fed baby is best, research shows that most infants obtain all they need for optimal growth and development consuming breast milk alone until around 6 months of age. Breast milk contains a rich diversity of health-promoting microbes, which is not replicated in infant formula. If your baby does consume formula, consider choosing one that contains pre- and probiotics. Choosing to continue breastfeeding beyond infancy may have lasting health benefits to the microbiome, since the first 3 years of life are when the majority of its composition is established.

Proper timing of complementary foods

Early introduction of complementary foods (especially before 3 months of age, no matter an infant’s size/weight) is associated with increased risk for gastrointestinal infection and food allergy. From a gut maturity/microbial colonization stage, this makes sense. Wait until baby is at least 4 months old, but use his/her developmental readiness to decide when to offer complementary foods; for most infants this is around 6 months old. Baby should be able to sit upright in a high chair with good head and neck control, display an interest in food and eating, open her/his mouth when food is offered, and be able to move food from the front of the tongue to the back. (Spitting food back out reflexively indicates baby’s still not ready; wait another week or two and try again.)

Baby’s microbiome is also influenced by mode of delivery. (If safely possible for you/baby, plan for vaginal delivery to confer beneficial microbes from the birth canal). If your baby/toddler requires antibiotics at some point, consider supplementing with infant-approved probiotic drops in consultation with your baby’s healthcare provider.

Early Childhood Microbiome

It’s likely that the same lifestyle factors that are beneficial to the adult microbiome have a positive impact on the early development of your child’s, too. Opportunity to be physically active, good oral hygiene, and healthy foods will all promote establishment of a richly diverse microbiome. Offer mostly foods that are rich in nutrients and minimally processed, with plenty of variety.

Learn how to take care of mom and baby's microbiome - and important part of immune development and health through their lives! | Calgary dietitian Sarah O'Hara guest posts on Ignite Nutrition Blog about gut health in pregnancy


Cook, MD. Exercise and gut immune function: evidence of alterations in colon immune cell homeostasis and microbiome characteristics with exercise training. Immunology & Cell Biology. 2016; 94(2): 158-163.

Dunlop et al. The maternal microbiome and pregnancy outcomes that impact infant health: a review. Adv Neonatal Care. 2015; 15(6): 377-385.

Santacruz et al. Gut microbiota composition is associated with body weight, weight gain and biochemical parameters in pregnant women. BJN. 2010; 104: 83-92.

Tamang et al. Review: diversity of microorganisms in global fermented foods and beverages. Front Microbiol. 2016; 7: 377.

Ursell et al. The interpersonal and intrapersonal diversity of human associated microbiota in key body sites. Journal of allergy and clinical immunology. 2012; 129: 1204-1208.

The maternal microbiome plays a role in influencing certain pregnancy risk factors and infant health outcomes. such as increased risk for preterm delivery, preeclampsia, gestational diabetes, and excess weight gain in pregnancy. Learn to take care of you and baby's microbiome! | Calgary dietitian nutritionist gut health specialists Ignite nutrition guest post Sarah O'Hara

Categorized: Gut Health & IBS, Women's Health

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