Microbiome – Understanding what microscopic critters have to do with pregnancy, birth, & baby – Notes from Pathways Connect Kelowna May 2018 Gathering

Where do we even start?  This is a topic I could discuss for days. It is near and dear to me academically, clinically, and personally.  During my master’s degree in clinical nutrition, I studied and wrote papers on the gut-brain axis, the microbiome, and neurodevelopmental disorders (which are my permanent passion focus).  Clinically, I work exclusively with pregnant moms and babies, which is arguably the most crucial phase in microbial health and, therefore, all health. Personally, I had my daughter via C-section birth and that weighed very heavily on me at that time and now.  This is going to be a topic that I obsess about for the foreseeable future and likely beyond because I am not going to wait for anyone else to catch up.  I want what is best for my daughter. Because I care so much and read too much about this, it sometimes gets a little heavy. I am really not a pessimist on this topic. I am very hopeful and very proactive. So please, if you are feeling down, give me a loud sigh and I will know to lighten up.


The human microbiota consists of the 10-100 trillion symbiotic microbial cells harboured by each person. The bulk of it is found as bacteria in the gut but it is also made up of all of the bacteria, viruses, parasites, and fungi all throughout your body – in your mouth, on your skin, within your bowels, and surrounding your womb. The human microbiome also includes the genes coded within these cells, which are unique and very different from our own, but still impact our health status. 


There are at least 1000 answers to this question and multiple books, articles, and videos created to help explain why. I think this list from Turnbaugh gives a good overview of the impacts of the microbiota that are currently well understood.

The microbiome is important for:

  • Harvesting otherwise inaccessible nutrients/energy from the diet and synthesizing vitamins (without which we would die);
  • Xenobiotic metabolics and other metabotypes (without which we would die);
  • Gut epithelial cell renewal and protection;
  • Maturation and maintenance activity of the innate and adaptive immune systems; *This is a big deal!  Keep this one in mind as you continue.
  • Cardiac size (which I know little to nothing about, but I think is neat because it highlights how far reaching these impacts are); and
  • Behaviour and association with neurodevelopmental and psychiatric disorders (which is a BIG deal in terms of rearing children and maternal mental health).

Bottom Line: There are implications in absolutely every field of study in human health, from gastroenterology to metabolic to immunology to psychiatric to developmental to perinatal. These bugs matter and we are in this together.

At AltaVie, we focus on pregnancy and pediatric care.  So why are we talking about this?  We don’t prescribe antibiotics. We don’t work with C. difficile. What’s the deal?

Our in-utero, birth, and early development exposures have arguably the largest impact on our microbiome of any other experiences at any other time.  Vaginal versus section birth, antibiotic exposure (in-utero, at birth, or in the first 2 years), and breastfeeding versus formula all have well-established and lasting impacts on our microbiome and, as a result, our metabolic and immunologic health.

Although there is a growing body of evidence in support of the in-utero transfer of microbiota from the placenta and amniotic fluid to the fetus, many scientists consider birth to be the initial seeding of our microbiome. Your mother’s intestinal and vaginal flora, her diet, any medications she may have been on, your birth environment, and the type of delivery that brought you into this world all played their part on shaping who you are today, as well as your risk factors for many health conditions.  When a baby is born vaginally, their microbial cultures match those of mom. Within hours of delivery, the newborn’s “sterile” gastrointestinal tract is full of enterococcistaphylococcistreptococci, and enterobacteria. These early settlers set the stage; they alter the oxygen content and pH of the intestine, making it more fertile breeding ground for the anaerobic microbial colonization to come.  Eventually, it will be the BifidobacteriumLactobacillus, and Bacteroides families that will take favourable reign over a stable, rich, and diverse micro-kingdom.

Poor maternal diet, prenatal medication use (in particular, antibiotics and antidepressants), teratogenic toxin exposures, Caesarean-section deliveries, and formula-feeding are all commonplace in our modern world today. By no means am I saying that all these are evil. Each one has their place and the potential to save lives. However, there is one defining factor that they all have in common. They all disrupt the development of normal intestinal microbiota, a condition known as dysbiosis.

Intestinal dysbiosis predisposes infants to GI distress (which means more fussing for you), infections, eczema, and allergies. In the long-run, this early imbalance in tiny bugs plays a role in the development of allergies and asthma, susceptibility to infections, inflammatory bowel diseases, autoimmune conditions, diabetes, obesity, and certain types of cancer. Yikes.



Enough background. Let’s get practical.



  • Address any and all imbalances. If you have a history of antibiotic use, high chronic stress load, yeast infections, SIBO, IBS, or any other GI disorder, fix it.
    • Do your own research, take ownership, do the work, & seek professional help.
  • Plan a 3- to 12-month period focus on building your health BEFORE trying to conceive.
    • Take your high-quality supplements religiously.
    • Nourish your body with nutrient-dense foods.
    • (I know it sounds simple, but seriously.)
    • Build up your stress response.
    • Establish good sleep habits.
    • Increase your physical activity.



  • Eat well, when you can. It’s ok to “survive” early morning sickness, especially if you built up your nutrient stores during the preconception phase. However, as soon as possible, reestablish healthy eating patterns.
    • High vegetable fibre. Avoid excess sugar and starch. No trans fatty acids. Lots of good healthy fats and routine protein throughout the day.
  • Take a probiotic, at least during the last trimester.
    • I recommend Lactobacillus reuteri & L. rhamnosus, at least 1 billion CFU.
  • Consider GBS prevention and early conservative treatment.
  • Stress support. High stress negatively impacts your microbiome and your baby.
    • 15 minutes a day laying still with hands on belly listening to music.



Bacterial vaginosis, a form a dysbiosis, is known to create a slew of complications related to birth. I remember the first lecture I listened to when I learned this a few years ago and I was absolutely blown away.  An imbalance in vaginal microbes is associated with premature rupture of membranes, preterm delivery, and low infant birth weight, all which come with their own bag of worms. There is also now research connecting dysbiosis (not specifically vaginal) with diabetes (including gestational) and hypertension, which can cause high birth weight and low birth weight, respectively.  None of these are to be taken lightly, but fortunately, there is a very healthy and broad impact that you can have on them with diet and lifestyle. If you have watched the documentary Microbirth, you will remember that they cover what are considered the 3 biggest impacts on setting up a healthy microbiome for life.

  • – Vaginal Birth
  • – Early Skin-on-skin Contact
  • – Exclusive Breastfeeding


That's obviously not a complete picture, but in a nutshell, those are the biggies that can either work for or against you. To reiterate: I am never EVER here to shame anyone.  I know that 1/3 of babes in North America are born via CS and that not everyone can breastfeed. I am here to educate and empower so that we can do our best for those babes too.


Both mom and babe are very vulnerable to yeast infection during the first few months, especially if there was any antibiotic use during labour.  We also know from research in the fields of psychology and neurology that imbalances in our microbiome impact how we feel.  They alter genetic expression related to neurotransmitter synthesis and control.  There is a lovely cyclone effect of high cortisol negatively impacting healthy microbes and unhealthy microbes increasing inflammation and levels of cortisol, your primary stress hormone, so you can see how we get into trouble postnatally.


We best advice for postnatal mom is to keep it simple.

  • Set realistic expectations for yourself and ask for help.
  • Get outside! Be social. Seek care for any perinatal mood disruption.
  • Enlist support in HEALTHY meal prep and planning. Focus on high healthy fats and protein (not fast-acting, blood-sugar yoyoing, survival-mode carbs).
  • Take your supplements. It is very hard as a new mom to eat enough, let alone enough nutrient-dense, healthy foods.
    • Prenatal MVM
    • Omega-3 EFA (2 g/d – This is important for baby brain – baby’s and yours.)
    • Probiotic (continue Lactobacillus supports early on, take an antibiotic-specific probiotic if you were exposed during labour, and then follow up with a broad-spectrum, high-quality probiotic supplement).
    • Vitamin D (4000-6000IU/d so that you get some conference into breastmilk)
  • Sleep!



We know our birth choices are a big deal, but BY FAR, the most stabilizing and influential component to a healthy microbiome is breastfeeding.  It is restorative to a large degree.

  • Breastfeed
    • Do not “top-up” lightly. Mix fed baby’s poo microbes are more like those of formula fed than breastfed babes.
  • Probiotics
    • BioGaia for first 6-12 weeks
    • UltraFlora Baby or some mix with Bifidobacterium species afterward
  • Skin on skin. Lots. With mom & dad. & the dog. 😉
  • Stress Support – Early SNS & HPA development have a HUGE impact on future health and learning.
    • Consider colic
    • Address food reactions/sensitivities/allergies
  • Wait until 6 months or full developmental readiness to introduce solids
  • Avoid medications, especially antibiotics, ideally for at least 2 years.







The old adage earns a new layer of depth. The several trillion symbiotic microbial cells and their genetic material outnumber our own by large margin. And guess who feeds them?  If you consume a diet high in sugar and saturated fat, you are feeding the wrong crowd.  The garden that you water will be the garden that grows!  You are providing the fuel source, so choose to preferentially feed those that are helping you out.  What does that mean in the real world?  It means a diet low in sugar, void of trans fatty acids, high in fibre, high in vegetables, with ample healthy fats. Yup, that’s it. Grandma was right. Eat your broccoli.


PROBIOTICS.                      Common. You knew I was going there.

You knew I was going to come around to probiotics. They are the most obvious way to directly influence the bacterial balance in our intestinal tract and they are just so darn popular these days.  I think part of the reason that they have gained in popularity so quickly (besides the MOUNTAIN of research supporting their usage) is because our society loves the idea of being able to take a pill to solve all our problems.  It seems deeply ingrained, Inception-style. Well, if that is your approach, I have good news and bad news. The bad news is that taking a probiotic is not going to rapidly and magically undo all of your previous chemical exposures and it is NOT going to override a crappy diet. The good news is, it is going to do a lot of good.


Coming back more specifically to pregnancy and birth, mom supplementing with specific strains of probiotics during pregnancy (especially during the third trimester) will help colonize her newborns GI tract.  Oral probiotics can restore normal vaginal flora in women with bacterial vaginosis and GBS. This is important not only for the infants initial seeding exposure, but studies are even showing that it is associated with premature rupture of membranes, preterm delivery, and low infant birth weight. So which probiotics should you take? Lactobacillus rhamnosus is a good place to start; this strain, when taken during pregnancy and continued on for the first 6 months, can decrease the risk of eczema by about 50%.



Don’t take my word for it. Educate and stand up for yourself. Explore your options.

  • Challenge GBS testing protocols, IAP, elective CS, any and all interventions (so you at least know what you are getting into).



If it is at all within your capacity, I urge you to breastfeed your babe for as long as you can reasonably manage.  Breastfed infants have microflora dominated by the Bifidobacterium species, whereas the microflora of formula-fed infants shows considerably less ideal species and less consistent community organization. As you have figured out by now, this impacts our health long-term. Not only does breastmilk have all of the nutrition that your baby needs, it delivers immune cells, enzymes, and oligosaccharides to your baby. Breastmilk contains both commensal bacteria which are important for baby’s gastrointestinal microbiota development, as well as prebiotics and the preferential fuel sources for the ideal bacterial to thrive. Breastfeeding reduces the risk of allergies, autoimmune conditions, obesity, inflammatory bowel disorder, and potentially even cancer.  Plus, it is cheaper.

How long do you need to breastfeed for to confer these benefits to your children? The World Health Organization (WHO) urges mothers to breastfeed for two to five years.  If that sounds daunting, a recent article in JAMA Pediatrics found that many benefits were established by seven months. This is good, considering baby should be exclusively breastfed (or formula-fed, if unable) for six months. No early food intros!



Address imbalance and proactively prevent excessive stress for mom and babe. The impact on the microbiome, inflammatory load, learning capacity, overall health, and a thriving life experience are huge.



Unless you have a very vulnerable preemie, don’t be too paranoid about your baby getting dirty and being exposed to bugs. This is the world we live in and most early exposures actually have a positive impact on baby’s immune system.



I have no clever conclusion. I know this is way too long for a 45-60-minute talk, so I will leave it at this and we will cover what we can. Hopefully, we will dive into some tangents that you find interesting as well.


About Amanda Stevens

Dr Amanda Stevens is a chiropractor and clinical nutritionist whose practice focuses entirely on paediatric and maternity care. She works with families through pregnancy and onward to infancy and childhood. She is passionate about thriving early development and a uses a multimodal approach for problem-solving and wellness care that is specific to each patient that walks through the door.

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