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Cultivate, Preserve, and Protect your Baby’s Microbiome

how to give babies healthy gut flora

Cultivate, preserve, and protect your baby's microbiome from the start

Cultivate, Preserve, and Protect your Baby’s Microbiome

There is an entire universe living inside your digestive system, and it is absolutely essential to your overall health, vitality and well-being.

I talk with my clients a lot about intestinal microbiome health, and you may have noticed that I always recommend fermented foods containing probiotics as part of a healthy diet as well. New studies are coming out all the time that show the connection between our gut biome and all of our body’s functions.

Furthermore, the health of your microbiome is set very early on in life, and among other things, influences the development of your immune system. If your gut biome is disrupted or does not develop properly early on, it can lead to all kinds of issues related to inflammation, allergies, food intolerances, and autoimmune diseases. It can impact your hormones, your fertility, your weight, even your mental function. New connections between gut health and overall systemic health are being discovered all the time.

If you’re pregnant, you have an extra responsibility to give your baby’s intestinal microbiome the best possible start. Just like everything you’ll face as a parent, things may not always go as planned. You probably won’t be able to avoid all potential disruptions to your baby’s microbiome, but simply being aware of those disruptors and knowing how to reduce their impact can give your baby a powerful start to a lifetime of good health.

Biggest Risks for Baby’s Microbiome

The biggest risks to your baby’s intestinal microbiome health are:

  • Antibiotics in pregnancy/labor or while breastfeeding
  • Cesarean birth
  • Lack of breastfeeding for at least the first 4 months of life
  • Antibiotics given to your baby in the first 2 years of life

You may notice that all of these risks are pretty common. Over 30% of births in the US are by cesarean. Not all moms are able to breastfeed. Sometimes the risk of deadly infections requires antibiotics. But in each of these scenarios, there are things you can do to help counter the negative effects of microbiome disruptors.

What can you do?

First of all, you’ll want to do everything possible to maintain your own health while pregnant to help you avoid these risks in the first place. Protecting the health of your OWN gut is an important first step, and a healthy diet is the best way to do that.

Here’s what your meals should look like while pregnant:

  • Fermented vegetables like kimchi, sauerkraut, and naturally fermented pickles, or a fermented beverage like kefir water or kombucha. Make sure your fermented vegetables are refrigerated and do not contain preservatives or vinegar.
  • A serving of high quality protein such as 100% grass-fed beef, lamb, bison; wild caught fish and seafood; organic, pasture-raised chicken, turkey, duck, pork, or eggs. Purchase the highest quality organic protein you can afford.
  • Clean fats from coconut oil, grass-fed butter or cultured ghee, avocados, olive oil and/or raw nuts & seeds.
  • Several servings of colorful, varied organic vegetables, served raw, steamed, or lightly sauteed.
  • A large mug of bone broth.


Start taking a probiotic now! There are possible complications associated with pregnancy that may require you to take an antibiotic, which can destroy the microbiota in your gut biome. Taking probiotics will not only help replace your gut flora if that happens, but a healthy gut biome bolsters your immune system, which may prevent you from contracting an infection requiring an antibiotic in the first place.

If you do end up needing to take an antibiotic, then rejoice because you’ll have been taking probiotics all along, and you’ll just continue taking them now. If you are just now reading this post because you’ve been prescribed an antibiotic, start taking a probiotic right away (and continue taking it throughout your pregnancy and while breastfeeding!).

This is the probiotic I recommend if you have to take antibiotics: MegaSporeBiotic (Click on REGISTER in upper right corner, then click PATIENT, then enter code SJS2018 when asked for Patient Direct code to order). Start with 1 capsule daily and work up to 2 capsules daily over a 7 day period. Continue on 2 capsules per day.

Add in Saccharomyces Boulardi: 2 capsules per day. S. boulardii is actually a beneficial yeast rather than a bacteria, so it’s particularly useful during antibiotic treatment because the antibiotics can’t kill it. S. boulardii is also preferable under these circumstances because there’s no risk of it harboring genes for antibiotic resistance and later transferring those genes to pathogenic bacteria.

Also include glutamine powder: 3 heaping teaspoons mixed in water, three times daily + Collagen Powder: 1 tbsp, 3x/day on empty stomach to heal the gut and support the regrowth of your beneficial intestinal flora.

Increase Vitamin D to 10,000 IU per day.

You will also want a quality prenatal vitamin! My number one recommendation is the Prenatal Pro Essential Packets. These all-in-one prenatal packets contain your prenatal multivitamin, a broad-spectrum multimineral and a high quality omega-3 fish oil. The prenatal packets contain potent levels of all necessary vitamins and minerals that play a part in the intricate processes of pregnancy.

Reduce Toxins

Environmental toxins like heavy metals, pesticides, pollutants, and endocrine disruptors in plastics also impact the health of your gut. Your intestinal microbiome is one of the first lines of defense your body has to filter out harmful toxins. The more toxins you (and your baby) are exposed to, the harder it is on your gut microbiota. It’s impossible to avoid all exposure, but there are many steps you can take to reduce the toxins in your home, and to reduce your exposure to them elsewhere as well:

  • Switch to stainless steel or glass storage containers for your food and beverages. Drink lots of filtered water to help flush your system regularly.
  • Avoid canned food completely, and packaged food whenever possible.
  • Get rid of non-stick cookware and switch to cast iron, stainless steel or ceramic cookware instead.
  • Buy organic fruits, vegetables, and animal products. Purchase the highest quality food you can afford, from a local organic farm if possible (if the animals ate it, you’re eating it too).
  • Switch to soaps, shampoos, and cleansers that don’t contain phthalates, parabens, or sodium lauryl sulfate. Check labels at your local health food store—these are actually pretty easy to find. The EWG Skin Deep website is a great resource for this.
  • Avoid areas where you might be exposed to any chemical fumes, like auto-repair shops, hair and/or nail salons, freshly painted rooms, etc.

Cesarean Births and Vaginal Swabbing

One important way your baby will get exposure to microbes is in the birth canal, but babies born by cesarean miss out on this critical exposure. A procedure to correct this, called Vaginal Swabbing (or Microbiome Seeding) has become popular in recent years, and it’s definitely something you’ll want to talk to your midwife or OBGYN about.

The process is pretty straightforward: before the c-section takes place, a sterilized piece of gauze is placed in the mother’s vagina and left in place for about an hour. The gauze is removed prior to surgery and kept in a sterile container. After the baby is born, the gauze is wiped over the baby’s face (including eyes, nose, and mouth) and all over the baby’s body, to simulate a vaginal birth.

One problem with this is that many c-sections are unexpected—so even if you’re planning a home birth, I recommend talking to your midwife and letting them know you want to do a vaginal swab in the event of a c-section. That way, if there is an expected complication during delivery, your midwife will know to take a swab before surgery if there is time to do so. Even if you aren’t able to swab, you can make sure your baby is exposed to beneficial bacteria through immediate skin-to-skin contact and breastfeeding.

Check out this resource from BellyBaby for detailed Vaginal Swabbing instructions.

What about Preemies?

It’s important for you to be prepared for the fact that not every birth goes as planned. You can do everything “right,” and you still may not have the birth experience you envisioned. If your baby is born early via cesarean, you may not get the chance to do a vaginal swab, or even to have skin-to-skin contact and breastfeed immediately. If your baby is early or there are other complications, you may be in for some unexpected time in a sterile NICU (Neonatal Intensive Care Unit) environment, and may not even be able to hold your baby right away.

It’s important that you talk to your midwife, doula, and/or OBGYN about this possibility because there are still important steps you can take to cultivate a healthy gut microbiota for your baby. Many NICUs are giving preemies probiotics these days, but it may be something you have to request. Once your baby is ready, you can still give daily “kangaroo care” (where your infant is cuddled skin-to-skin on you or your partner’s chest and secured with a blanket, infant carrier, or wrap) to give your baby exposure to healthy microbes.

Remember that even if you can’t have a “perfect” birth experience, there are ALWAYS things you can do to give your baby the best start possible!

After your baby is born

If at all possible, breastfeed exclusively for least the first four months. Your baby will get exposure to important microbes from your breast, so even if your baby has trouble latching and you need to supplement with bottle feeding, make sure to continue to offer your breast, even if your baby only latches for a moment or two.

If you do bottle-feed, choose glass bottles. Even BPA-free plastic bottles contain chemicals that can leach into breast-milk or formula.

You’ll also want to give your baby as much skin-to-skin contact as possible, and encourage your partner to do the same. Daily kangaroo care is important for every baby’s health and well-being, and the skin-to-skin contact gives your baby exposure to a variety of healthy microbes. Plus, babies LOVE it!

If your baby was born by cesarean section or either of you have to take antibiotics, I highly recommend supplementing your baby with infant probiotics: ½ teaspoon daily. Breast-feeding mothers can add powder to expressed milk or place small amounts on nipple or finger.

What if I can’t breastfeed?

Breastfeeding is not right for every mom and baby. If, for whatever reason, you decide that formula is necessary, here’s the formula I recommend. Also be sure to provide plenty of skin-to-skin time/kangaroo care multiple times per day (feeding time is the perfect time for this), and to supplement with the infant probiotics listed above (you can add it directly to formula).

In a nutshell

  1. The gut microbiome is absolutely critical to your baby’s life-long health.
  2. There is plenty you can do before and after your baby is born to protect and preserve the microbiome
  3. Probiotics, breastfeeding, and reducing exposure to toxins are all powerful ways to nurture and protect your baby’s microbiome..

Let’s Talk!

I’d love to use this space as a forum of sorts, providing inspiration and community among my readers, so … I want to hear from you!

Are you pregnant now, or do you have a new baby?

Did you/do you take a probiotic while pregnant?

Have you or your baby had to take an antibiotic? Were you able to supplement with probiotics?

Spread some gut health lovin’! Sharing is caring, and I bet you have some friends who would love to read this too :).

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Let’s Meet!

Looking to have a more in-depth conversation about you or your baby’s gut biome health? Schedule a consultation with me!

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