Bacteria & Birth: Why They’re Good Together

Heather Dessinger

This post contains affiliate links.
Click here to read my affiliate policy.
bacteria and birth

No Daddy’s In The Room, Please

I’m sure you are mature enough to handle this. You probably caught your firstborn child in your rough, manly hands and then nuzzled him/her against your chiseled, manly chest while giving your gorgeous wife a postnatal foot massage. It’s not you I’m worried about.

Truth be told, I’d just be more comfortable if I could talk with my fellow mamas alone for a few minutes. So help me out here and pretend your supersecret Batman pager went off and slip out quietly, okay?

(Scans room) . . . . Alright mamas, looks like it’s just us now. A couple of weeks ago I made a promise to tell you how to promote healthy digestion and immune function in babies. I am going to keep that promise today and will be using lots of fun words like vagina, cream applicator, and suppository. Bless your heart, you deserve some practical DIY info after listening to me rave about letting your baby eat bugs. So let’s get down to business, shall we?

Wait, Why Does This Matter Again?

The fancy term is Micrometabolic Imprinting in Infancy, which basically says that despite what Purell would like us to believe, we need bacteria in and on our bodies to survive. You can read more about this symbiotic relationship here, but I’ll give you the the cliff notes version:

When they pass through the birth canal, babies get a “first meal” of good and bad bacteria from their mother. (If they are delivered by caesarean the bacterial profile changes with less beneficial and more pathogenic stuff . . . a topic for another day.)

When we have primarily beneficial bacteria in our birth canals it provides babies with the strains they need to digest food, keep pathogens in check, support the immune system and even create vitamins such as K2. On the other hand, pathogenic bacteria can cause diarrhea and colic in the short term, with more serious effects later on.

“Long-term consequences of neonatal intestinal dysbiosis may include allergies, asthma, increased susceptibility to infections, inflammatory bowel diseases, diabetes mellitus, obesity, and colon cancer.

Olmstead, Snodgrass, Meiss and Ralston:  Micrometabolic Imprinting in Infancy

So despite the widespread belief that everything within a 100 mile radius of our newborn baby should be sanitized, boiled, or wrapped in plastic, introducing bacteria is really a vital milestone in promoting a baby’s health. But not just any bacteria! GOOD bacteria!!

Unfortunately, we live in the age of stress, antibiotics and junk food, so a birth canal populated with beneficial bacteria is not something most of us should take for granted (including me). So on your baby’s birth day why not give them the gift that will last a lifetime . . . a properly colonized birth canal. Yep, I really said that. Isn’t it a wonder Hallmark hasn’t snatched me up to write greeting cards by now?

Oh, you want suggestions for how to actually do this??? Well, here you go!

Easy At-Home Methods for Introducing Beneficial Bacteria to the Birth Canal

Many moms choose to do one of these methods on a daily basis in the last weeks of pregnancy:

  • Insert unpasteurized, plain yogurt or kefir into the vagina with a small spoon or spatula or v@ginal cream applicator. Insert at night and wear a pad.
  • Insert a probiotic suppository using an encapsulated probiotic supplement such as Biokult. No need to take the probiotic out of the capsule

Ideas For Nurturing Beneficial Gut Flora After Birth

  • Don’t bathe your baby too often! Newborns that have passed through the birth canal have their mothers good AND bad bacteria on their eyes, mouth, ears and hands that go in the mouth. As mama breastfeeds she will pass on antibodies to fight the pathogenic stuff. However, if this bacterial mix is washed off and the baby acquires a different set of pathogenic microbes (say if the baby is taken to a nursery and washed, then exposed to a blanket that has foreign pathogens on it), the process for keeping pathogens in check becomes more complex. Baby has to pass the microbes to mama, who makes the antibodies and passes them back to baby. It’s a lovely system when babies get older, but in their first days it’s better to avoid that scenario and allow their bodies to recuperate from the birth experience.
  • If at all possible, breastfeed. Studies show that the beneficial strain bifidobacteria is predominant in breastfed infants, while formula fed infants “possess a more haphazard microbiota that includes Bacteroides,staphylococci, E. coli, clostridia, and bifidobacteria.¹  
  • And take your probiotics! Mothers have specific immunological mechanisms that ensure the transfer of their own enteric bacteria to their babies, so make sure you’ve got the good stuff to give!

Next time we’ll talk about nourishing older babies and toddlers with yummy, probiotic rich foods (Coconut kefir AND healthy soda? Oh my!)

What did I miss? What do you want to know more about?

Related Posts

About HEATHER

Heather is a holistic health educator, herbalist, DIYer, Lyme and mold warrior. Since founding Mommypotamus.com in 2009, Heather has been taking complicated health research and making it easy to understand. She shares tested natural recipes and herbal remedies with millions of naturally minded mamas around the world. 

Leave a Comment

85 thoughts on “Bacteria & Birth: Why They’re Good Together”

  1. Yes! I always suggest colonizing the birth canal too…in just those same ways 🙂 LOVE how you spell v@gina, btw! 😉 I also suggest applying some powder probiotics (both native and transient) to the nipple in order for baby to ingest them from the start too. And having an eye dropper of cultured veggie juice to put a drop in baby’s mouth is something I will do as well. Great article….as always! I always enjoy your introductions! 🙂

    Reply
    • Ah yes, don’t want to get banned by Google, do I?!?! I remember you mentioning that eye dropper idea before. So brilliant! Using it in a future post 🙂

      Reply
  2. Sometimes, there’s a little part of me that wishes I had known all of this before I had my little guy. :’) But, mostly, I’m just amazingly excited to do better the 2nd time around. And, there’s also a lot of “Man, I wish Mommypotamus was my neighbor.” Thanks Heather! Enlightening, as always!

    Reply
    • I didn’t know this the first time around either, Heather! Don’t worry, there are ways to promote good bacterial colonization in older children. Stay tuned!

      Reply
  3. As always, awesome post. I wish more people were aware of the importance of colonization at birth. Thank you for putting this out there!!!

    Reply
  4. Great article! My son will be 11 this winter and I’m on a 1-2 year plan for another child with my new husband. It’s amazing how much more information there is now compared to when I was pregnant in 2000. Maybe not more information, but more accessible. Thanks for the info!

    Reply
  5. Heather – You are such a hoot! I hope you are coming to the market this week. How hard would it be to get you guys to move to East Texas? Don’t you want to come to the country?
    Miss Sky should have a very healthy immune system in spite of her cesarean start. She definitely doesn’t get bathed “too” often, and makes a point of adding to her GI flora on a regular basis. She was caught munching on goat pellets a couple of weeks ago. Not much I could do after the fact. Of course she does eat well, too, plenty of raw milk and all : )
    Great post, thanks for the laughs.

    Reply
    • Ramy – Yes, we’ll be there! And I think it would be very hard to get Daddypotamus to move to the country, but we’d love to visit! And eek! Goat pellets!!! I found Micah splashing in the toilet a few days ago . . . not much I could do either, lol!

      Reply
  6. I do not have any children yet, but plan to in the future- i find this article very good to add to my bank of knowledge. Just one question – so once they baby is born, do you just recommend that they be wiped down or should they just be left as is for a few hours? I guess since I am inexperienced here I am abit unsure of how this should work to leave the beneficial bacteria from the canal on the baby..

    Thanks!

    Reply
    • Directly after a baby is born, the baby should be placed on the stomach or chest of his mother if possible. Yep, he’ll still be covered in fluids and possibly some meconium. A mother’s instinct in this situation will be to wash her baby. A midwife or doctor should provide a thin, recently sterilized blanket or towel to help keep the baby warm and for the mother to wipe him clean. Besides preserving whatever bacteria were already on the baby, this is an important part of post-birth bonding between mother and baby. Wiping the baby with a clean damp rag to wash him should be enough of a bath in the first couple of weeks, done only as needed. I hope I’ve answered your question. 🙂

      Reply
  7. I’ve always had success with getting rid of v@ginal infections (that’s fun!) using a clove of garlic. I usually bruise or slash the outside of the clove to get more juiciness, it doesn’t burn, and insert. You know it’s working when you can taste it in the back of your throat 🙂 This would be a great first step in improving your bacterial terrain. Maybe do this for a week then follow up with the probiotic introduction. A midwife I know uses a similar protocol to minimize the chances of GBS. Of course limiting sugar and refined carbs is important, too, or you’re just feeding the bad bacteria while you try to compete for real estate with the good. And lots of probiotic foods and drinks like Bubbies sauerkraut or pickles if you’re not up for making your own, water and/or dairy kefir, fermented salsa (super easy!), etc. If you’re concerned about being GBS+ or having bad bacteria issues you might look into a probiotic enema. Haven’t done one myself but would seriously consider researching it if I was pregnant and thought I had issues. What better way to wash away the bad and replace it with the good in an area that’s hard to reach by mouth 😉

    If I had no reason to suspect bad bacterial overgrowth in my body, such as not having digestive issues, eczema, or fungal/yeast problems (e.g. athletes foot/yeast infection), then I might hold off on introducing the probiotics in either powder or fermented food form until the baby is a little older. How much older, I don’t know. But we know so little about what bacteria strains make a healthy baby gut that I wouldn’t want to mess with it too much. That being said, my last one was born via cesarean and while I did B. infantis and possibly L. reuteri (he had reflux) when he was a few months old, if I knew what I know now and it had been an option I would have dosed him with that ASAP and been more consistent. If I had to do it again or was making recommendations to someone else who has to have a cesarean birth I would request antibiotics to be given to me at the time of surgery instead of an hour before which is becoming new protocol (reduces mom’s risk of infection some) and request immediate skin-to-skin in the OR before baby is taken to the warmer to be wiped down, measured, etc. That might allow some improved chance of picking up mom’s skin flora instead of the hospital’s towel and glove flora (eww). There, that can get you started on your cesarean birth post 🙂

    Reply
  8. Great post, except for your squeamishness and/or prudishness. What gives? You have a vagina. Women have vaginas. What’s the big deal? I subscribed to your blog because I expected enlightened discussion, and for the most part, that’s what you deliver. But seriously, censoring the word vagina? Seriously?! Like it’s a nasty, dirty thing that God mustn’t hear you type? Or something?

    Reply
  9. PS: no need to publish my comment. I’m not trying to call you out in public, just seriously puzzled and dismayed by the censorship and expressing that via comments here.

    Reply
    • Hi V! I went ahead and approved your comment but greatly appreciate your sensitivity in not wanting to call me out. Knowing a persons motivation is not to wound makes critiques so much easier to respond to!

      Anyway, truth be told, I wasn’t intending to censor. Although I did up front mention that I get a little nervous about using the word in public, that’s typically when I’m standing in front of a room full of husbands and wives teaching a class. Public speaking is intimidating already and the fact is, I feel a little funny about it . . . . mostly because I see discomfort wash over the faces of my class. I am very sensitive to how my words affect people, and this post was just an honest reflection of that.

      However, the spelling in this post was largely an attempt not to get flagged as an “adult” website by Google. There are just so many times you can use the word before hey notice!

      Reply
  10. I’m confident that your blog is a long way from being classified as “adult” by the Google crawl-bots. Your post (and the excellent discussion) on circumcision and your posts about breastfeeding and so on … provided a wealth of keywords that allow the search engine to classify your blog accurately. You really have nothing to fear here, so here’s one voice encouraging you not to treat the female reproductive system like a dirty word. You didn’t spell it p3nis in your post about circumcision, did you?

    Reply
  11. Your use of vagina spelling made me laugh! Thanks for the info. I love this blog and find that my hubby reads it often! But, he probably didn’t read this one. Just a quick funny story about vaginas. We were at birth class while Angela Friesen was teaching for Donnellyn and she started the birth slide show. The first pic was a lady’s vagina upside down since she was in the “all fours” position. My husband looked at me and said is that….I said yep and we both just lost it in the laughing dept. We were laughing so hard I couldn’t breathe. Angela had to ask us if we were okay. It was hysterical and we laugh everytime we think of birth class!

    Reply
  12. I was wondering if you suggest not washing a newborn for the first 24 hours with anything even water? I had a waterbirth with my last baby and I was wanting to do a waterbirth for this one due in January. Not sure now if it would be better to get out of the tub for the birth or even do without the tub for laboring. Just curious of the effects of being immersed in water, even dechlorinated water and the colonization of the good flora. Especially since I know I am still working on improving my gut health with the Gaps Diet (we started 2 years before I became pregnant with #3). Thank you!

    Reply
  13. Hi Karen! I have two waterborn babies . . . and hope to have at least one more! I don’t have any studies to back this up, but I think that if you don’t scrub them or put soap on them a lot of the bacteria will stay intact. My reason for thinking this goes back to a post I did on Vitamin D. Our skin makes vit D from the sun but it doesn’t absorb it right away. It actually takes 24-48 hours after we were in the sun for the bloodstream to reach it’s highest levels. Unfortunately, most of us shower right after being outside and wash all that good Vitamin D off! I was distressed when I read this (who wants to go without a shower for two days!!!) but then I learned that you can rinse with water and just use soap on the groin/armpit areas and most of the Vitamin D will stay intact. As long as the water exposure is brief I’d say it’s a similar scenario with birth.

    Reply
  14. Hi, glad you’re getting this information out there. I also read, in the GAPS book, about smearing yogurt on your armpits and nipples. I tried it (I’m 6 mo pregnant) and it had a cool side effect: I didn’t need to use deodorant anymore! I’ll definitely be smearing and inserting the yogurt as I get closer. Thanks for your post

    Reply
  15. So let’s talk probiotics. What kind and how much and when? (the kind I’ll need to take orally after birth. Or should I start taking them now at 36 weeks?)

    Reply
  16. I was just thinking about all this last night! I found this article: http://articles.mercola.com/sites/articles/archive/2012/06/25/mmr-vaccine-caused-autism.aspx?fb_ref=fbLike&fb_source=home_oneline

    About halfway down the page the article starts talking about how gut flora affects the brain, and boy was that an eye-opener!

    After I read that I started wondering how on earth I can go about making sure my kids have healthy gut flora, and now this morning you post this…. I guess this won’t help the ones who have already been born, and I’m not having any more, but I can pass this on to everyone I know who IS having more kids….

    Reply
  17. This is great! Thanks. I’ve been wondering about this, because my youngest had colic terribly, and I’d like to avoid it this time. I wish I knew all I know now about gut flora! Thankfully, only 5 weeks on GAPS has already reversed several of his allergies. Now, with a baby coming in about 3 months, I want to make sure the baby gets a good dose of good bacteria when he’s born!

    Reply
  18. Great post! You actually don’t need anything fancy to insert yogurt, you can just use a needle-less syringe. If you buy Green Pastures fermented cod liver oil in liquid form, you will have the perfect applicator for this!

    Reply
  19. So, when inserting a encapsulated probiotic, does it matter the kind? I mean, obviously a high quality one, but are there particular kinds that you can insert? I’m pregnant, and I don’t want to stick something up there that I’m not supposed to!

    Reply
  20. Hi Heather! This is so great… Thank you. What would your recommendation be if Strep B Positive caused antibiotics at birth? I am hoping to avoid them this go round… But in the case I can’t… What would your recommendations be? My first child is the textbook case of damaged gut flora and the allergies… Had I only known 🙂 Thank you!

    Reply
  21. Hi Analise! I am not a medical doctor and am not qualified to give medical advice, but I was GBS+ with both my pregnancies. My midwife the first time advised me to do a chlorahexadine wash. I didn’t know about proper colonization back then so I said okay. For my second pregnancy my new midwife (the old one retired) was fine with me doing garlic and probiotic suppositories to increase my good bacteria count naturally so that they would naturally keep the Strep B population low. I’d eaten fantastic during my pregnancy and incorporated a lot of immune boosting foods toward the end, so I felt pretty confident that my baby would be fine with the exposure (after all, it’s a pretty normal part of vaginal flora for many women around the world)

    We skipped antibiotics/washes and just watched my son closely after he was born to make sure there were no complications. We delayed cord clamping to make sure he had the full infusion of everything he needed to start life, and everything worked out okay for us. I can’t say what decision is right for another family, but that’s what we felt the most peace about after talking things through with our care providers.

    Reply
  22. I did a clorahexadine wash while in labor with my second. She ended up with GBS (late onset though) – and spent 2 weeks in the hospital. I truly believe that occurred because I didn’t understand that she would get her first gut immunity from me. I made it sterile- which made her susceptible a week later.

    Reply
  23. Me too! Catching it was a God thing. They tried to send me home because she didn’t seem “sick enough” – but my mommy gut said something was wrong (I’m NOT a rush to the doc mom). Next day after her blood work came in (they had admitted her and started her on IV antibiotics) – I was told IF I had taken her home- she probably wouldn’t have made it- because her count was MUCH higher than what was apparent by her symptoms. Since she was a full week old when she got sick- I was told the chances of it being because of delivery were very very slim. That it’s more likely that it was just from contact with me and her daddy (we were the only ones around her after birth till 1 week). Based on what I know now- I think she didn’t get a good colonization during birth- and didn’t have anyway to fight it off later. As a side note- I had NONE of the markers for high risk. My GBS was low (positive- but not high numbers-), no fever, no long term ruptured membrane (waters broke right at delivery). This was before my “real food conversion”. I’m pretty hardcore about fermented foods now- and their importance. Esp being pregnant again.

    Reply
  24. I’m definitely going to pin this for baby #2! What are your thoughts on babies getting washed right after birth. My son was given a bath about 30 minutes after he was born. Would you suggest waiting to bathe a newborn and for how long. Maybe with the next I’ll just have him or her wiped with a warm wash cloth and not use soap.

    Reply
    • Good question, Carissa! In my book on feeding babies I recommend that parents NOT bathe their newborn babies! Soap is very alkaline and destroys not only the good bacteria but also the acid mantle that deactivates pathogens on contact. I rinse with warm water and only wash the diaper area regularly – the rest just gets cleansed as needed. Hope that helps!

      Reply
  25. Thank you for this, Nicole Rice! I admit I am surprised that the good bacteria from your breast milk and the GBS didn’t cancel each other out but it is very helpful to have this story to share with other moms. I have met moms who did not test positive for GBS whose children ended up in the hospital with it. And then there are moms like me who were GBS positive through multiple pregnancies with no negative effects. I don’t think the association is as linear as mainstream protocols would indicate.

    Reply
  26. One final thing to consider is what types of first foods to offer. According to Dr. Campbell-McBride, bone broths and stewed meats are ideal because they help coat the gut and prime digestion. The Weston A. Price Foundation also has some good suggestions, but if gut flora is an issue I’d probably start with Dr. Campbell-McBrides recommendations. More on getting started with solids at https://mommypotamus.com/when-should-my-baby-start-solids/

    Reply
  27. Heather, Did you already talk about promoting good bacteria in older children? Just wanted to make sure I didn’t miss it. Mine are 9 and 5. I open a floragen4kids capsule into whatever I can, but I never really know how much they are really getting, especially if they don’t finish the drink i hid it in. just ordered some probiotics that come in a little pearl that they can swallow, I do their omegas that way too, but looking to see what else you recommend. Thanks!

    Reply
  28. Thanks. My daughter is nearly 4, food allergies, eczema, and soft poo from day one. I was given loads of antibiotics during labor and for a few weeks after, while breast feeding. I would like to reverse her gut flora. Thanks for the info and any more you post.

    Reply
  29. I don’t have kids yet and am not pregnant, but I just wanted to drop a comment after perusing your site for hours on end… thanks so much for having all this information out there. I feel so lucky to have waited to have children, because now I am learning so much important stuff! You and Wellness Mama changed my mind about circumcision, by the way. Previously, I would have gone ahead and done it because my husband is, and he’s never had any problems, so he would have been okay with it too… so thanks, on behalf on my future sons.

    Reply
  30. My babe broke out with a rash with pureed beef and spit up non stop after a runny egg yolk 🙁 Not sure what to do but give fruit/veg for first foods now…

    Reply
  31. I did started with broth and egg yolk I do some vegetables and lil bits of meats and we been fine. i also give him infant probiotics and fermented cod liver oil and sometimes coconut oil he loves both flavors. when he gets somo diahrea or vomits I up his probiotics right then and he gets better the same day. and i eliminate any food that caused it for at least 2 weeks

    Reply
  32. Heather, I was wondering how a water birth affects the babies first dose of beneficial bacteria since most of us have chlorinated water? Thanks

    Reply
  33. Yikes, Christina Smith! Have you done a skin test with him to see if he’s okay with broth? Dr. Campbell-McBride says it’s so good for babies who are showing a tendency toward food sensitivities.

    Reply
  34. He is okay with chicken broth 🙂 And I’ve been giving him Baby Biotic. Just not okay with the runny eggs and pureed beef so far. He did well with avocado and banana. Not too sure where to go from there… maybe a cooked egg yolk?

    Reply
  35. If it were me I’d pass on the yolks and consider maybe some chicken. Also, I’d do a skin test on the beef just in case it was something else that caused a reaction that day. It COULD be the beef, but since it is not all that allergenic it might be worth double checking.

    Reply
  36. I was wondering about the quote: And take YOUR probiotics! Mothers have specific immunological mechanisms that ensure the transfer of their own enteric bacteria to their babies, so make sure you’ve got the good stuff to give!

    I’ve heard the probiotics don’t get passed through breastmilk to baby, but your quote seems to suggest otherwise? I’d love to hear your insights! I’m trying to decide whether to give my baby (4 weeks) probiotics or perhaps she gets them through my taking them.?

    Reply
  37. Now that your tea is hopefully taking effect let’s think on that last thought for a moment. – Direct vaginal contact with chemicals, dyes and perfumes. If you apply Aloe Vera gel on the affected areas it can help reduce the itching and burning caused by the infection.

    Reply
  38. Vanessa Peng Lutz – I’ve been thinking I need to do a whole series on birthy stuff. Vitamin K shot, eye ointment, etc. Will add it to the list!

    Reply
  39. Thanks! I know the saying, ‘Do better when you know better’, but I STILL wish I had known with my three kids… We did no baths and had home births, but we could have done better. Thanks for the wealth of knowledge.

    Reply
  40. Jennifer Wentzell – I feel the same way! I did things differently with each of my births due to what I’ve learned over the years. <3

    Reply
  41. I have a quick question… I know you said you’d get to colonizing c section babies later, but I would love a tiny bit of info on that now. My sister just had to have a c section and on top of that her baby had to go to the NICU, so she didn’t even get to SEE him for like 5 hours, let alone spend time skin to skin. He’s big and full term and otherwise healthy, but he had a growth in his lungs that was inhibiting his breathing, so they had to take care of that. She’s been pumping (and producing plenty, esp for a brand new first time mom, she was pumping 2oz at a time the first day!) so I can only imagine that once he can eat he’ll get breastmilk, but at the moment he is being fed through his IV because he’s intabated. So he’s going to need plenty of help once he gets out of the hospital. My sister is totally on board with all this stuff but is understandably too tired and overwhelmed to be thinking about these things right now, so what should I tell her to give him? Just regular kids probiotics? Any other tips? Thanks, and btw awesome post! I’m also pregnant and my #1 concern with this child (my 3rd) is healthy gut flora, because my first two had food allergies and their related issues when they were younger (which we healed through diet!). The more I read the more it seems like literally EVERYTHING is connected to gut flora- digestion, general immunity, brain function, likelihood of developing chronic illness, pretty much every health related thing I can think of. So you’ve given me a few more tools to hopefully give my baby the best chance at a good colonization at birth- thanks!

    Reply
  42. One of the things I disliked about my son’s hospital birth is how they bathed him right away. They took all the vernix and my smell off him. I feel that’s why we struggled a little bit with breastfeeding in the beginning. If I have another child I plan to not be in the hospital.

    Reply
  43. Love this. I worked really hard to prep my birth canal and tested neg for strep B the second time which was so exciting.
    However my son was born in the caul. I’m wondering if this prevented him from getting those good bugs??
    If so I might ask them to break my bag next time.
    Thoughts?

    Reply
  44. Hi there, I was wondering What your thoughts were on the antibiotics they drop in newborns eyes after the come out of the womb? They say it’s important as to prevent infection from bacteria in the birth canal, but I am not convinced.

    Reply