12 - 48 Months

How to boost your baby’s biome

“Vaginal bacteria are not the same bacteria that’s in the air, so it’s clear that when babies are born through C-section or vaginal, their first moments’ bacteria are totally different. That obviously has an influence on the microbiome and every interaction that baby has from that moment on, will keep shifting their microbiome.”

Meenal Lele, author of “The Baby and the Biome”

We hear a lot about the first 3 years of a baby’s life — how critical those years are to brain development. But today’s guest, the author of The Baby and the Biome, would argue that the same window is just as critical for our gut. Probiotics may have a role in keeping that system healthy. But are probiotics helpful to babies? And what about when you’re pregnant? Jessica Rolph, your host, welcomes Meenal Lele, founder of Lil’ Mixins.


[1:39] When do babies pick up their first dose of bacteria? 

[2:54] How does birth affect this bacterial environment? How does the introduction of bacteria differ between a C-section and a vaginal birth?

[4:56]  What can people who have C-sections do to replicate the bacteria that’s introduced during a vaginal birth?

[5:58] Should parents bathe their babies right away, or is there any benefit to letting them go unbathed for those first few days? 

[7:18] What are significant sources of good bacteria for your baby to build their microbiome in those first weeks? 

[9:18] What kind of probiotics does Meenal recommend for mixing into formula? How do you work those into breast milk?

[11:11] When our babies start to eat solid foods, should we supplement with probiotics? 

[12:51] What are other benefits of probiotics and supplementation?

[14:22] What would Meenal do if she had a baby now, knowing everything she knows?

[17:18] Why have human microbiomes lost microbial diversity?

[21:52] Jessica shares her top takeaways from the conversation with Meenal.


Jessica: Welcome, Meenal.

Meenal: Thank you so much for having me. I appreciate it.

Are babies sterile before birth

Jessica: So I read somewhere that babies are sterile before birth, so they don’t really have a microbiome yet when they’re in utero. When do babies pick up their first dose of bacteria? Am I right about this? 

Meenal: It’s not totally clear actually, it’s one of those things that’s really hard to study because if you try to sample… We can’t really sample very well a baby inside, in utero, and then every time we try to… If we try and sample the amniotic fluid or something, we’re always going to be pulling bacteria from the air and other things onto that sample, and so it’s really hard to tell. But the basic idea is, yeah, it’s a sterile environment. And that’s mostly because if you think about it, your inside organs, they’re sterile, we don’t have… You don’t have bacteria on your kidney because it’s inside your body, you do have bacteria on your skin ‘cause that’s outside your body. At the same time, there is a ton of bacteria in the urogenital tract and in the vagina, so then a baby in that sense is still somewhat interacting with the mom’s bacteria, because that bacteria that’s in the vaginal tract can actually can get up the uterus basically, and affect how the baby is developing in utero. So it’s kind of complicated, but for the right way to think of it is, I believe, is that the baby is kept somewhat sterile, and yet they’re still being influenced by the mom’s bacteria.

Building microbiome from birth

Jessica: That’s so interesting. And then what about the process of birth? Whether it’s C-section or a vaginal birth, what happens with this bacterial environment at birth for the baby? 

Meenal: Yeah. So when you’re born, you’re immediately exposed to your mom’s bacteria, and if you think about it, the vagina sort of expands and like a glove, it completely covers the baby as it’s on its way out, and so the baby’s getting completely smooshed in their mother’s bacteria. And in fact, they say it’s on purpose that the babies are born facing backwards and that most women defecate a little bit during while they’re pushing and the baby is supposed to eat a little bit, it’s a true fecal transplant, and that seeds… That’s what’s supposed to seed their gut. Their very first gut seeding is directly from the mother.

But then when you’re born by C-section, you have to keep a C-section very, very sterile, ‘cause now we’re cutting inside, again, we’re not supposed to have bacteria on the inside organs, and so they give you a ton of antibiotics for good reason, and you should get them, and they keep the operational theater sterile. And so then the first bacteria baby is exposed to are the air bacteria that end up on the surgeon’s gloves, and the bacteria that are naturally on the clean blanket that’s put down on the table where they lay the baby down immediately and things like that.

That’s the baby’s first exposure to bacteria. It’s a completely different set, your vaginal bacteria are not the same bacteria that’s in the air. And so it’s very clear that when babies are born in different ways, their first moments bacteria are totally, totally different. That obviously has an influence and yet again, every interaction that baby has from that moment on, will keep shifting their microbiome, so it’s not the last thing, it’s not the only word in this either.

Vaginal swabbing for c-sections

Jessica: This is so fascinating. I guess my question is, is, what can we do? I’ve heard about people who have C-sections in doing what they can do to replicate this bacteria that’s introduced during a vaginal birth, I’ve heard about swabbing… Can you talk to this a little bit in more detail? 

Meenal: Yeah, it’s interesting, the NHS in the UK, they actually give guidance to mothers on how to do this, and there are a couple of studies going on right now in the US about, could we create guidance around this too, but basically involves… You get sterile gauze, and if you’re going to have a C-section, you basically shove it into the vagina and let it get soak up all the vaginal fluids during birth, or maybe not during birth, actually, I think that you take it out before the C-section, but then basic, and you keep it in a sterile or just a clean zip lock bag will do kind of thing. And then right after the baby is born, you basically swab them with it, so you swab their skin with those vaginal fluids, you can actually swab kinda their lips and their nose in the exact same way that the baby would kinda scrape all that stuff up and you can, to some extent, you can replicate it.

When to bathe a newborn

Jessica: So interesting, and then what about giving your baby a bath? So I think I knew some of this when I had my babies, and I had this intuition that maybe bathing them right away, or is there any benefit to letting them sort of stay a little dirty for those first few days? 

Meenal: There is more than a little benefit to letting them stay dirty, and I have this very visceral memory of my first, my older son. And when I say this, I want to be clear, I’m not speaking ill of any of the folks, the hospital that he was born in, everyone was lovely to us, and was doing their absolute best, but I just remember watching them wash him, and kind of really scrub him and just thinking at the time like, “That seems unnecessary. He hasn’t been doing much.” But actually in the UK and a lot of Europe, you just don’t bathe babies for two weeks, they’re born with this Vernix caseosa, if I’m pronouncing that correctly. And you just let it slowly absorb and that’s it, it’s like this goopy white stuff and then it slowly absorbs into the skin, but it’s almost like imagine putting a thick layer of Vaseline on them or something when the moment they’re born and then letting that just kinda ride and that’s really… That keeps your skin from losing water and from getting bacterial infections in those first critical couple of weeks, and so yeah, there’s really no reason to wash them for a really long time.

Ways to boost your baby’s gut health

Jessica: So post-birth, let’s talk about post-birth, so let’s say you had a C-section, what are the significant sources of good bacteria for your baby to build their microbiome? Is it skin on skin, is it formula, breast milk, how do they get inoculated? 

Meenal: The bigger thing after they’re born, the bigger thing to worry about is really their gut bacteria, and that is about making sure that they’re getting the right inputs, not as many negative inputs as possible, so what are the right inputs? Like you said, breast milk. If you’re giving them, formula, a probiotic supplementation can be really helpful, even if they’re drinking breast milk, unfortunately today, because of our… Just our moms, like those of us who are breastfeeding or I was a few years ago, the breast milk we were giving our babies is fundamentally different than it was maybe even a generation ago. So a probiotic supplementation can be useful and we can talk specifically ‘cause that’s like saying take vitamins, which is not particularly useful advice, it matters which probiotics, which bacteria.

So you definitely want your baby to be drinking breast milk or formula, getting in there, getting that stuff in their diet. The big thing really to think about in those first six months, though I say, it would say is the opposite, which is try to limit their exposure to antibiotics, and now, I don’t mean to be very clear, antibiotics should be used when they are necessary. The key is to try and prevent the need for the antibiotics. So to the extent that you are not smoking in the house, something that causes ear infections, you’re feeding your baby their bottle lying down on their back, that can cause the milk to wash back up and again, cause an ear infection. Even for most ear infections you get, the baby gets, is really about talking to the doctor and saying, “Hey, is this one that would just maybe go away on its own, and could we try giving it a couple days and not using the antibiotics?” Those sorts of things are actually more protective of the baby’s microbiome than anything is not wiping it out, not putting the bleach on the counter of their growing gut.

Which probiotics make sense in early infancy

Jessica: First of all, I have couple double quick questions on this. One is, what kind of probiotics do you recommend for mixing into formula or how would you mix that into a infant’s diet if you’re breastfeeding and not pumping? So that’s my first question.

Meenal: So which probiotics make sense in early infancy? So there’s two that have good data. B. Infantis, B. Infantis is a bacteria that has been proven to help a lot of babies in early infancy, and so that specific strain for babies, you can look for they sell it, and for a baby who is breastfeeding, it doesn’t take a lot, so it can be a couple of drops that are just like you give them Vitamin D, you can put a couple drops on the nipple and then the baby can drink it, actually, you could just squeeze it into their mouth from the dropper, or if they’re formula-feeding, you can put it in a bottle. The other bacteria that has actual clinical data behind it, is L. Rhamnosus. And L. Rhamnosus, when taken by mother in the last trimester of her pregnancy, and then by mom and/or baby during the first six months has been shown to cut the risk of eczema by up to 50%. So those are the only two that really have good clinical data behind them. That doesn’t mean those are the only useful ones, we can only answer these questions kind of one clinical study at a time.

Jessica: That’s great. So you’re saying that when you’re pregnant, you should take L. Rhamnosus, and there’s in some kind of probiotic, especially in the last trimester, and then when you’re breastfeeding, take these probiotics yourself, it will transfer into your breast milk? 

Meenal: Yes, it transfers into the breast milk and babies can take it too, actually. They found some of the strongest effect when both mom and baby were taking it, but either one taking it is also quite helpful.

Jessica: Great. And so can drop it in their mouths as newborns, and it’s safe, and then as they grow, so they start… Let’s imagine that they’re starting to eat solid foods, what should we continue to do as far as supplementing with probiotics? 

Meenal: After a baby has started solid foods, there’s less data around how much probiotics help. And I think that a lot of this has to do with the fact that it’s a lot harder to study the benefits of probiotics once someone’s eating. Your food really, really changes the make-up of your gut bacteria, and it influences it quickly. So one of my favorite studies, and this is a bit of a side note, one of my favorite studies showed that when you had immigrants move from another country like Laos and come to the US, their gut bacteria had almost completely switched over and was like an American within two weeks of arriving here, and that’s how rapidly food can affect your gut bacteria. So once a baby’s eating solid foods, a lot of what’s the make-up of their gut is just going to be controlled by are they eating a lot of vegetables and fruits, and high fiber foods. That’s it.

So does a probiotic help, I think is a harder question again, because it’s going to be harder to show the benefit, it’s going to have less influence by nature. When the baby’s just on breast milk or just formula feeding, then it’s easier, it’s such a pure food that it’s easier to see the benefit of a probiotic, and so there isn’t great data after that point. So I will say that after the six-month time period, I don’t know the clinical literature nearly as well, and I wouldn’t feel comfortable making any recommendations there.

Benefits of probiotics

Jessica: And if we talked about the benefits of probiotics and supplementation for eczema, what else? What are the other benefits why should somebody bother? 

Meenal: Probiotics have only… This is really interesting. So with L. Rhamnosus, they actually did a lot of clinical studies trying to understand if they could prevent a whole host of different diseases, and the only one that really showed up was eczema, specifically atopic dermatitis, that over and over, you could see the same benefit, and they’re not really sure why you don’t get the benefit for, let’s call it wheeze or asthma or a food allergy. I think there’s just a bajillion different bacteria out there, so we’ve just not even scratched the surface of other ones that we can be studying, and so I’m sure there are other ones out there, but we just don’t really have them today. When it comes to food allergy prevention, we know that early allergen introduction is very protective, like up to 97% protective in some cases against food allergy, when it comes to asthma, for example, a lot of that has to do with not using… The fewer antibiotic insults a baby has had the better, the lower the risk of asthma and their exposure to air pollution. The less air pollution they’re exposed to, the lower the risks for asthma.

So once you get past those earlier stages, as I’m saying it’s the more and more influences on a baby, the harder it gets to control them, and that’s why those first six months can be so critical ‘cause they’re just doing so few things and you actually have a lot of control over each one.

Jessica: And so what would you do if you had a baby right now, knowing all that you know…

Meenal: Yeah, if I… Now knowing everything I know, I mean, I would take those probiotics, for example, in pregnancy, and I used to think probiotics were utter garbage, and that doesn’t mean people can’t be selling you completely useless probiotics, it just means that… There turns out to be data there where I thought there wasn’t, so I would take those probiotics in pregnancy because there’s no risk to you as a pregnant mother and to the baby, and if you get a 50% cut in eczema, that’s awesome. I would definitely leave my baby alone. I think one of the few things we did right with my older son was use cloth diapers, and the big reasons for cloth diapers is actually because they have far fewer chemicals on them, if you’re using the pure cotton cloth diaper, you’re not covering their urogenital tract area in a bunch of chemicals. But we were using a lot of the mainstream soaps in our house, and it turns out a lot of chemicals that are in products, we now know are actually very disruptive to not only the adult skin, but then 10 times so for baby skin.

We now buy all in crunchy cleaning products, so we just try and use vinegar, and it is just as few chemicals as we can in the house because I sort of was always under the impression that, Hey, this stuff has been studied, it’s been great, but they haven’t been.

They just sort of… They’ve been studied in the very, very obvious place, like if you put this on your skin will you die, and the answer is no, but there’s so many second and third order effects to the chemicals we’re exposed to that are really, really hard to study, and I get that. But so then those studies haven’t been done, and so I actually think what they call the precautionary principle. I don’t think that you should go… You have to go completely overboard in terms of being safe, but there are a lot of things that you can say this moment in my life, Do I need to be exposed to this? Do I need to do it this way? And if the answer is no, then you can just make that choice not to.

Microbiomes and our environment

Jessica: That’s so helpful. It feels intimidating, but then when you can start going through one by one and just downgrading or just going a little bit more natural in skin care and in home care, it’s not an endless… They’re not endless categories to take on. So is this related to how the human microbiomes have lost microbial diversity, is this why because we have cleaning products and we have chemicals in our skin care. I heard that Western microbiomes in humans consists of 15%-30% fewer species than non-Western microbiomes, like, What’s going on here with our diet? With our environment… Could you talk to this a little bit.

Meenal: Yeah, I don’t know that I know the answer to that. What I can say is, there’s a few things that can be affecting… And you hit on them. So our pollution, that can… Pollution can kill your microbiome, it can kill a certain bacterial strains, that could be a cause of it, two is our diet, our diets are significantly more restricted than they have historically been, so typically, you wouldn’t have… You would eat a lot of different kinds of foods. You definitely wouldn’t eat nearly as much sugar as we eat today, and sugar can actually be really toxic to certain kinds of bacteria and then promote other kinds of bacteria, but we need the first kind to help us survive, so if we’re eating too much sugar, we’re actually helping bacteria we don’t need and can actively hurt us thrive.

And then our diets in terms of how refined the foods are and things like that, again, the bias for bacteria that we don’t want or that we aren’t evolved to work with. And I use this example of, I think maybe I even say this in the book, there’s always this idea that we want to talk about bacteria as good and bad, even throughout this small chat, right, I’ve probably said good bacteria and bad bacteria like 50 times, but that’s not necessarily a useful way to think of it, because there are just bacteria that our bodies and our genetics have come to be comfortable working with and be symbiotic with, and other ones that we don’t know how to work with, and so we just have to bias for the ones that we know how to work with, ‘cause that’s just part of who we are truly.

So there’s the pollution, there’s the diet, and then honestly, the last big thing is the antibiotics. Martin Blaser, Dr. Martin Blaser wrote a book called “Missing Microbes,” that really opened my mind to this a bunch of years ago. But yeah, we consume antibiotics at a rate that you would have no… You would never believe. If I remember correctly, by the age of 30, the average American has had something close to 30 doses or 30 courses of antibiotics, it’s crazy, and that’s not even counting the antibiotics that we eat on a daily basis that are… ‘cause they’re just in your meats and in the milk. So I would say probably our antibiotic over-usage is the single biggest issue that we face, and in Sweden, I believe they did a concerted effort to try and reduce the number of courses of antibiotics people were getting, and they were able to cut out 75% of them, so like three out of four courses of antibiotics humans get are unnecessary, and yeah so that’s… I actually, my guess is that that’s probably the single biggest issue.

Jessica: Well, just to normalize, thanks for everyone here, I just started a course of antibiotics yesterday for a bladder infection, it was kind of urgent, I tried the DIY for a couple of days, it wasn’t working, just wanted to really feel good, and I had chocolate for breakfast, so I have a lot to learn, a lot to improve on. We’re all on a path.

Meenal: To that point is, again, I just want to be really, really clear that stopping unnecessary use of antibiotics does not mean that you shouldn’t take the necessary ones. If you had an infection that could have killed you right, don’t forget that through most of human history, we had a much shorter lifespan also, so trade-offs and you should take… You should clear the infections you have with antibiotics, but the problem is we take a lot of antibiotics we don’t need. Like I said, there’s no reason for the antibiotics in our meat or in our dairy, and a lot of us rush to take antibiotics when we actually have a virus, and it wouldn’t help any way… Right. So that’s what they found in Sweden, is 75% were unnecessary, meaning the antibiotics didn’t do anything positive either, but when you’re sick and you have a bacterial infection, you got to take the antibiotics, you can’t risk the death that could come on the other side.

Jessica: Yeah, well, thank you. My mom’s voice was in my ear when I was kind of prolonging this infection. It has been fascinating talking to you today, It’s been such a pleasure. Thank you so much for sharing all this wisdom.

Meenal: Yeah, thank you so much for having me. It’s really awesome to chat with you.

Here are some of my takeaways from the conversation with Meenal:

  1. The bacteria that lives in the mother’s birth canal plays a role in seeding the baby’s gut. Babies born by C section can be swabbed in the same fluids to achieve a similar exposure to bacteria. The NHS in the UK actually gives guidance to mothers on how to do this.
  2. The white coating that covers newborn babies is the Vernix caseosa (vur-nuhks kay-sow-suh) and helps to protect the babies skin during those first few days outside of the womb. There is no need to wash this protective coating off your newborn. It will eventually be absorbed. In the UK and much of Europe, the recommendation is to wait 2 weeks before bathing a newborn.
  3. In early infancy, the focus should be about getting the right inputs. You might consider supplementing breastmilk/formula with a probiotic. Meenal recommends taking L rhamnosus during pregnancy and giving it to the baby after birth. B. Infantis is the other probiotic that has been proven to help babies in early infancy. 
  4. Once a baby is eating solid foods, the makeup of their gut is going to be most influenced by the fruits, vegetables and other high-fiber foods they are consuming. There isn’t great data to suggest that probiotics do much after the six month mark.
  5. Check the chemicals in the soaps and other products you are using while pregnant and on your baby. Some can disrupt healthy bacterial growth. Pollution, diet and antibiotics are three areas to examine when trying to enhance our own microbiome and that of our children.

Learn about how your baby’s brain is developing during those first 1000 days on the Lovevery blog


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Kate Garlinge

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Posted in: 12 - 48 Months, 18 - 48 Months+, Family Relationships, Social Emotional, Child Development, Behavior, Parenting

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