Infant Gut Microbiome + 5 Ways to Improve Infant Gut Health
You may have landed on this page looking for answers because your baby is struggling with colic, diaper rash, or eczema. If so, you had good intuition because it may be time to focus on your infant’s gut health.
In this article we’ll dive into:
what exactly the infant microbiome is
where it comes from
how important it is for lifelong wellness
tips for how to improve infant gut health naturally
what to do in the case of common issues like not breastfeeding or antibiotics
This topic is actually the impetus for founding Flora & Fauna Nutrition.
Before I started F&F, I was a microbiologist and product developer for a probiotics company. One of our products was this incredible probiotic that is given to premature infants and has been clinically studied over and over showing it helps save lives.
I felt so lit up about how fundamental the early development of the microbiome is for the health of babies, so that is why I wanted to specialize and work with this population specifically.
So without further ado, let’s jump into one of my favorite topics!
photo credit: Dragos Gontariu
The infant microbiome
The microbiome comprises all the genes of bacteria and other microscopic organisms, known as microbes, that reside in and on our bodies (for simplicity's sake, I’ll use microbiome to refer to the bacterial communities themselves too).
Babies have distinct microbiomes all over their body—gut, mouth, skin, etc.— but today we’re focusing on the gut microbiome because of its far-reaching impacts.
The hallmark of the healthy infant microbiome is that it comes to be dominated by a type of bacteria called Bifidobacterum. You may have seen this type of bacteria in your probiotic. It is definitely one of the good guys, and infants' guts should be majority colonized by it.
Where does the infant microbiome come from?
It will depend on myriad factors but in the case of vaginal delivery, it comes mainly from the mother. And in the case of c-section from the hospital and skin microbes. It also starts to shift based on feeding mode (breastmilk or formula).
It is not exactly clear exactly when the microbiome starts developing. It was thought that the fetus was sterile inside the womb. Some new research has shown microbes present in the amniotic fluid, meconium, cord blood and placenta of healthy pregnancies, not just those of pre-term births, but it’s possible this may just be contamination or flaws in experimental design. I’m excited to see what more we learn about this in the future!
But the main event for the colonization of the infant microbiome undoubtedly happens during delivery and the days and weeks post-birth. How it develops is impacted by mode of delivery, whether antibiotics are administered, how the baby is fed and what they eat when starting solids.
How the infant microbiome shifts over their first weeks, months and years of life
Baby is getting seeded with a diverse set of microbes beginning immediately, but which ones dominate change over the course of the first weeks.
At birth, there is a huge inoculation event that is happening, which depends on the type of delivery. Babies born via vaginal delivery are mainly seeded with their mother’s gut and vaginal microbes, while babies born via cesarean delivery are mainly seeded with skin and hospital-associated microbes.
After about three weeks, babies' guts should start to become dominated by Bifidobacterium, that beneficial bacteria I talked about before. The rate of this will also depend on feeding mode, with more dominance by bifidobacteria with exclusive breastfeeding.
Then another explosion in diversity happens when baby starts solids. These microbes were likely there in small amounts, but when the right food source comes along they can really take over. Feeding this diversity from the very beginning is excellent for not only gut health, but increasing the chances baby will have a more adventurous palate as they age.
Related: Do this when starting solids to reduce the likelihood of very selective eating
Right around 3-5 years old, your child’s microbiome will start to equilibrate and resemble that of an adult.
The importance of infant gut health for setting up lifelong wellness
The gut microbiome does many important jobs for our babies. It is key in preventing potentially pathogenic bacteria from taking over, helping to absorb all the nutrients from the milk or food they drink and it is fundamental in the proper development of the immune system.
But having a healthy gut microbiome does not just affect your baby’s health in the short-term.
Studies have shown infant gut health is linked to risk of developing health issues into adulthood, the most common of which are immune-related, neurological and metabolic disorders.
Signs of poor gut health for baby
Signs that your child may be in need of some gut health TLC are:
colic
skin issues like eczema and frequent diaper rash
allergies
And once they start eating solids:
food sensitivities
constipation
diarrhea
Nobody wants their child to suffer from any of these symptoms, but making changes early on can make all the difference for their long-term well-being.
An epidemic of ‘missing microbes’ in today’s infants
There is actually an epidemic of missing microbes in our infants in the U.S. and other parts of the western world.
There has been a decline in Bifidobacterium in the U.S. associated with increased cesarean births, antibiotic use and decreased breastfeeding. This decline is correlated with an increase in immune-related conditions like allergy, asthma and eczema.
There is one type of bacteria in particular called Bifidobacterium longum subsp. infantis (B. infantis), which is considered to be the hallmark of a healthy breastfed infant microbiome and is shown to be critical for proper immune development and intestinal barrier integrity.
This particular Bifidobacterium has uniquely evolved to thrive on breastmilk and colonize the infant gut. It helps to repress pathogens, is anti-inflammatory and it helps calibrate the innate immune system.
But the alarming thing is that a 2022 study showed that here in the U.S., some communities have zero percent of babies that actually have this bacteria present in their microbiomes.
Meaning this gut species, which has been shown to calibrate the immune system and proven critical for optimal development, has gone extinct in some communities.
This is in contrast to other countries around the world where the percentage is much higher, sometimes topping 90%.
The main thought is that the trend of decreased breastfeeding that peaked in the 70s here in the U.S. drastically reduced the growth and prevalence of this organism. B. infantis thrives on human milk oligosaccharides (HMOs) found in breastmilk, which is why it can be outcompeted and go missing if breastfeeding is not prioritized.
So this is why you may have been hearing that immune conditions like eczema, asthma and allergies are on the rise. It's hypothesized that the increase in these immune-related issues is due to improper calibration of the immune system from a lack of bifidobacteria in early infancy.
But all is not lost—keep reading below to find out ways you can help improve your child's gut microbiome and include this critical component, especially if you aren't able to breastfeed.
How to improve infant gut health naturally
Start in pregnancy
Ok, I get this isn’t exactly helpful if your baby is already here and crying for hours on end due to colic, but its importance is so fundamental that I have to mention it here. For optimal gut health for baby, you’re going to want to start in pregnancy.
The beneficial bacteria that is the main colonizer of the infant gut, Bifidobacterium, starts rising in healthy pregnancies alongside progesterone. So things are definitely building the entire pregnancy for optimal microbiome development for your baby. Which is why I tell all my clients to focus on gut health in pregnancy - preferably preconception! Read all about how to benefit yours and baby’s gut health during pregnancy in this blog post.
Related: Gut health during pregnancy & why it matters
We all know some parts of birth are out of our control, so if you end up needing to have a c-section or antibiotics—take a deep breath. All is not lost. Following the advice in the next few points will be important for bringing things back into balance.
That being said, if you have a choice, I encourage you to read over the evidence-based natural birth practices recommended by the World Health Organization and Lamaze International that lead to less intervention and higher potential for natural birth progression with less impacts on your baby’s microbiome.
photo credit: Josh Willink
2. Prioritize breastfeeding
Breastfeeding is the single most important thing you can do for the health of your infant’s microbiome. Especially if you had a c-section birth—but definitely any mode of delivery— exclusive breastfeeding can help to establish proper microbiome development in your baby.
So much so that by 6-months, this study found that there was no significant difference between the gut microbiome composition of exclusively breastfed babies born via c- section or vaginal delivery. This was not the case for mixed-feeding.
We know breastmilk has evolved to be the perfect food for babies, but it also was designed to feed another critical thing.
A full third of breastmilk is made up for human milk oligosaccharides (HMOs), and babies cannot even digest them! That means that mom is using hard-earned energy to create food specifically to feed—you guessed it—baby’s gut bacteria.
B. infantis in particular is able to consume HMO better than other bacteria out there (even other Bifidobacterium species) so if given a diet of breastmilk, it will thrive.
It consumes HMO in a way that does not allow for the growth of less beneficial bacteria and actually helps to keep pathogens at bay.
3. Be in the right environment
I know many of us, especially in the US, have been taught that we should be sanitizing and disinfecting everything to be healthier and keep our babies from getting sick, but the truth is that the bacteria and other microorganisms in our bodies are critical to our health. So, over-sanitizing may be doing more harm than good.
The increase in sanitizers and disinfectants can decrease the abundance of bacteria in our guts and skin, and also allow for less opportunities for our children to come into contact with neutral microorganisms that help to calibrate the immune system early on.
A study even found that sanitizing pacifiers via chemical means was linked to a higher incidence of food allergy.
A good wash of your hands and items with an all-natural soap is a good measure against undesirable microorganisms, but beyond that, loading lots of chemical disinfectants around our babies should be avoided as much as possible.
And as someone with a son who still puts literally EVERYTHING in this mouth, I know how anxiety inducing it can be. But rest assured this is a beneficial process for babies. When infant saliva is combined with breastmilk, it produces antimicrobial compounds that help to protect babies as they are exploring.
I’ve said it before, but it bears repeating—nature is so clever! Often times we just need to trust in the natural processes that have evolved to protect us.
Babies were designed to explore like this for healthy development. Even more reason to consider the products you are using in your home, so you can feel confident your baby is not ingesting potentially toxic chemicals while exploring their new environment.
Likewise, spending ample time outdoors in nature helps to bring baby in contact with tons of different microorganisms, which has a benefit for their microbiome and immune system development. So get outside as much as possible and let baby (safely) explore to help further develop the gut microbiome.
4.Start solids right
There is a developmental explosion that happens when baby starts solids. This window of time is also a hugely important time for microbiome development.
From day 1 of starting solids, your baby's microbiome starts its shift towards its adult-like state that'll be reached around 3-5 years old. Their gut bacterial diversity is increasing, and supplying a wide-variety of nutrient-dense food for their palates and gut microbes will set them up for optimal health and well-being.
You can check out my Ultimate Guide to Starting Solids which includes all this information and more, and includes 90 days unlimited Q&A while you start the process!
Related: Top 12 foods to start baby-led weaning
5. Consider probiotics
Like I said before, sometimes the circumstances of our birth and child’s infancy are out of our control—emergency c-sections, low milk supply or tongue ties leading to difficulty breastfeeding, siblings bringing home infections that require antibiotics. For these things and more, probiotics can be an excellent insurance policy.
Specifically to help reinstate B. infantis into our infant communities, I am a proponent of taking B. infantis-containing probiotics while breastfeeding, and exploring giving it to your baby too if indicated by one of the signs of poor gut health above.
As always, speak to your healthcare provider if considering supplements for you and your baby.
For pregnancy and breastfeeding some excellent options include JarrowDophilus Prenatal Probiotic, and for infants, their infant probiotic drops. Both of these include a clinically studied B. infantis strain (M63) that was isolated from a healthy breastfed infant and shown to help healthy development of the infant microbiome.
I can’t breastfeed— help!
As someone who struggled with breastfeeding in the beginning due to my son's tongue tie, I feel you. Sometimes it just isn’t in the cards—and that's OK.
In that case, the type of formula you choose can have huge benefits. Choosing a formula that contains oligosaccharides which feed the beneficial infant gut bacteria like bifidobacteria is a great choice. Also, try to choose a formula that does not contain corn syrup because that can have negative effects on the microbiome and can shift the proper development.
Kendamil organic is a great option because it actually contains those HMOs we discussed earlier. Similac pro Total 360 Care contains HMOs and no corn-syrup but doesn’t have grass-fed milk like Kendamil.
Happy Baby Organic formula is a great option for sensitive tummies because it contains grass-fed A2 milk protein and contains galactooligosaccharide (GOS), the most preferred oligosaccharide after HMOs. It also contains a clinically studied probiotic strain B. breve M16v, which helps promote the healthy development of the infant microbiome for babies that are not breastfed or born via cesarean.
I (or my baby) had to use antibiotics around birth or during their first year—is their gut health doomed?
Short answer—no. The microbiome is quite resilient when fed the proper things.
So if still exclusively milk feeding, prioritize breastfeeding for however long, or however much, you are able—every ounce counts!
If formula feeding, consider the type of formula I mentioned above, because those are going to be optimal to continuing to nourish the right gut bacteria.
If baby has already started solids, diet is going to be critical in the weeks following antibiotic treatment while the microbiome is rebounding. Try to limit added sugar as much as possible, as sugar—even natural kinds!— preferentially feed the not so beneficial bacteria.
Also add in as much diverse plant food as possible. And it doesn’t necessarily mean veggies because I know this can be tricky! Whole grains, spices and herbs, and fruits all count as plants too!
Fermented foods like dairy or coconut yogurt are excellent options and tend to be pretty well accepted by most babies and toddlers.
The probiotics I mentioned earlier would also be beneficial here too.
Bringing it all together
Nurturing your infant’s gut health is one of the most powerful ways to support their lifelong health.
From birth, the tiny ecosystem of microbes plays a crucial role in the development of their digestion, immunity, metabolic health and more.
Whether through vaginal birth, breastfeeding, an enriching environment or a diet rich in diverse, gut-friendly nutrients, there are many ways to encourage a thriving microbiome. Following the easy step for how to improve infant gut health outlined here are a huge step in the right direction.
And if challenges arise—like the need for antibiotics or difficulty breastfeeding—there are still plenty of ways to support their gut health, from formula choice & probiotics to mindful nutrition. Every small step you take now lays the foundation for a healthier future.
If your child is showing signs of needing some gut support, or you are pregnant and just proactively want help to best support their microbiome, reach out—I’d love to support you on this journey! You can book your 20-minute clarity call here.
