You’ve probably heard of the far-reaching implications of the gut microbiome, the trillions of viruses, bacteria, and fungi that live inside us, and may even be taking steps to enhance your microbiome, like eating yogurt or taking probiotic supplements.

personally, I’m aiming for a tie-dye microbiome
But what is a healthy gut microbiome, anyway? What are we trying to achieve with our microbiome-friendly diets and practices? While this billion+ dollar question remains largely unanswered, most people agree that the more microbial diversity we have in our guts, the better. However, Evolve Biosystems has provided a very different and convincing answer to a subset of this question, defining a healthy baby gut microbiome.
At last week’s Translational Microbiome Conference (which I paid for out of pocket – yes, I’m that much of a microbiome fanatic), I learned about Evolve’s large research efforts to define a healthy, or evolved, baby gut microbiome.
By studying babies from every population in the world (the slides featured some pretty adorable pictures), researchers were surprised to find that in stark contrast to the diversity of adult microbiomes, baby microbiomes are dominated by a single bacterial species. Up to 80% of the microbiome of breastfed, healthy babies is a single species: Bifidobacterium longum subspecies infantis, which we’ll call “Baby Bif.” This Baby Bif is the exact same organism found in babies all around the world, confirming that it’s beneficial for babies of all genetic backgrounds. Babies colonized by Baby Bif enjoy fewer health and behavioral problems than those who do not, showing that this ancient bacterial species is critically important to properly shape developing humans.

while these babies look different, they’re colonized with the exact same Baby Bif!
Where does Baby Bif come from? Not surprisingly, this bacteria is passed from mother to baby during birth, but surprisingly, this species is not present in the vaginal microbiome, only in the colonic microbiome of adult women, confirming that this species is passed from mother to baby by fecal oral transfer. Gross, but true (and important)!
Lots of research has examined the microbial differences between babies born vaginally, who get microbiome transfers from their mothers, and those born via C-section. The bacteria of C-section babies more closely resembles the skin bacteria of the people around them in the delivery room, while the vaginally-delivered babies have bacteria that resemble their mothers’, and this microbial difference is believed to be responsible for the increased incidence of diseases in C-section babies. For example, studies that have tracked C-section babies reveal that they have a 29% increased risk for irritable bowel syndrome (IBD), an 18-32% increased risk of allergy/asthma, a 20% increased risk of Type 1 Diabetes, and a 68% increase in early childhood obesity. These stats are especially important because C sections account for ~30% of births in the US, 50% of births in China, and up to 80-90% of births in South American countries.
So how do we ensure that C-section babies receive proper starting microbiomes to increase their likelihood of good health? Recent research has shown restoration of the skin microbiomes of C-section babies that were swabbed with vaginal fluid, which is an important step in improving infant health. However, in this procedure, babies won’t get Baby Bif, since it comes from mothers’ colonic bacteria. Furthermore, even a subset of babies born vaginally don’t have Baby Bif, as this bacteria is very sensitive to antibiotics, and since most women have had 15-20 courses of antibiotics before giving birth, many mothers don’t have the Baby Bif to pass onto their children.

this scenario is problematic for many reasons, including its attack on Baby Bif!
So how do we change the standard of care to ensure that babies have their Baby Bif, which performs innumerable important functions for baby development? This is where companies like Evolve are stepping in to make both probiotics (live Baby Bif for mothers), and prebiotics (the food that Baby Bif eats) for babies.
To create prebiotics for Baby Bif, researchers studied human milk, which is a complex mixture whose components either feed babies or feed microbes. 85% of the total energy in breast milk (lactose, proteins, etc) is digested by babies, while the other 15% of milk energy, called human milk oligosaccharides (HMOs), cannot be digested by babies, but instead feeds babies’ bacteria. Importantly, studies have shown that only Baby Bif grows in the presence of HMOs, and other bacterial species cultured in HMOs die. Unfortunately, current baby formulas do not contain HMOs. Therefore, even if babies receive Baby Bif from their mothers, this crucial bacteria fails to grow when babies are only fed formula.

Quick review: babies born vaginally and breastfed have the highest bacterial quantity and diversity; bacteria do not flourish in vaginally-born babies that are not breastfed; and babies born via C-section start off with fewer and different bacteria.
Evolve developed a baby formula, the first to contain HMOs, and recently concluded a clinical trial showing that Baby Bif flourished in babies with this HMO-supplemented formula, similarly to those who were breastfed. This stable colonization of Baby Bif correlated with significant beneficial metabolic changes for babies. Similarly, Evolve is currently running a trial to evaluate the efficacy of “prenatal probiotics.” That is, researchers are giving Baby Bif to mothers who don’t have it in hopes that it will be passed onto their children. Fingers crossed that this intervention is successful!
So what are the takeaways for future parents to ensure optimal health for their children? Hopefully soon, mothers will be able to get tested for the presence of Baby Bif, and if they don’t have it living inside them, they can ingest specialized prenatal probiotics. If possible, vaginal births, breastfeeding for 6-12 months, and encouraging your kids to play in the dirt is a great way to strengthen their microbiomes and set them up for great health 🙂

As a big baby, I continue to play in dirt as much as possible!
So, when will Evolve be able to offer prenatal baby bif and how much will it cost? Fascinating!
Glad you found this interesting! I just emailed David Kyle, the CEO of Evolve, to as your great questions – I’l let you know what I hear!
Very interesting luckily products are being developed to help expectany mothers have baby bif… All this is going on inside our bodies and most of us are unaware of the crutial processes to ensure good health! Thank you for presenting this current research
Glad you found it interesting, and I’ll continue to post all about about baby health and the microbiome as research becomes available!
I realise this is late, but did you come across any information about the microbiome of babies born by C-section and breastfed? There’s no graphic for them! Both of my children were born by C-section then breastfed for over a year. I’ve read mixed information as to whether breastmilk contains any beneficial bacteria or only prebiotics.
Also I’ve heard that babies may be exposed to their mother’s bacteria in utero before birth, after the amniotic sac ruptures – so my baby born by emergency C-section could have received more bacteria than my friend’s baby who was born vaginally but ‘in the caul’. Do you have any thoughts on this?
Thanks for the interesting article.
Thanks for reaching out! From my research, breastfeeding restores almost all the beneficial bacteria that would have been delivered via fecal inoculation during C-section, and you’re correct in that they also received bacteria in utero. Ben Greenfield writes extensively about gut healing for babies born via C-section (he has two sons who were delivered that way), and he has an excellent podcast for which you can ask questions: https://bengreenfieldfitness.com/article/digestion-articles/how-to-fix-your-gut/
This post was very informative because I’ve always wondered what the term ‘good bacteria’ means especially when it comes to my baby’s health. I like how you included a quick review that summarizes the information. I look forward to more information on this topic, the research you have included is very impressive and you should keep it up.
Thanks Ronny – and happily, Evolve just shared the results of a scientific study showing that their probiotic helps colonize babies with the beneficial bacteria, and the colonization is enhanced by breastfeeding…
http://msphere.asm.org/content/2/6/e00501-17?lipi=urn%3Ali%3Apage%3Ad_flagship3_feed%3BfvuDyQlpTsmb%2BgFQYgJD2g%3D%3D
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