What is a healthy gut microbiome?

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!