Infant & Toddler Health

What We’ve Learned About Kids and the Human Microbiome

What We’ve Learned About Kids and the Human Microbiome
Kid's Microbiome

It seems like we’re hearing a lot about bacteria these days. And for good reason.

The human microbiome (the inner universe of microorganisms in and on the body) is being studied and understood more than ever before. From helping us absorb nutrients from our food to supporting the health of our immune system, the microbiome (and its trillions of inhabitants) is truly a unique cosmos of the microscopic.

New, cutting-edge research is finding that the microbiome (particularly in the gut) plays a key role in just about every aspect of our health and longevity, especially during childhood.

In fact, there is growing recognition that the microbiome is directly linked to infant and childhood development and immune function—creating a major shift in focus on how the microbiome relates to pediatric health.

This is great news! It’s allowing us to grasp a better understanding of the human body and how we can help our kids develop strong immune systems to help them stay healthy throughout their lives. And it’s all about that good bacteria!

So, here’s what we’ve learned:

How the Human Microbiome Develops and Evolves

The intestinal microbiome goes through some seriously radical changes throughout infancy and childhood that can have lasting effects on adult health later on.

Let’s break it down:

  • The placenta harbors a variety of bacteria, so our first true exposure is in the womb.1
  • Right before we’re born, our GI tracts are mostly sterile and aerobic, just waiting for introductory bacteria to make themselves at home and begin colonizing.
  • During the birth process, especially in a vaginal delivery, our body picks up bacteria from our mother.
  • Within the first days and weeks of life, the presence of oxygen and milk shifts the composition of the gut microbiome to enable populations of new and different bacterial colonies, with strains like Bacteroides, Bifidobacterium, and Clostridium moving in.
  • As we move into the first years of life, a variety of environmental and dietary factors contribute to the overall health and balance of our microbiome.

The gut microbiome is home to an astronomical array of colonies and combinations of bacteria and other microorganisms. Different variables can affect the microbiome’s overall composition in our first weeks of life, and researchers are discovering that certain bacterial strains can support child development when it comes to various aspects of whole-body health.

How Diet & Environment Affects the Microbiome During Childhood

Factors like method of delivery (vaginal or C-section), environment, first foods (breastmilk or formula) and diet can alter the intestinal microbiota of infants—which can then affect the overall immune system and general well-being of the baby.

Method of Delivery

The mode of delivery can have an oh-so-profound effect on the structure of the infant microbiome.

For example, studies indicate that vaginally delivered newborns exhibit bacterial communities including Lactobacillus, Prevotella, Escherichia, Bacteroides, Bifidobacterium, and Streptococcus, while some infants delivered via C-section demonstrate a reduced incidence of Bifidobacterium (a naturally occurring bacteria that helps support digestion and the immune system).2 

Breast Milk and Infant Formula

We’ve long been singing the praises of breast milk. And here’s why:

It’s made up of immunoglobulins, cytokines, growth factors, lysozyme, lactoferrin, and HMOs (human milk oligosaccharides), among other incredible things. HMOs are abundant carbohydrate components in breast milk that function similarly to prebiotics, stimulating the growth of Bifidobacterium and other helpful bacteria.

Your body specifically calibrates your milk to pack in the nutritional proportions your growing baby needs based on signals your body receives from your baby’s saliva. Pretty cool, huh? Breast milk composition can even change depending on the temperature outside or if your baby requires more hydration at a particular time—it’s like custom-made nutrition and life support.

We've also learned that formula fed infants experience a larger amount of C. difficile in the intestinal microbiota, which can be associated with some negative effects later in life.3

When formula feeding, it can be helpful to supplement with a probiotic formula designed for children to help account for bacteria not present in standard formulas that may be able to support your child’s foundational health.


When your child is suffering, you want whatever will kill the harmful bacteria, fast. And antibiotics can wipe out all of the inhospitable bacteria but they have a way of getting rid of all the good bacteria, too. While antibiotics are a medical necessity in many cases, they are also present in our food supply—leading to an overuse of the drugs, which can take a toll on our bodies.

The negative impact of antibiotics is pronounced for infants under 12 months, with significant reductions in Bifidobacterium and Bacteroides, and reduced bacterial diversity in general. Without enough diversity, children may not have the building blocks they need for strong immune defenses.

How to Support a Healthy Microbiome

As we learn more about how the human microbiome works, we can strategically encourage microbial health by including probiotic supplements.

Combining probiotics and a healthy whole food diet rich in prebiotics may be the key to maintaining a balanced microbiome. 

It’s wise to choose a probiotic formula specifically designed with kids in mind; one that doesn't include sugary, probiotic gummy snacks! Did you know that most probiotics for kids (liquids, powders, gummies, chewables) don’t have much of a chance of surviving the harsh, acidic environment of the stomach? It’s one reason why many probiotics on the market aren't actually delivering the live organisms they promise.

That’s why we created our PRO-Kids formula, which is the first ingestible probiotic for children. It’s a teeny-tiny micro pearl, so even very young children can swallow it. PRO-Kids are also made with two patented technologies, LiveBac and BIO-tract, that help ensure your probiotics have a long shelf-life (with zero refrigeration required—you’re welcome!) and that the beneficial organisms make it past stomach acids and into the GI tract, where they can really get to work for your kiddo.

We strive to give our kids the best foundation for a healthy life, and we’re excited to gain further insight and understanding into how the microbiome can support our kids for a lifetime of health.


1. Aagaard, K., Ma, J., Antony, K. M., Ganu, R., Petrosino, J., & Versalovic, J. (2014). The Placenta Harbors a Unique Microbiome. Science Translational Medicine, 6(237).

2. Blustein, J., & Liu, J. (2015). Time to consider the risks of caesarean delivery for long term child health. BMG, 350(Jun09 3). doi:10.1136/bmj.h2410

3. Penders, J., Vink, C., Driessen, C., London, N., Thijs, C., & Stobberingh, E. E. (2005). Quantification of Bifidobacterium spp., Escherichia coli and Clostridium difficile in faecal samples of breast-fed and formula-fed infants by real-time PCR. FEMS Microbiology Letters, 243(1), 141-147.


Julie Hays is the Communications Director here at Hyperbiotics. Health writer and mama of two little girls, Julie's on a mission to empower others to live lives free of the microbial depletion many of us face today. For more ideas on how you can maximize wellness and benefit from the power of probiotics, be sure to subscribe to our newsletter.