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, like bacteria, in and on the body) is being studied and understood more than ever before. From extracting nutrients from our food to influencing the health of our immune systems, the microbiome (and its trillions of microbes) 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 pediatrics.

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

It appears that 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
  • When we’re born, our GI tracts are mostly sterile and aerobic, just waiting for introductory bacteria to make themselves at home and begin colonizing.
  • Within the first days and weeks of life, the presence of oxygen and milk shifts the composition of the gut microbiome to populate new and different bacterial colonies, with strains like Bacteroides, Bifidobacterium, and Clostridium.
  • 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 there is a growing recognition of how certain bacterial strains can support a developing child 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 have found that vaginally delivered newborns exhibited bacterial communities including Lactobacillus, Prevotella, Escherichia, Bacteroides, Bifidobacterium, and Streptococcus, while some infants delivered via C-section demonstrated a reduced instance of Bifidobacterium sp (a naturally occurring bacteria that helps promote digestion and boost the immune system).2 This is just one illustration of how different factors can alter the micro-makeup of the gut.

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 an abundant carbohydrate component in breast milk and function similarly to prebiotics, stimulating the growth of Bifidobacterium sp and other helpful bacteria.

Your body even 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? Breastmilk 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 medicine and life support.

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

It can be helpful when formula feeding to supplement with a probiotic 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 bad bacteria - fast. And antibiotics can wipe out all of the bad bacteria but it has a way of getting rid of all the good bacteria too. And while antibiotics are a medical necessity in many cases, antibiotics are also present in our food supply - leading to an overuse of these 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. When there isn’t enough diversity, it could potentially place children in harm’s way when it comes to having a strong immune defense.

How to Restore a Healthy Microbiome

As we learn more about how the human microbiome is affected, we can strategically manipulate it by including supplements like probiotics and prebiotic foods.

Combinations of probiotics and diet may be the keys to manipulating and reshaping a balanced microbiome. Probiotics are live microorganisms that stimulate the growth of good bacteria - and they’re great for kids!

If you can, it’s best to choose a probiotic specifically designed with kids in mind. And I’m not referring to those sugary, probiotic gummy snacks, either. 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 many probiotics on the market are simply ineffective.

That’s why we created our PRO-Kids formula - it’s actually the first ingestible probiotic for children. It’s a teeny-tiny micropearl, so even very young children can swallow them. They’re 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 things like bacteria (and the microbiome) can affect our kids and improve pediatric care.


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.

This Healthy Living section of the Hyperbiotics website is purely for informational purposes only and any comments, statements, and articles have not been evaluated by the FDA and are not intended to create an association between the Hyperbiotics products and possible claims made by research presented or to diagnose, treat, prevent, or cure any disease. Please consult with a physician or other healthcare professional regarding any medical or health related diagnosis or treatment options. This website contains general information about diet, health, and nutrition. None of the information is advice or should be construed as making a connection to any purported medical benefits and Hyperbiotics products, and should not be considered or treated as a substitute for advice from a healthcare professional. Always seek the advice of your physician or other qualified health professional with any questions you may have regarding a medical condition.

Posted in Infant & Toddler Health, Kids & Probiotics, Mom + Child, Summer, Top Articles