Your Baby’s Gut Microbiome: The Foundation of Healthy Digestion and Immunity



noun, plural mi·cro·bi·ota.

a [modifiable] army of 100 trillion microbial cells that we depend on to stay alive: influencing the way we eat, think, and function.

We’ve come a long way in the last few decades in our understanding of what we can do to establish a healthy immune system and prevent childhood illnesses at the same time. We learned that handwashing is the best way to prevent disease but that playing in the dirt may actually be good for your child’s health. There are so many “suggested” ways to maintain your new baby’s health e.g. “breast is best”, antibiotics early on can be harmful, and that a vaginal birth is preferred over a C-section in order to establish a healthy microbiome for your baby.12 The current focus of the scientific community is how we can help our little ones cultivate a strong and healthy microbiome, even if the mother is unable to produce enough breastmilk or if an emergency C-section prevented her from being able to introduce a healthy microbiome to baby.3

What is the Microbiome and How Does it Affect Your Baby's Health?

Simply put, the microbiome is the combined genetic makeup of all of the yeast, bacteria, and fungus that happily coexist in and on our bodies.4 Most of these microorganisms are considered “commensal” – they neither harm us nor provide any true benefit other than taking up real estate that might otherwise be taken by harmful microbes. Some microorganisms, however, are considered “probiotic” – they provide enormous benefits to us and having them take up residence early on in life can protect us from infection or even allergies.5

Babies are sterile inside of the womb and only begin to have their own microbiome at the moment of birth. Ideally, they are bathed in a fabulous cocktail of vaginal microbiota from head to toe and then minutes later are popped onto the breast where their pristine guts are colonized immediately with the antibody-rich golden nectar of prebiotic-rich colostrum. It’s not long before that colostrum gives way to breastmilk that contains a probiotic strain that is so connected to the human baby’s gut health – Bifidobacterium longum infantis. This strain helps to modulate our immune systems, keep the lining of our gut strong and healthy, and alleviate the symptoms related to: constipation, gassiness, abdominal pain, irritable bowel syndrome (IBS), atopic dermatitis, and eczema.6

The Power of Breastmilk

This breastmilk is so powerful, that even the smallest amount given to your baby, even after a C-section, can offset the negative effects of missing out on the microbial benefits of vaginal birth.7 Turns out that pumping also falls behind on the scale of the beneficial microbial transfer. The strains of bacteria and yeast that live on your skin are introduced to the baby once they begin breastfeeding and help to protect them from harmful bacteria that want to take up residence. Later on, when the baby begins to take on more solid foods, it’s definitely beneficial to include some probiotic foods in order to establish a healthy microbiome early. During the first 3 years of life, the foundation of the gut microbiome is being laid.8 If this foundation-building is disrupted by severe illness or antibiotics, the child is much more likely to develop autoimmune and metabolic disorders later in life.9

So if you’re worried about how to help give your little one the best start to overall microbiome health, here’s what to keep in mind: opt for vaginal birth, if at all possible, avoid taking antibiotics while pregnant or breastfeeding, and if you’re able to breastfeed at all, every little bit is beneficial and can offset the negative effects of a C-section, formula feeding, or even antibiotic treatment. And after your little one starts eating solid foods, try a very wide variety of fruits, vegetables, beans (don’t forget hummus), and probiotic foods (yogurt, sauerkraut, kimchi, kombucha). You may be surprised by what they like!

What Can Parents Do?

Of course, we understand that an “easy” birth experience isn't always the case. There are several factors that may cause your baby to not be, “bathed in a fabulous cocktail of vaginal microbiota from head to toe.” So what should the rest of us do?

Good question, good nutrition and high-quality supplements are some of the keys to your child growing up healthy and happy. Here is what the Harvard Medical School says about nourishing your kids10:

Most of the same strategies for healthy eating that work for adults also work for children. Children need the same nutrients as adults, but in different amounts.

Healthy diets for all ages are based on what the 2010 Dietary Guidelines for Americans call nutrient-dense foods from different categories. These include:

Fruits and Vegetables. A variety of fresh, canned, frozen, or dried fruits and vegetables that cover the color spectrum: red tomatoes and strawberries; oranges and carrots; yellow squashes and bananas; leafy greens, avocados, and limes; blueberries; and purple grapes and eggplant. As a rule, the richer the color, the healthier the food.

Grains. Whole grains, such as oatmeal, brown rice, quinoa, or whole-grain bread.

Protein. Fish and other types of seafood, poultry, poultry, beans and other legumes, nuts and seeds, and lean meats.

Dairy Foods. Low-fat milk, cheese, yogurt, and other dairy foods.

Fats. Don't fear fats—as long as they are healthy fats from foods such as fish, nuts, seeds, and vegetable oils.

At the same time, it's best to limit a child's intake of foods with:

Added sugar. Sweetened breakfast cereals, sodas, juices, pastries etc...

Solid fats. Hot dogs and other fatty meats, full-fat dairy foods, and many prepared foods

Added salt. Chips, bread, and many processed and prepared foods

We know that finding the right mix of nutrition for your child can be extremely difficult, especially if you have a picky eater (almost every toddler) and you don’t have the time to cook delicious organic, colorful foods every day (almost all of us). That’s where us our partners at Sun Genomics can help.

Optimal immune performance starts in your gut.

Can you trust yours?

We've partnered up to provide you a complete Immuno-biome Analysis, and improve you your little one's gut health with Custom Probiotics, here's how:


1. Identify: Your unique gut microbiome with our remote immune-biome efficiency analysis.
  • Schedule a 45 minute tele-health visit with one of our primary care providers here
  • We'll review your health history intake form together + come up with a wellness plan to get you to your goals
  • Next, we register you with Sun Genomics portal to send you your remote microbiome sampling kit.
  • You'll send back a stool sample in a pre-paid envelope, and their scientists extract the DNA and apply our patented methodology combining whole-genome shotgun sequencing with a built-in-house bioinformatic pipeline.


2. Optimize: Your bacterial profile with a customized probiotic and tailored dietary insights.
  • In about 6 weeks, you'll receive the complete gut microbiome analysis with personalized scores through an online customer interface identifying the unique gut bacteria that makes you, you!
  • Additionally, Sun Genomics will provide a complete 30 consultation with a registered dietician, as well as
  • A thorough lists of foods to enjoy, minimize, or avoid and the rationale of why.
3. Improve: Health outcomes: ↓inflammation ↑energy ↑sleep ↑mental clarity ↑weight loss ↑skin vibrance ↑overall wellness.
  • After about another week, you'll get a three-month supply of precision probiotics manufactured just for you in the GMP facility in San Diego, California!

Every parent wants what’s best for their child and that’s where understanding the microbiome, gut health, nutrition, and healthy supplements can make the difference.