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

Author Image Katie Thomson MS, RD | Cofounder

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 hand-washing 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.[1][2] 

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]

Baby Boy reaching for square baby puree meals

What is the Microbiome?

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 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 a vaginal birth.[7] Turns out that pumping also falls behind on the scale of beneficial microbial transfer. The strains of bacteria and yeast that live on your skin are introduced to 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]

baby lying down with mouth open

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 (yoghurt, sauerkraut, kimchi, kombucha). You may be surprised by what they like!

Get 20% Off Square Baby!

Square baby - infant food - starting solids at 6 months

Use code "GUT20" at checkout for 20% off your first order!*
*new customers only

What can you do? 

Of course, we understand that an “easy” birth experience may not be how it happens.  There are several things 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. Most of the same strategies for healthy eating that work for adults also work for children[10].

So, what exactly should my baby be eating for optimal health and a happy gut?

The Academy of Pediatrics stresses the importance of offering a variety of textures and foods, especially fruits, veggies, whole grains, legumes, and pureed meats to help baby develop their palate, get essential nutrients, and learn to love a variety of foods.  They also note that there is no “perfect order” to introduce foods.

We love Dr Tanya Altmann’s book, “What to Feed Your Baby” that outlines the 11 Foundational Foods she recommends as a pediatrician a spokesperson for the Academy of Pediatrics.

Book title what to feed your baby

Dr Tanya is a champion for gut health and believes in daily probiotic use from foods like yogurt and kefir or supplements, especially in the winter months in which babies are more likely to catch a cold or virus. She notes, “Probiotics have been shown to help everything from constipation to acid-reflux.”

In addition to offering foods with probiotics like yogurt with live active cultures, you should also feed your little one high-fiber foods like fruits, veggies, and whole grains to FEED the good bacteria.

avocado and eggs pureed into baby food by square baby

Here’s Dr Tanya’s Top 11 Foundational Foods that support gut and overall health and development:

  • EGGS. The perfect single-ingredient food. Healthy source of protein, fat, and other nutrients like iron and biotin that are essential for infant growth and development. You can find Eggs in Square Baby’s “Veggie Scramble” and “Pumpkin Spice Eggnog”
  • PRUNES. Can help with constipation, a very common tummy problem for babies.
  • AVOCADOS. High in potassium, fiber, and heart-healthy monounsaturated fats. You can find Avocados in Square Baby’s “Avocado Greens” and “Veggie Scramble”
  • FISH. Fatty fish like Salmon are a great source of protein, Vitamin D (important for building bones, preventing illness, and lowering certain disease risk, including cancer), and omega-3 fatty acids, especially EPA and DHA (great for brain & eye development). You can find Salmon in Square Baby’s “Salmon Mash”
  • YOGURT, CHEESE & MILK. Dairy products are packed with 9 essential nutrients like calcium, potassium, phosphorus, protein, Vitamin A, D, B12, riboflavin, and niacin. While babies should not have regular cow’s milk in their first year (focus on breastmilk or formula until at least 12 months), yogurt and cheese can be introduced at 6 months of age. You can find Whole Milk Greek Yogurt in Square Baby’s “Beet Berry”, “Mango Rice Pudding”, “Greenie Baby”, “Peachy Oatmeal”, “Pumpkin Spice Eggnog”
  • NUTS and NUT BUTTERS. A great vegetarian source of protein, Vitamin E, and healthy monounsaturated fats. And contrary to previous recommendations, introducing nuts early does not put your child at risk of becoming allergic. Actually, studies are now showing that introducing potentially allergenic foods like peanuts earlier may decrease the chances of later developing an allergy. You can find Peanuts in Square Baby’s “Peanut Pumpkin Pie”
  • CHICKEN and/or BEANS/LENTILS. All are healthy sources of protein! Infants need an iron and zinc source at about 6 months of age, and chicken is great source. And legumes like beans or lentils are high in fiber, protein, vitamins, and minerals. You can find Chicken Bone Broth in Square Baby’s “Mango Coconut Chicken”, “Apple Curry Chicken”, and “Harvest Feast” and Beans or Sprouted Lentils in “Apple Rosemary Lentils”, “Minty Green”, “Spinach Dahl”, “Avocado Greens”, and “Peanut Pumpkin Pie”.
  • SUMMER BERRIES/WINTER CITRUS: Both are high in fiber and rich in vitamins, minerals, phytonutrients, and antioxidants like Vitamin C that help with vision, brain development, and disease prevention. You can find berries in Square Baby’s “Beet Berry”, and “Baby Blues”
  • GREEN VEGETABLES: Nutrient-dense powerhouses! That means calorie for calorie, foods like spinach, kale, green beans, and broccoli pack more nutrition than most foods. You can find loads of Green Veggies in Square Baby’s “Minty Green”, “Spinach Dahl”, “Avocado Greens”, “Apple Rosemary Lentils”, and “Greenie Baby”
  • WHOLE GRAINS. Whole grains like oats, brown rice, barley, and quinoa are a great source of dietary fiber, which aids in a healthy digestive system and feeds the healthy bacteria in our intestines. You can find a variety of Whole Grains in every Square Meal, including sprouted brown rice, sprouted amaranth, sprouted millet, sprouted quinoa, barley, and oats.

Get 20% Off Square Baby!

Square baby - infant food - starting solids at 6 months

Use code "GUT20" at checkout for 20% off your first order!*
*new customers only

    We know that finding the right mix of nutrition for your child can be extremely difficult, especially if you have a picky eater (just about every toddler) and you don’t have the time to cook delicious organic, colorful foods everyday (almost all of us).  Don’t worry! Square Baby and Sun Genomics have got you covered!

    probiotics for baby

    Square Baby offers on-demand delivery of our Square Meal System–a foolproof way to give your baby 100% daily nutrition! Rooted in nutrition science, our team of Registered Dietitians and Pediatricians create tailored meal plans to offer 100% of your baby’s daily fruits, vegetables, grain, and protein servings based on USDA recommendations.  This takes the guess work out of nutrition and meal prep  — making it easier to feed your child healthy and great tasting foods!  Boom. 

    healthy green puree baby food and baby food jars stacked by square baby

    Sun Genomics’, Floré combines whole genome DNA analysis with precision probiotics custom formulated based on a persons’ unique DigestiveDNA™. The customer’s microbiome journey begins when they register for the customer portal and receive their microbiome sampling kit. Once the customer provides a stool sample, Sun Genomics’ scientists extract the DNA and apply our patented methodology combining whole genome shotgun sequencing with a built-in-house bioinformatic pipeline. The customer then receives their microbiome analysis through an online customer interface identifying the bacteria within their gut as well as a three-month supply of precision probiotics manufactured in the GMP facility in San Diego, California.

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

    This blog post is for information purposes only and shouldn’t be used as personal, health, nutritional, or medical advice. Always consult with your pediatrician before making any decisions about your child’s health or readiness for various foods.











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