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Baby's First Biome

A Guide to Babying Their Biome

By Denise Cartwright, CRUDE Founder/CEO

As soon as a baby is born, millions of bacteria begin to colonize its tiny body — making their new home in the baby’s gut, mouth, skin, ears, and in between their toes.

These microscopic bacteria are transferred from mom to babe during birth, and afterward as she holds the baby close, skin-to-skin. From the very beginning, human life is dependent on bacteria, our “invisible organ” whose importance we’re only just beginning to understand.

The human body has as many if not more bacterial cells than human cells —most of which are harmless, and many of which are helpful. Research is increasingly uncovering the wide ranging effects that these bacteria, our microbiomes, have on our bodily health — from gut and skin health to mental health and the prevention of allergies. Our resident flora, or microbiome, is responsible for helping develop and train our body’s immune system, teaching it to respond to our body’s needs over the course of our life. 

The first 1000 days of a baby’s life provides an important window of development for the microbiome. Studies suggest, for instance, that the state of a baby’s microbiome in the first two years of life may predict later risk of obesity and increased risk of metabolic and autoimmune diseases such as type 1 diabetes and asthma. The microbiome may also be particularly important in the development of the newborn brain, with potential outcomes ranging from effects on cognition, anxiety, mood, and sociability. There’s a lot we still don’t know about the microbiome, but research is beginning to uncover some interesting clues about how our lifestyles and environment could affect the complex bacterial universes on each of us. We did our research and compiled our favorite science-backed insights to help you navigate (and cultivate) your baby’s biome. 

Bring on the Fiber

Beyond the early months of infancy and breastfeeding, a diet high in fiber is associated with a healthier, more diverse gut microbiome. The introduction of a diet rich in complex carbohydrates can help feed the child’s healthy bacteria and create an environment in the gut for them to thrive — protecting the child from inflammation and pathogenic bacteria. This goes for mom, too! A high-fiber diet could be one of the most foundational ways to help gut bacteria flourish in humans of all ages.

Protect Baby’s Natural Oils

The skin naturally produces a thin, oil-based “shield” called the natural moisture barrier. This barrier maintains the skin’s proper pH and bacterial balance, and retains essential moisture in the body. At least in the case of pre-term babies, this protective barrier is literally life-saving. The skin is a significant entry point for life-threatening bloodstream infections, and a weak moisture barrier allows allergens and irritants to more easily enter the body, leading to higher rates of disease. Research from Stanford’s Gary Darmstadt shows that sunflower oil effectively strengthens this barrier, reducing neonatal mortality by 27% and hospital acquired infection by 50%. This is huge, and shows the value of keeping baby’s skin properly moisturized with safe ingredients— but it’s also important to take it one step further, by taking steps to ensure that you’re not stripping the babe’s protective oils to begin with.

Soaps & Antibiotics: Proceed with Caution

Soaps and sudsing cleansers unnecessarily strip the skin’s natural moisture barrier of its resident bacteria. Washing your hands with soap is an important measure for preventing the spread of disease, but soap is far too aggressive for chronic full-body use, especially for babies. To protect baby’s biome, it’s important to avoid harsh cleansers that strip nature’s protective goodness. Antibiotic exposure also alters the microbial profiles of both mom and babe, and should be used with discretion at all ages to avoid disrupting the body’s beneficial bacteria and risking antibiotic resistance. This is especially important during the first few years of a child’s life as their microbiome is developing — proceed with caution and definitely consult your doc regarding any potential health concerns. 

Go Outside (and consider pets)

Exposure to germs in childhood is thought to help strengthen the immune system and protect children from developing allergies and asthma. The best way to help your nature thrive could be to, well, get out in nature. It may also be helpful to bring nature inside the home — having pets has been associated with increased microbial diversity. Both having pets and time spent in nature have proven to boost mental health by decreasing the stress hormone, cortisol — which is also a bonus for your biome. Elevated levels of cortisol have been shown to trigger a negative change in the microbiome, switching once friendly bacteria into harmful, pathogenic ones. Maintaining emotional homeostasis could help us maintain bacterial homeostasis — it’s truly all connected, isn’t it? 

Breastfeed (when possible)

Possibly the biggest influence on baby’s biome is what they’re fed. Breast milk, nature’s perfect baby formula — is full of hormones, antibodies, and you guessed it, beneficial bacteria. These invisible helpers colonize the infant’s gut and set the course for the baby’s growing immune system and metabolism. Emerging research suggests that breastfed infants are less likely to be colonized by potentially pathogenic organisms like C. difficile and E. Coli bacteria, and direct breastfeeding without a pump is associated with a higher overall bacterial richness and diversity.

And breast milk’s brilliance doesn’t end there — backwash from nursing babies may even trigger infection fighters in mom, changing the composition of the breast milk itself to support baby’s immune system. This adds to the long list of reasons breastfeeding should be normalized and supported in work and public spaces, but there are many reasons it’s not always possible to breastfeed your babe. If it’s not happening, don’t fret — pumped milk and formula still offer the other goodness and nutrients found in breast milk. Probiotics and prebiotics are also increasingly being used in baby formula; ask your doctor if they can help you find one that’s safe for your baby.


We’re committed to providing the education that support you, your family, our biomes, and our living planet — and we think that starts by trusting, rather than interfering, with nature’s brilliant regenerative systems. We’d love to know how you’re promoting bacterial diversity and homeostasis in your life and with your family, so don’t hesitate to comment or email us at with your tips and suggestions. Happy seeding!

About the Author

Denise Cartwright is the Founder and CEO of CRUDE, and a Master Esthetician with 12+ years of experience. A lifelong Utahn, she's passionate about the natural world, plant medicine, and wellness. Check her out on Instagram @dkcartwright.

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