The microbiome begins at birth by Dr. Dee | Feminine Systems Health Series

“We’re not born alone. We’re born with a bacterial blueprint.”

When we think of birth, we imagine the first cry, the first breath, the warmth of a mother’s chest. But behind the scenes, something profound is unfolding—a baby’s body is being seeded with microbes that will shape their health for decades to come. This is the birth of the microbiome.

What is the Microbiome?

The human microbiome is a vast, intelligent ecosystem of trillions of microbes—mostly bacteria, but also viruses, fungi, and archaea—living in and on us. The gut microbiome, in particular, plays a critical role in digestion, immunity, brain development, and even hormonal balance.

But what most people don’t realize is this:
Your baby’s microbiome starts forming the moment they are born. And the way we birth, feed, touch, and nurture in those early days has a lifelong ripple effect.

There are a lot of health conditions which are associated with “gut microbiome”.

Diseases	Microbiome Association
Digestive	IBS, IBD, Celiac, Colon cancer, SIBO
Immune	Type 1 Diabetes, RA, MS, Lupus, Asthma
Metabolic	Obesity, Type 2 Diabetes, NAFLD
Neurological	Depression, Anxiety, Autism, Parkinson's, Alzheimer's
Skin	Eczema, Psoriasis, Acne
Hormonal	PCOS, Endometriosis, Infertility, GDM
Miscellaneous	Chronic fatigue, Long COVID, Cancer response, Kidney disease

Birth: The First Bacterial Transfer

During vaginal birth, the baby is naturally exposed to the mother’s vaginal and gut flora. This isn’t contamination—it’s colonization. Babies born vaginally receive Lactobacillus and Bifidobacterium, two foundational bacteria that help establish a balanced immune system and gut lining.

In contrast, babies born via C-section often miss this initial seeding. Instead, they pick up skin-based bacteria from the surgical environment—Staphylococcus, for example—which can lead to a higher risk of allergies, asthma, obesity, and metabolic diseases.

That’s not to say C-sections are bad—sometimes they’re life-saving. But awareness gives us the power to make restorative choices.

Breastfeeding: Nature’s Prebiotic Blueprint

Breastmilk is more than food. It’s information. Rich in human milk oligosaccharides (HMOs)—which babies can’t even digest—breastmilk is designed to feed gut bacteria, not just the baby.

These HMOs selectively nourish Bifidobacterium infantis, a superhero microbe that helps reduce inflammation, digest milk sugars, and protect against pathogens.

Even one drop of colostrum—the golden first milk—is like a probiotic shot for your baby’s future.

Skin-to-Skin & Sensory Seeding

Microbiome health is also influenced by touch, environment, and maternal closeness. Skin-to-skin contact, kangaroo care, and exposure to the family home (rather than hyper-sterile NICUs or overuse of antiseptics) help babies build microbial resilience.

In rural India, grandmothers used to rub babies with oils and herbs passed down over generations—not just for softness, but to expose the baby’s skin to healthy family flora.

We lost this wisdom to modern “germophobia.”
It’s time to reclaim it with evidence-backed reverence.

Formula Feeding & Antibiotics: What to Know

If breastfeeding isn’t possible, or if antibiotics are needed, don’t panic. What matters is what we do next:

• Choose formulas with added prebiotics and probiotics.
• Consider probiotic supplementation (under pediatric guidance).
• Avoid unnecessary antibiotics in infancy unless clinically indicated.
• Support the mother’s gut health too—it’s all connected.

Simple Rituals to Support the Baby’s Microbiome:

• Prioritize vaginal birth when safely possible.
• Delay first bath by at least 24 hours.
• Breastfeed exclusively for the first 6 months if possible.
• Practice skin-to-skin for at least 1 hour a day in the first month.
• Introduce solids mindfully (including fermented foods like kanji or curd rice in later weaning stages).
• Protect and nourish the mother’s gut too—her flora is the baby’s foundation.

Let’s raise a generation of microbiome-rich, immune-resilient, gut-wise children—starting from the very first breath.