Building Your Microbiome from Birth

Part of the The Secret World Inside You exhibition.

Part of The Secret World Inside You exhibition. 

You inherited all your human DNA from your parents—but your microbiome is more complicated. 

Rendering of a fetus in the womb with the umbilical cord still attached.
Babies in the womb encounter no microbes until they are born.
© AMNH/B. Peterson

Most babies get their first big dose of microbes at birth, while traveling through the birth canal, then pick up more while breastfeeding. Early microbes helped shape your immune system, your digestive system, even your brain. 

In the Womb

Exposure to bacteria before birth could be deadly for a fetus. So for nine months it grows in a nearly sterile “safe zone.” Since the fetus can’t eat or breathe, it gets everything it needs from its mother’s blood, including oxygen and nutrients. 


To get from the womb to the world, most babies make their way out through the birth canal. This is a big day for baby and microbiome alike, because unlike the womb, the birth canal is chock full of bacteria. 

A newborn baby held by a medical professional wearing gloves and a smock.
Newborn babies get their first microbiome from their mother during birth.
Wikimedia Commons

During that journey, a newborn baby gets completely covered with bacteria, giving it a brand-new microbiome.

Some evidence suggests that births by Cesarean section may impact a baby’s immune system, and could be a factor in the development of conditions including food allergies and asthma.

Early Years

Perfected by millions of years of evolution, mammalian breast milk contains the exact nutrients a baby needs—and the right bacteria, too. And breast milk doesn't feed just the baby. It also feeds the baby’s microbiome. 

These bacteria, and others that feed on breast milk, jump start the baby’s immune system and digestive system, help prevent infection and even affect brain development.

The early microbiome trains the body’s immune system to attack potentially dangerous microbes but leave benign ones alone.

Rites of Passage

An exposed pregnant belly.
Big life changes, like a pregnancy, can alter a person’s microbiome.
Wikimedia Commons

Your microbiome can change in big ways at various stages of your life. The biggest shifts occur when you have a major change in diet, but adolescence, pregnancy, and old age can also alter your microbiome. So can malnutrition, disease, and the use of antibiotic drugs.

Return to The Secret World Inside You main exhibition page.