Building Your Microbiome from Birth

Part of The Secret World Inside You exhibition. 

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

Baby in Womb

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. 

Being Born

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. 

Human Newborn

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

Pregnant Woman

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.