The community of bacteria that populate our intestines, called the gut microbiome, plays an important part in regulating metabolism and immune responses. However, little has been known about how the microbiome develops in childhood and the sorts of things that affect its development positively and negatively.

What we do know is that babies and children who lack a diverse population of bacteria in their microbiome in childhood are more likely to develop asthma, allergies, diabetes and obesity later in life. And now two studies suggest that treatment with antibiotics, cesarean delivery and the use of formula can all reduce the desirable diversity of bacteria in the gut.

Cesarean delivery, treatment with antibiotics and formula feeding can reduce the number of different types of bacteria in the infants’ gut microbiome.

In the first study, researchers from New York University followed the development of the microbiome in 43 infants for two years after birth. They collected stool samples from the infants 12 to 24 hours after delivery and then every month for the first year of their lives.

Samples were collected every six months during the second year. Vaginal swabs, rectal swabs and stool samples were collected from each mother twice: once before giving birth and once afterward.

The researchers found that cesarean delivery, treatment with antibiotics and formula feeding can reduce the number of different types of bacteria in the infants’ gut microbiome. They also report that breastfeeding, skin contact and the diversity of the bacteria of the mother’s own microbiota, which populates the infant gut during vaginal birth, appear to influence the development of a healthy diversity of gut microbes in babies.

In a second study, researchers in the U.S. and Finland collected stool samples from 39 babies every month for three years. They found that antibiotic therapy reduced gut microbiome diversity and led to a temporary rise in genes related to antibiotic resistance.

They also noted that all infants delivered via cesarean section and about 20 percent of those delivered vaginally lacked Bacteriodes, a type of bacteria that regulates intestinal immunity. Children treated with antibiotics also had a less diverse and less stable gut microbiome.

The average American child receives three courses of antibiotics before the age of two, and as the NYU researchers point out, “The hidden costs imply the need for careful consideration in children with less severe illnesses.”

It may be a good idea to check with your child’s pediatrician before giving your child antibiotics that may be left over in your medicine cabinet from the last time he or she was sick or before asking for a prescription. Although cesarean section delivery and antibiotics both offer real benefits, neither comes without risks to a healthy infant gut and the long-term health it can help establish.

Both studies are published recently in Science Translational Medicine.