Modern human habits, she said, can interfere with this early exposure at every turn; babies may be born by cesarean section, without exposure to the birth canal and its bacteria; they may be bottle-fed instead of breast-fed; they may sleep far away from their mother; and they may well be treated with antibiotics for one infection or another. (The American Academy of Pediatrics recommends breastfeeding for the first year of life, and recommends that infants should sleep in the same room as their parents but on separate safe surfaces to reduce the risk of sleep-related deaths.)

In a study published in 2016, on which Dr. Dominguez-Bello collaborated, scientists profiled the microbial development of a group of babies in the United States, examining the ways in which their bacterial populations were affected by mode of birth, by formula feeding versus breast-feeding, and by antibiotic exposure. In her research in the Amazon basin of South America, she said she has found that in rural houses and huts, most of the bacteria are related to the surrounding environment. In such settings, she said, the mother is more likely to carry the baby, and to sleep with the baby, both of them exposed to bacteria from plants and soil.

As houses become more enclosed and more subdivided, she said, spaces are increasingly separated by areas of use, and the speed at which outside air replaces inside air is decreased. “What happens is, we reduce the exposure to external environmental bacteria, so we become the main source of bacteria, our skin, our mouth, we shed bacteria, and the house becomes highly humanized, most of the bacteria in a house in a city will be human,” she said.