Two new studies of more than 80 infants together offer a clearer picture of how antibiotics, along with birth mode and diet, can disrupt the development of the gut microbiome. Children repeatedly treated with antibiotics during the first few years of life not only showed lower microbial diversity, but also harbored antibiotic resistance genes, temporarily, after treatment. Further studies are needed to probe the long-term consequences of these gut microbiome disturbances, which have previously been linked to obesity, diabetes, asthma, and to allergies later in life. The community of bugs that resides in our intestines plays a critical role in regulating the body's metabolism and immune defenses. However, how the gut microbiome develops during early childhood is not fully understood. Less still is known about how the infant microbiome responds to and recovers from environmental perturbations, including those from antibiotic treatment, cesarean section (versus vaginal delivery), and formula feeding (compared to breast-feeding). Antibiotic treatment among children is routine in most parts of the world, with the average American child receiving three courses of antibiotics by age two. To gain more insights into the possible consequences, Nicholas Bokulich and colleagues tracked the microbial development of 43 U.S. infants for two years after birth, collecting their stool samples as well as additional samples from their mothers before and after birth. They found that antibiotics, cesarean delivery, and formula feeding can delay infants' microbiome development and reduce bacterial diversity. The mother's own microbiota, which is known to populate the infant gut during passage through the birth canal, may also influence the healthy development of the infant's microbiota, as may breast-feeding and skin contact.
In a second study analyzing stool samples collected from 39 children over three years, Moran Yassour and colleagues also found that repeated antibiotic treatment reduced gut microbial diversity and even led to a transient rise in antibiotic resistance genes. In the first few months of life, all infants born by cesarean section and, unexpectedly, about 20% of those born by vaginal delivery lacked Bacteroides, bacteria known to help regulate intestinal immunity, suggesting that birth mode and other factors can strongly influence bacterial diversity. Antibiotic-treated children also had less diverse and less stable microbiota at the level of both species and strain. Furthermore, the researchers detected antibiotic resistance genes that rapidly peaked in abundance following antibiotic treatment, before sharply declining. Interestingly, for reasons not fully understood, some infants as young as two months old harbored antibiotic resistance genes, even without any exposure to antibiotics. In related audio files, authors Yassour and Ramnik Xavier highlight the findings' public health implications for infants and children who are routinely treated with antibiotics.