Metagenomic survey of the gut microbiome of term infants in the United States reveals widespread dysbiosis, absence of B. infantis, and high abundance of antibiotic resistance genes.. Metagenomic survey of the gut microbiome of term infants in the United States

During the neonatal period, the gut microbiome plays an important role in protecting infants from infections while favoring the development of the immune system. However, there are few studies surveying the gut microbiome of term infants across the United States during this critical developmental window. To address this gap, we performed a multi-site survey to profile the gut microbiome of term infants in five states using shotgun metagenomics. Our survey found that Bifidobacterium are less abundant among term infants than generally assumed, B. infantis was missing in 97% of the population, resulting in a limitation of human milk oligosaccharide utilization capacity. Antibiotic resistance genes and bacteria associated with inflammation and gut dysbiosis are also widespread in the United States, independent of location, age, and diet. These findings may provide additional insight into the current state of the term infant gut microbiome and the potential risks for infant health and development.