Antibiotics, birth mode, and diet shape microbiome maturation during early life

Abstract

Early childhood is a critical stage for the foundation and development of both the microbiome and host. Early-life antibiotic exposures, cesarean section, and formula feeding could disrupt microbiome establishment and adversely affect health later in life. We profiled microbial development during the first two years of life in a cohort of 43 US infants, and identify multiple disturbances associated with antibiotic exposures, cesarean section, and diet. Antibiotics delayed microbiome development and suppressed Clostridiales, including Lachnospiraceae. Cesarean section led to depleted Bacteroidetes populations, altering establishment of maternal bacteria. Formula-feeding was associated with age-dependent diversity deviations. These findings illustrate the complexity of early-life microbiome development, and microbiota disturbances with antibiotic use, cesarean section, and formula feeding that may contribute to obesity, asthma, and other disorders.

The role of early life nutrition in the establishment of gastrointestinal microbial composition and function

“…; however, effects of feeding on Lactobacillus abundance are inconsistent across other studies. Increased proportions of Lactobacillus, 25,26,48,54 as well as greater abundances of L. gasseri 28,47 in BF compared to FF infants have been reported, whereas other studies found opposite results 16,52,53 or reported intergroup variability and instability over time. 27,43 A greater prevalence 15 and higher proportion 24 and total counts 16,46 of C. difficile in FF compared to BF infants, as well as, significantly more Peptostreptococcaceae, 31 Akkermansia, 15 Veillonella, and Enterococcus 28 have been described.…”

“…Many studies have reported that BF infants are colonized with higher proportions of microbes from the phylum Actinobacteria and less Firmicutes than FF infants. 23,25,26,28,33 Other studies report that BF infants have similar levels of Actinobacteria and Firmicutes 28,30 but lower proportions of Bacteroidetes 31,36 and Proteobacteria 26,28 compared to FF infants.…”

“…15,23,31,33 Exclusive breastfeeding is inversely related to alphadiversity in 3 mo-old infants. 23 Conversely, exclusive breastfeeding and breastfeeding duration, 23 as well as predominant breastfeeding for the first 3 mos, 25 are positively related to alpha-diversity at 12 mos. Many studies have reported that BF infants are colonized with higher proportions of microbes from the phylum Actinobacteria and less Firmicutes than FF infants.…”

“…In addition, virulence factors of the microbiota of BF and FF infants affect the expression of immunity and defense genes in the host GI epithelium, 30 potentially contributing to programming of the intestinal immunological tone. More recently, Bokulich and colleagues 25 showed maturational differences, measured by age-dependent stages characterized by specific taxa that serve as markers for the rate of microbiota development, in BF and FF infant microbiota. These assessments are of interest to researchers as delayed development is often linked to physiological perturbations.…”

Impact of Early-Life Antibiotic Use on Gut Microbiota of Infants

“…Antibiotics use during infancy is closely associated with the changes in the composition of gut microbiota which last for more than 6 months. To resolve the origin of gut microbiota and thoroughly research the possible impact of antibiotics use and other environmental factors on gut microbiota, a team of researchers from the Massachusetts General Hospital (MGH) and the Broad Institute selected a cohort of 43 U.S. infants and analyzed microbial development during the first 2 years of life systematically [19]. They identified multiple disturbances associated with antibiotic exposures, cesarean section, and formula feeding.…”