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

By Nicholas A. Bokulich, Jennifer Chung, Thomas W. Battaglia, Nora Henderson, M. Jay, Huilin Li, Arnon D. Lieber, Fen Wu, G. Perez-Perez, Yu Chen and 5 more. Science Translational Medicine, 2016

1,267 citations recorded by the source corpus.

A longitudinal study of intestinal microbiota in children and their mothers shows that antibiotics, cesarean section, and infant formula alter patterns of microbial acquisition and succession during the first 2 years of childhood. Snapshots of the developing infant gut microbiota The intestinal “microbiota,” that is, the community of microbes inhabiting the human intestinal tract, undergoes many changes during the first 2 years of life. Bokulich et al. now show that this pattern of development is altered in children who are delivered by cesarean section, fed formula, or treated with antibiotics, compared to those babies who were born vaginally, breast-fed, or unexposed to antibiotics. Future studies will determine whether these disturbances influence the health of these babies. 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 2 years of life in a cohort of 43 U.S. infants and identified multiple disturbances associated with antibiotic exposures, cesarean section, and formula feeding. These exposures contributed to altered establishment of maternal bacteria, delayed microbiome development, and altered α-diversity. These findings illustrate the complexity of early-life microbiome development and its sensitivity to perturbation.

Subfields: Gastroenterology, Molecular Biology, Public Health, Environmental and Occupational Health

View Paper: https://www.semanticscholar.org/paper/0192801c452e999872773610694a8e90e033551c

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Citations in the corpus

U.S. immigration westernizes the human gut microbiome (2018, methodology): “We also performed extensive analysis and modeling of differences in dietary intake, as diet is known to be a strong driver of microbiome variation (Bokulich et al., 2016; David et al., 2014; Muegge et al., 2011).”
Natural history of the infant gut microbiome and impact of antibiotic treatments on strain-level diversity and stability (2015, background): “Another study published in this issue (54) compared a similar number of children with and without antibiotic treatments, using a population born in the United States that had a higher rate of cesarean deliveries than our cohort.”
The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota (2017, background): “This is due to a rapid decrease of bifidobacteria, being replaced in relative abundance by Bacteroides spp. and members of the Lachnospiraceae and Ruminococcaceae families.”
Antibiotics as Major Disruptors of Gut Microbiota (2020, background): “Numerous studies have shown links between changes in the composition of the gut microbiota and diseases, including recurrent diarrhea associated with C. difficile, some bowel disorders (including IBD), colorectal cancer, non-alcoholic steatohepatitis, type 2 diabetes, obesity, and advanced chronic l”
A new antibiotic selectively kills Gram-negative pathogens (2019, neutral): “Disrupting the microbiome by antibiotics, especially early in life, is a major concern, given the important role of symbiotic bacteria in many aspects of human health, such as shaping the immune system during development 14 .”
Maturation of the Infant Microbiome Community Structure and Function Across Multiple Body Sites and in Relation to Mode of Delivery (2017, neutral): “Since other studies have not reported maternal gestational nor Type II diabetes as characteristics of their cohort, we cannot directly compare nor speculate as to whether their findings might be a result of confounding or co-linearity 24,40,42–44 , 52 .”
A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome (2017, background): “Several studies have reported significant differences in the diversity and composition between vaginally versus C-section-delivered infants [101, 105, 106, 108], with vaginally born infants harboring an early microbiome that resemble that of the vagina, while the microbiomes of C-section infants ref”
The gut microbiome: Relationships with disease and opportunities for therapy (2018, background): “, 2018), early-life diet (Bäckhed et al., 2015; Bokulich et al., 2016; Stokholm et al., 2016), antibiotic use (Bokulich et al.”
Role of the microbiome in human development (2019, background): “80 Lack of maternal microbiota exposure at birth, as happens in the C-section born, leads to alterations in the microbiota of babies 30 49 and in fatty acid and bile acid metabolism.”
QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data (2020, methodology): “In this tutorial, we use the QIIME 2 command-line interface, and focus on processing and analyzing a subset of samples from the Early Childhood Antibiotics and the Microbiome (ECAM) study (Bokulich, Chung, et al., 2016).”
An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography (2016, background): “Recent studies have found significant overlap in species between mothers and their infants over the first year of life (Backhed et al. 2015; Bokulich et al. 2016), and many microbial taxa that are heritable (Goodrich et al. 2016).”