Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability.

Sci Transl Med
Authors
Abstract

The gut microbial community is dynamic during the first 3 years of life, before stabilizing to an adult-like state. However, little is known about the impact of environmental factors on the developing human gut microbiome. We report a longitudinal study of the gut microbiome based on DNA sequence analysis of monthly stool samples and clinical information from 39 children, about half of whom received multiple courses of antibiotics during the first 3 years of life. Whereas the gut microbiome of most children born by vaginal delivery was dominated by Bacteroides species, the four children born by cesarean section and about 20% of vaginally born children lacked Bacteroides in the first 6 to 18 months of life. Longitudinal sampling, coupled with whole-genome shotgun sequencing, allowed detection of strain-level variation as well as the abundance of antibiotic resistance genes. The microbiota of antibiotic-treated children was less diverse in terms of both bacterial species and strains, with some species often dominated by single strains. In addition, we observed short-term composition changes between consecutive samples from children treated with antibiotics. Antibiotic resistance genes carried on microbial chromosomes showed a peak in abundance after antibiotic treatment followed by a sharp decline, whereas some genes carried on mobile elements persisted longer after antibiotic therapy ended. Our results highlight the value of high-density longitudinal sampling studies with high-resolution strain profiling for studying the establishment and response to perturbation of the infant gut microbiome.

Year of Publication
2016
Journal
Sci Transl Med
Volume
8
Issue
343
Pages
343ra81
Date Published
2016 Jun 15
ISSN
1946-6242
DOI
10.1126/scitranslmed.aad0917
PubMed ID
27306663
PubMed Central ID
PMC5032909
Links
Grant list
P30 DK043351 / DK / NIDDK NIH HHS / United States
R01 AI062773 / AI / NIAID NIH HHS / United States
R01 DK060049 / DK / NIDDK NIH HHS / United States
R01 DK092405 / DK / NIDDK NIH HHS / United States
U54 DK102557 / DK / NIDDK NIH HHS / United States
Additional Materials