Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability
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Author(s)
Yassour, Moran
Vatanen, Tommi
Siljander, Heli
Hämäläinen, Anu-Maaria
Härkönen, Taina
Ryhänen, Samppa J.
Franzosa, Eric A.
Vlamakis, Hera
Huttenhower, Curtis
Gevers, Dirk
Date Issued
June 2015
Journal
Science Translational Medicine
Publisher
American Association for the Advancement of Science (AAAS)
Citation
Yassour, Moran, Tommi Vatanen, Heli Siljander, Anu-Maaria Hämäläinen, Taina Härkönen, Samppa J. Ryhänen, Eric A. Franzosa, et al. “Natural History of the Infant Gut Microbiome and Impact of Antibiotic Treatment on Bacterial Strain Diversity and Stability.” Science Translational Medicine 8, no. 343 (June 15, 2016): 343ra81–343ra81.
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Author's final manuscript
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.
MIT Department
Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics
Institute for Medical Engineering and Science
Massachusetts Institute of Technology. Department of Biology
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DOI of Published Version
https://doi.org/10.1126/SCITRANSLMED.AAD0917
