Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 116, Issue 43, Pages 21392-21400Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1907567116
Keywords
antibiotics; gut microbiota; aggregation; population dynamics; bacteria
Categories
Funding
- Kavli Microbiome Ideas Challenge
- American Chemical Society
- American Physical Society
- Kavli Foundation
- National Science Foundation (NSF) [1427957, 0922951]
- M. J. Murdock Charitable Trust
- National Institutes of Health (NIH) [P50GM09891, P01GM125576-01, F32AI112094, T32GM007759]
- National Institute of Child Health and Human Development [P01HD22486]
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Antibiotics induce large and highly variable changes in the intestinal microbiome even at sublethal concentrations, through mechanisms that remain elusive. Using gnotobiotic zebrafish, which allow high-resolution examination of microbial dynamics, we found that sublethal doses of the common antibiotic ciprofloxacin cause severe drops in bacterial abundance. Contrary to conventional views of antimicrobial tolerance, disruption was more pronounced for slow-growing, aggregated bacteria than for fast-growing, planktonic species. Live imaging revealed that antibiotic treatment promoted bacterial aggregation and increased susceptibility to intestinal expulsion. Intestinal mechanics therefore amplify the effects of antibiotics on resident bacteria. Microbial dynamics are captured by a biophysical model that connects antibiotic-induced collapses to gelation phase transitions in soft materials, providing a framework for predicting the impact of antibiotics on the intestinal microbiome.
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