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Updated: Oct 21, 2025
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Quantitative Polymerase Chain Reaction-based Analyses of Murine Intestinal Microbiota After Oral Antibiotic Treatment
Published on: November 17, 2018
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Quantifying rapid bacterial evolution and transmission within the mouse intestine
Kimberly S Vasquez1, Lisa Willis2, Nate J Cira2
1Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Cell Host & Microbe
|September 2, 2021
Summary
Understanding gut microbiota evolution is key. This study reveals rapid, predictable selection and transmission dynamics of Escherichia coli strains in mice, highlighting the interplay between host environment and microbial evolution.
Area of Science:
- Microbiology
- Genomics
- Evolutionary Biology
Background:
- Gut microbiota colonization and transmission dynamics are poorly understood due to challenges in high-resolution strain tracking.
- Previous studies lacked the ability to track individual microbial strains and their evolutionary trajectories within the gut.
Purpose of the Study:
- To investigate strain-level dynamics and selection processes during gut microbiota colonization and transmission.
- To identify genetic factors driving microbial adaptation within the host intestinal environment.
Main Methods:
- Introduction of hundreds of barcoded Escherichia coli strains into germ-free mice.
- Quantification of strain-level dynamics and metagenomic changes using high-resolution tracking.
- Whole-genome sequencing of isolates to identify genetic variations and linked alleles.
Main Results:
- Rapid and reproducible selection of mutations in motility and metabolite utilization genes within days.
- Coprophagy (consumption of feces) led to similar barcode distributions across co-housed mice, indicating transmission.
- Population genetics modeling predicted significant fitness advantages for certain mutants and daily migration rates.
- Ciprofloxacin treatment revealed interplay between selection and transmission, including selection for resistance during bottlenecks.
Conclusions:
- Gut microbiota evolution is shaped by a combination of rapid, deterministic selection and environmental transmission.
- High-resolution strain tracking is crucial for understanding microbial population dynamics and adaptation.
- The study provides a framework for dissecting the evolutionary forces governing the intestinal microbiota.
