Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment

Yael R. Nobel, Laura M. Cox, Francis F. Kirigin, Nicholas A. Bokulich, Shingo Yamanishi, Isabel Teitler, Jennifer Chung, Jiho Sohn, Cecily M. Barber, David S. Goldfarb, Kartik Raju, Sahar Abubucker, Yanjiao Zhou, Victoria E. Ruiz, Huilin Li, Makedonka Mitreva, Alexander V. Alekseyenko, George M. Weinstock, Erica Sodergren and Martin J. Blaser ()
Additional contact information
Yael R. Nobel: New York University School of Medicine
Laura M. Cox: New York University School of Medicine
Francis F. Kirigin: New York University School of Medicine
Nicholas A. Bokulich: New York University School of Medicine
Shingo Yamanishi: New York University School of Medicine
Isabel Teitler: New York University School of Medicine
Jennifer Chung: New York University School of Medicine
Jiho Sohn: New York University School of Medicine
Cecily M. Barber: New York University School of Medicine
David S. Goldfarb: New York University School of Medicine
Kartik Raju: New York University School of Medicine
Sahar Abubucker: The Genome Institute at Washington University
Yanjiao Zhou: The Genome Institute at Washington University
Victoria E. Ruiz: New York University School of Medicine
Huilin Li: NYU Langone Medical Center
Makedonka Mitreva: The Genome Institute at Washington University
Alexander V. Alekseyenko: New York University School of Medicine
George M. Weinstock: The Genome Institute at Washington University
Erica Sodergren: The Genome Institute at Washington University
Martin J. Blaser: New York University School of Medicine

Nature Communications, 2015, vol. 6, issue 1, 1-15

Abstract: Abstract Mammalian species have co-evolved with intestinal microbial communities that can shape development and adapt to environmental changes, including antibiotic perturbation or nutrient flux. In humans, especially children, microbiota disruption is common, yet the dynamic microbiome recovery from early-life antibiotics is still uncharacterized. Here we use a mouse model mimicking paediatric antibiotic use and find that therapeutic-dose pulsed antibiotic treatment (PAT) with a beta-lactam or macrolide alters both host and microbiota development. Early-life PAT accelerates total mass and bone growth, and causes progressive changes in gut microbiome diversity, population structure and metagenomic content, with microbiome effects dependent on the number of courses and class of antibiotic. Whereas control microbiota rapidly adapts to a change in diet, PAT slows the ecological progression, with delays lasting several months with previous macrolide exposure. This study identifies key markers of disturbance and recovery, which may help provide therapeutic targets for microbiota restoration following antibiotic treatment.

Date: 2015
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DOI: 10.1038/ncomms8486

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