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Cell Host Microbe. 2015 May 13;17(5):553-64. doi: 10.1016/j.chom.2015.04.006.

Antibiotics, pediatric dysbiosis, and disease.

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Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA.
Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA.
Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA. Electronic address:


Antibiotics are by far the most common medications prescribed for children. Recent epidemiological data suggests an association between early antibiotic use and disease phenotypes in adulthood. Antibiotic use during infancy induces imbalances in gut microbiota, called dysbiosis. The gut microbiome's responses to antibiotics and its potential link to disease development are especially complex to study in the changing infant gut. Here, we synthesize current knowledge linking antibiotics, dysbiosis, and disease and propose a framework for studying antibiotic-related dysbiosis in children. We recommend future studies into the microbiome-mediated effects of antibiotics focused on four types of dysbiosis: loss of keystone taxa, loss of diversity, shifts in metabolic capacity, and blooms of pathogens. Establishment of a large and diverse baseline cohort to define healthy infant microbiome development is essential to advancing diagnosis, interpretation, and eventual treatment of pediatric dysbiosis. This approach will also help provide evidence-based recommendations for antibiotic usage in infancy.

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