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Antibiotics and the gut microbiota
Sheetal R. Modi, … , James J. Collins, David A. Relman
Sheetal R. Modi, … , James J. Collins, David A. Relman
Published October 1, 2014
Citation Information: J Clin Invest. 2014;124(10):4212-4218. https://doi.org/10.1172/JCI72333.
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Review

Antibiotics and the gut microbiota

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Abstract

Antibiotics have been a cornerstone of innovation in the fields of public health, agriculture, and medicine. However, recent studies have shed new light on the collateral damage they impart on the indigenous host-associated communities. These drugs have been found to alter the taxonomic, genomic, and functional capacity of the human gut microbiota, with effects that are rapid and sometimes persistent. Broad-spectrum antibiotics reduce bacterial diversity while expanding and collapsing membership of specific indigenous taxa. Furthermore, antibiotic treatment selects for resistant bacteria, increases opportunities for horizontal gene transfer, and enables intrusion of pathogenic organisms through depletion of occupied natural niches, with profound implications for the emergence of resistance. Because these pervasive alterations can be viewed as an uncoupling of mutualistic host-microbe relationships, it is valuable to reconsider antimicrobial therapies in the context of an ecological framework. Understanding the biology of competitive exclusion, interspecies protection, and gene flow of adaptive functions in the gut environment may inform the design of new strategies that treat infections while preserving the ecology of our beneficial constituents.

Authors

Sheetal R. Modi, James J. Collins, David A. Relman

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Figure 1

Microbial community-wide effects of antibiotics on the human gut microbiota.

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Microbial community-wide effects of antibiotics on the human gut microbi...
Antibiotic treatment alters the population structure of the indigenous microbiota, reducing bacterial diversity and redistributing member composition in both transient and persistent effects. Changes to the highly co-evolved microbial community architecture lead to changes in resource availability and species-species interactions, opening niches available for pathogenic intrusion and leading to the loss of colonization resistance. Antibiotics also select for antibiotic-resistant community members, enriching the presence of resistance genes in the microbiome. Treatment with antibiotics promotes the transfer of genetic information among bacteria by increasing conjugation, phage transduction, and plasmid mobility, primarily through the activation of cellular stress responses.
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