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TY - JOUR AU - Willing, Benjamin P. AU - Russell, Shannon L. AU - Finlay, B. Brett PY - 2011 DA - 2011/04/01 TI - Shifting the balance: antibiotic effects on host–microbiota mutualism JO - Nature Reviews Microbiology SP - 233 EP - 243 VL - 9 IS - 4 AB - Antibiotics have substantial direct and indirect effects on the intestinal microbiota; although some of the changes disappear soon after cessation of the antibiotic treatment, other changes remain indefinitely. Owing to their substantial effects on the microbiota, antibiotics have been used experimentally to identify groups of bacteria that correlate with changes in immunity and disease susceptibility.Throughout the course of evolution, the host has become dependent on its microbiota for many functions, including the maintenance of intestinal immune homeostasis. Changes in the microbiota that are induced by antibiotic treatment and are important to immunity include the loss of bacterial ligands that are recognized by the host, changes in the metabolites that are produced by the microbiota and the loss of specific bacterial signals.Studies using antibiotics have revealed that the microbiota not only contributes to development, but also is required for the maintenance of immune function. Many changes in immunity have been observed in response to antibiotics, including reduced secretion of antimicrobial peptides and changes in T helper cell populations. Changes in immunity that result from antibiotic treatment result in increased susceptibility to infection.Antibiotics have been used to implicate the gastrointestinal microbiota in a number of systemic biological processes, including elements of systemic immunity and extra-intestinal disease susceptibility. Antibiotics have linked the intestinal microbiota to models of allergies, autism, metabolic syndrome and multiple sclerosis.There are several challenges that need to be considered when using antibiotics to study host–microbial interactions. Direct effects on the immune system, reproducibility with respect to the duration and number of antibiotic exposures, antibiotic resistance and individualized responses to the same treatment all influence the outcome of antibiotic studies. Currently, most antibiotic studies remain correlative owing to the lack of targeted approaches available.There is a need to develop strategies to mitigate the effects of antibiotics on the immune system. Promising approaches include bacteriotherapy and exogenous immune activation with bacterial ligands. SN - 1740-1534 UR - https://doi.org/10.1038/nrmicro2536 DO - 10.1038/nrmicro2536 ID - Willing2011 ER -