Scientists reveal how gut microbes 'recover' after antibiotic treatment -- ScienceDailyWe also saw that as antibiotics removed bacteria and reduced their metabolic rates in the mouse gut, there was an increase in oxidising agents called electron acceptors," Reese explains. "This new environmental state meant that the microbial community which recolonised after treatment looked very different from the original community." The bacteria that appeared immediately following treatment, including some potentially harmful species, were able to take advantage of the electron acceptors to grow quickly. As they grew, they used up the excess resources, causing the gut environment to return to its normal state. However, this did not guarantee recovery of the original microbial community. "Antibiotics may drive some microbe species extinct in a gut community, so new microbial immigrants from outside the mouse -- in this case from an untreated mouse in the same cage -- were likely needed to return the microbiota to its original state," says senior author Lawrence David, Assistant Professor of Molecular Genetics and Microbiology at Duke University.