Competitive suppression in human gut microbiome samples in presence of broad and narrow spectrum antibiotics

The aim of this project was to investigate how broad vs narrow-spectrum antibiotics affect the fitness of a resistant bacterial focal strain in presence of microbiome samples from three human donors. We inoculated the focal strain into microcosms (described in Baumgartner et al. PLoS Biology, 2020) containing the gut community and supplemented them with either a broad or narrow-spectrum antibiotic. We sequenced the initial microbiome samples from each human donor (n=3) and all the microcosms with the gut community (n=27) after 24h.