The absolute gut microbiome alters host physiology, varies by gut architecture and disease, and predicts response to therapy

To study the effect of alterations in microbial density on the host, conventional C57Bl6 mice were treated with polymyxin B, ciprofloxacin, vancomycin, clindamycin, or ampicillin for 4 weeks. These antibiotic regimens result in a differential reduction in fecal microbial density. RNA-seq of whole tissue from the proximal colon was performed on the antibiotic treated mice, germ free controls, and non-antibiotic treated controls to interrogate transcriptional changes in the host. Overall design: colonic gene expression in mice given one of four antibiotics (ampicillin, clindamycin, polymyxin B, vancomycin; n = 3 per group), compared to control mice (n = 5) and germ-free mice (n = 4)