Given the differential impact of pr

Given the differential impact of probiotics and aFMT, as compared to watchful waiting, on the recovery of mucosal gut microbiome composition and function, we next sought to characterize the effect of the three post-antibiotics interventions on the host. To this aim, we performed a global gene expression analysis through RNA sequencing of transcripts collected from stomach, duodenum, jejunum, terminal ileum, cecum, and descending colon biopsies immediately after antibiotics treatment and 3 weeks later into the three post-antibiotic interventions (Figure 3A). Of note, antibiotics affected the transcriptional landscape across the GI tract, with the majority of differences between naive and antibiotics state observed in the descending colon (Figure 6A). Importantly, restoration of the antibiotics-naive host transcriptional landscape by the three post-antibiotics intervention arms mirrored our findings in the microbiome, as multiple genes across the GI tract that were significantly affected