Project description:Pseudomonas aeruginosa is known to tolerate antibiotic therapy during infection. This prevents clearance of infection and negatively impacts patient outcomes. Here, we report the transcriptome sequence of antibiotic-treated and untreated P. aeruginosa cultures and the differential gene expression observed when treated cells are compared to untreated cells.
Project description:The diverse bacterial communities that colonize the gastrointestinal tract play an essential role in maintaining immune homeostasis through the production of critical metabolites such as short chain fatty acids (SCFA), and this can be disrupted by antibiotic use. However, few studies have addressed the effects of specific antibiotics longitudinally on the microbiome and immunity. We evaluated the effects of four specific antibiotics; enrofloxacin, cephalexin, paromomycin, and clindamycin; in healthy female rhesus macaques. All antibiotics disrupted the microbiome, including reduced abundances of fermentative bacteria and increased abundances of potentially pathogenic bacteria, including Enterobacteriaceae in stool, and decreased Helicobacteraceae in the colon. This was associated with decreased SCFAs, indicating altered bacterial metabolism. Importantly, antibiotic use also substantially altered local immune responses, including increased neutrophils and Th17 cells in the colon. Furthermore, we observed increased soluble-CD14 in plasma, indicating microbial translocation. These data provide a longitudinal evaluation of antibiotic-induced changes to the composition and function of colonic bacterial communities, associated with specific alterations in mucosal and systemic immunity.
Project description: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.
Project description:Myeloid progenitors derived from antibiotic-treated mice have cell-intrinsic functional defects. In this microarray dataset, the transcriptomes of bone marrow myeloid progenitors from antibiotic-treated and control mice are compared. Myeloid progenitors from antibiotic-treated mice have a reduced interferon gene expression signature. These data suggest that tonic interferon signaling is sensed by myeloid progenitors and such signals are reduced in antibiotic-treated mice.
Project description:Sequencing reads of Escherichia coli K-12 control and antibiotic-treated cultures enriched (Cappable-Seq) and not enriched (Ultra directional) for the 5’ end of primary transcripts.