Project description:<p>Individuals vary widely in their drug responses, which can be dangerous and expensive due to treatment delays and adverse effects. Growing evidence implicates the gut microbiome in this variability, however the molecular mechanisms remain largely unknown. We measured the ability of 76 diverse human gut bacteria to metabolize 271 oral drugs and found that many of these drugs are chemically modified by microbes. We combined high-throughput genetics with mass spectrometry to systematically identify drug-metabolizing microbial gene products. These microbiome-encoded enzymes can directly and significantly impact intestinal and systemic drug metabolism in mice, and can explain drug-metabolizing activities of human gut bacteria and communities based on their genomic contents. These causal links between microbiota gene content and metabolic activities connect interpersonal microbiome variability to interpersonal differences in drug metabolism, which has implications for medical therapy and drug development across multiple disease indications.</p><p><br></p><p>Additional data related to this study can also be found by the following links;</p><p>- Raw sequencing data; <a href='https://www.ebi.ac.uk/ena/data/view/PRJEB31790' rel='noopener noreferrer' target='_blank'>ENA (accession no. PRJEB31790)</a></p><p>- Data for Figures; <a href='https://doi.org/10.6084/m9.figshare.8119058' rel='noopener noreferrer' target='_blank'>FigShare</a> </p><p>- Analysis pipeline schemes, scripts and input files for analzing data and generating figures; <a href='https://github.com/mszimmermann/drug-bacteria-gene_mapping' rel='noopener noreferrer' target='_blank'>GitHub</a> and archived <a href='https://doi.org/10.5281/zenodo.2827640' rel='noopener noreferrer' target='_blank'>Zenodo</a></p>
Project description:The aim of this experiment was to determine if the development of resistance to antibiotics can be driven by the concentration and speciation of Cu. Experimental setup was designed to investigate two hypotheses for which two strains of Gram- bacteria have been selected: - Do TE enhance AR in resistant bacteria? Resistant strain: Bioluminescent Pseudomonas aeruginosa PAO1 (Xen41, Tetracycline resistant) - Do TE induce AR in sensitive bacteria? Sensitive strain: Pseudomonas aeruginosa PAO1 (Wild Type)
Project description:We performed shallow whole genome sequencing (WGS) on circulating free (cf)DNA extracted from plasma or cerebrospinal fluid (CSF), and shallow WGS on the tissue DNA extracted from the biopsy in order to evaluate the correlation between the two biomaterials. After library construction and sequencing (Hiseq3000 or Ion Proton), copy number variations were called with WisecondorX.