The Complete Microbiome Workflow: Deciphering the Secrets of the Human Microbiome for Future Diagnostic Solutions

摘要

Human Microbiome is an exciting and rapidly expanding field of research, aimed at studying bacteria, fungi and viruses (beneficial as well as pathogenic) densely populating in our bodies. Human Microbiome project demonstrated that microbiome dysbiosis in gastrointestinal tract might eventually cause various diseases including Crohns, C.Diff, U.colitis, Diabetes and cancer. Correlation of Microbiome compositions to these chronic diseases promises a great deal for development of innovative diagnostics and therapeutics. We developed a new automated high-throughput Microbiome kit for purification of fecal Total Nucleic Acid (DNA and RNA) with superior yields and quality. This magnetic bead-based kit enables processing 96 stool samples on KingFisher Flex platform within just 1h. Gene expression analysis on these Total Nucleic Acid extractions, using TaqMan assays for diverse bacterial species confirmed superior depletion of inhibitors of enzymatic reactions and lowest Ct values vs other commercial kits. This presentation will highlight several case studies that were conducted utilizing the Ion Torrent platform for 16S sequencing to characterize the microbiome compositions in fecal samples originating from various donors. One case study explored the impact of diet on gut microbiome profile and NGS data indicated that the gut microbiome can respond to dietary perturbations, as we observed several shifts in the abundances of certain bacterial families in GI tract of a person, who was on a nutritionist recommended diet. Another case study was performed with fecal samples collected from a person taking probiotics, to explore whether there are any respective changes in the gut microbiome profile. 16S sequencing results detected a significant shift in firmicutes/bacteroidetes levels with the intake of probiotics. In conclusion, the workflow that we developed to harness the power of microbiome enables fast generation of metagenomic data for bacterial communities residing within human gut, which can be utilized as diagnostic biomarkers for certain diseases, and potentially lay the path towards future microbiome therapeutics. Articles from Journal of Biomolecular Techniques : JBT are provided here courtesy of The Association of Biomolecular Resource Facilities.