This application seeks funding to purchase a Qiagen QIAcube Connect System. This instrument is a cutting-edge, next generation benchtop automated DNA sample preparation system configured for microbiome workflow. It will be partnered with our existing Illumina MiSeq system (ShEEP funded, 2018) and our Eppendorf epMotion automated pipetting robot to eliminate tedious manual steps in DNA extraction, increase accuracy and reliability, and maximize throughput in our 16S rRNA gene sequencing projects. Like the MiSeq, the QIAcube will support studies of the gut microbiome by our VA-funded investigators. The QIAcube enables use of well-established QIAGEN spin-column kits currently in use in our lab (manual processing) so we can continue to use QIAGEN-based chemistry to increase efficiency. The QIAcube Connect integrates a centrifuge, heated shaker, pipetting system and a robotic gripper allowing full automation of more than 80 spin columns per run. The workstation has a built-in UV light for efficient decontamination of the worktable, critical when extracting nucleotides from samples in the same workspace. The workstation contains a tablet allowing for simplified sample preparation and provides real-time feedback on run progress. The barcode scanner on the QIAcube automatically uploads kit information to the screen, streamlining run preparation. The instrument also has a variety of pre-installed protocols for DNA isolation and purification and is based on existing approaches used in our QIAGEN reagents for sample lysis, binding, washing and elution. To give an impression of the effectiveness of this instrument, a recent 16S rRNA gene sequencing study in our lab involved 350 samples (fecal pellets). The manual processing of the samples to isolate DNA took a research associate 20 workdays to complete, working 8 hours per day. The QIAcube would reduce this preparation time (40 min per 48-sample run) to ~5-6 hr of instrument time. The QIAcube system will allow expansion of ongoing, currently funded research on the following projects of our 3 major and 2 minor users: 1) The Kuhn lab is studying the role of the gut microbiome in Gulf War Veterans Illness as well as in repetitive mild traumatic brain injury; 2) the Mateika lab is studying the role of serotonin in respiratory function in spinal cord injury and how respiratory and sleep alterations associated with spinal cord injury are modulated by the gut microbiome; 3) the Rossi lab is studying the role of high fructose intake via the diet in regulating blood pressure responses to salt, and we have already started a collaborative project with Dr. Rossi on this subject; 4) the Theis lab is collaborating with the PI on a VA funded project to study the role of the gut microbiome in Gulf War Veterans Illness. Dr. Theis is also the resident expert on 16S rRNA gene sequencing and bioinformatics and his expertise is critical to this program of research. Dr. Theis is a VA researcher in our R&D Service; and 5) the Hazlett lab is studying bacterial infections of the cornea and recent preliminary studies in her lab have uncovered participation of the gut microbiome in a Pseudomonas aeruginosa corneal mouse model. Dr. Hazlett is a VA researcher in our R&D Service (WOC). Together, these five investigators study some of the most prevalent clinical conditions affecting Veterans (i.e., GWVI, chronic effects of neurotrauma, spinal cord injury and dietary influences on hypertension). Emerging studies are showing that these same disorders are significantly modulated by the gut microbiome. The addition of the QIAcube to our existing gut microbiome instrumentation will not only increase sample throughput and add new and innovative dimensions to the individual projects, it will also enhance our ability to translate these findings to the clinic and improve the health care delivered to our Veterans.
The broad, long-term objectives of this ShEEP application for a QIAGEN QIAcube automated sample processor are to expand our growing program of research on the gut microbiome at the Detroit VAMC in support of Veterans health care issues. The QIAcube will be partnered with our 2018 ShEEP-funded Illumina MiSeq and our recently purchased Eppendorf epMotion automated liquid handling workstation to form a state- of-the-art platform for carrying out our 16S rRNA gene sequencing studies. The QIAcube is a critical add-on to our system and will maximize sample throughput and allow expansion of our ongoing VA-funded studies on Gulf War Veterans Illness, chronic effects of neurotrauma, spinal cord injury and dietary influences on hypertension. The QIAcube will complete the assembly of an automated and highly accurate 16S rRNA gene sequencing system, thereby adding an important dimension to the research of numerous VA funded investigators at our station.