The SDDRC awards Technology Development grants to advance new research technologies that overcome shortcomings of existing approaches and are broadly applicable to digestive diseases research.
Technology Development Grant ($25,000):
Jack Gilbert, PhD
Professor, Department of Pediatrics
School of Medicine
About the Awardee:
Dr Gilbert's research is focused on understanding how to apply advances in microbiome research into the clinic. A key aspect of this work is appropriate screening of microbiome profiles from various environments, such as biopsies. His primary research foci are gut microbiome and lung microbiome, where mucosal biopsies present with major human DNA contamination. He is committed to training graduate, postdoctoral and clinical fellows in his lab to provide the key expertise required to advance basic research and clinical practice. Fundamental to this goal is developing laboratory protocols that can be rapidly deployed into clinical trials to aid in the integration of microbiome science into practice.
Project Title: "Host depletion and benchmarking guidelines for mucosal biopsy microbiome studies”
Summary: The microbiome (bacteria, fungi, and other tiny organisms) of the mucus lining the gut is known to be different from the microbiome of stool, and to be important in many diseases including colon cancer and inflammatory bowel disease. However, samples of the mucosa have a lot of human DNA (typically, more than 99%). Sequencing the DNA to find out about the microbes is therefore very expensive because the vast majority of the DNA sequence data has to be discarded. In this project, different protocols will be tested for storing and removing host DNA from mucosal biopsy specimens (samples of the gut mucus). The results will tell us which already-collected specimens are useful for microbiome DNA analysis, and will also guide how to store new specimens going forward so that we can find out how the microbiome causes diseases that affect the gut.