SC18: Novel Technologies for Exploring the Human Microbiome
THURSDAY AUGUST 17 DINNER | 5:00 – 7:30 PM
Detailed Agenda
5:00 Bacteriophages for Infection Therapy and Microbiome Engineering
Ryan Honaker, Ph.D., Technical Manager, Epibiome
Phage therapy is a century-old idea that is currently experiencing a resurgence of interest, driven both by antibiotic resistance as well an increased understanding of the importance of the microbiome. Utilizing modern genomic and automation tools, a pipeline for phage discovery and characterization is under development, with the goal of creating safe and effective phage-based treatments for a variety of infections and dysbioses.
5:30 Fecal Microbiome Transplantation for the Treatment of Recurrent Clostridium Difficile Infection: the Role of Universal Stool Banks
Shrish Budree, M.D., Senior Clinical Research Fellow, Clinical Research, Openbiome
Clostridium difficile infection (CDI) is the most common healthcare-associated infection resulting in up to 29,000 deaths in the United States annually. The rate of treatment failure and recurrence of the CDI is high. Unfortunately, there are limited treatment options for patients with recurrent CDI. There is now mounting evidence that fecal microbiota transplantation (FMT), the infusion of healthy donor stool into the recipient’s intestinal tract, is an effective treatment for recurrent CDI, with efficacy rates as high as 91% when delivered via colonoscopy. It is theorized that FMT protects against toxigenic Clostridium difficile by restoring colonic microbial diversity and critical metabolic functions. Universal stool banks such as OpenBiome are crucial to enable safe access to FMT for the treatment if recurrent CDI. This talk will explore the role of FMT in the treatment of recurrent CDI and other diseases beyond CDI and the role of universal stool banks in achieving safe access to FMT.
6:00 Dinner Buffet
6:30 Use of the Microbiome as a Biomarker to Identify Patients with Colorectal Polyps
Patrick Gillevet, Ph.D., Professor and Director, Microbiome Analysis Center, George Mason University
Alterations in the colonic microbiota are likely to play a role in colonic neoplasia. Characterization of these complex changes could be used as a non-invasive biomarker to screen patients for premalignant lesions. A prospective study of patients undergoing screening or surveillance colonoscopy was performed to determine if a unique microbiome pattern could be used to identify patients with colorectal polyps (hyperplastic and adenoma). The results indicate that microbiome analysis combined with advanced machine learning methods could be used: as a biomarker to screen patients for polyps, to optimize the use of colonoscopy, and to reduce the associated health care costs.
7:15 Q&A
7:30 End of Course
Instructor Biographies
Ryan Honaker, Ph.D., Technical Manager, Epibiome
Ryan is a microbiologist who did his graduate work in microbiology at the University of Colorado, Denver studying transcriptional programs of dormancy in Mycobacterium tuberculosis, followed by a postdoctoral fellowship in the department of Microbiology and Immunology at Stanford where he was an American Cancer Society postdoctoral fellow. There he studied host-pathogen interactions and the progression to cancer that results from infection with Helicobacter pylori.
As one of the first employees of EpiBiome, Ryan has been designing phage therapies to provide antibiotic alternatives that will help prevent antibiotic overuse, with the overall goal of combating the growing and severe problem of antibiotic resistance in agricultural and human medicine. His research team is creating an automated high throughput pipeline to develop effective and quantitative phage isolation and characterization methods for application to therapeutic use.
Shrish Budree, M.D., Senior Clinical Research Fellow, Clinical Research, Openbiome
Dr. Budree is a pediatrician and pediatric gastroenterologist who trained in South Africa and is currently pursuing his PhD. His research is focused on the role of the intestinal microbiome in childhood disease. He completed his medical, pediatric and pediatric gastroenterology training at the University of Cape Town and the Red Cross Children’s Hospital in South Africa. He worked as a research fellow for a year on a large Gates Foundation funded pediatric cohort study based in Cape Town, South Africa. He then completed a microbiome fellowship in the Xavier microbiome laboratory at Massachusetts General Hospital and the Broad Institute of Harvard and MIT in Boston, in which he focused on 16S rRNA and metagenomic sequencing and analysis of the intestinal microbiome. Dr. Budree then joined OpenBiome as their senior clinical research scientist in July 2016. He is currently involved in numerous fecal microbiome transplantation (FMT) trials both in the U.S. and globally. His interest in fecal microbiome transplantation stems from both his clinical gastroenterology background and his current microbiome research.
Patrick Gillevet, Ph.D., Professor and Director, Microbiome Analysis Center, George Mason University
Dr. Gillevet received his PhD in Biochemistry from the University of Manitoba in 1982. He has had extensive training in microbiology, biochemistry, molecular biology, bioinformatics, and molecular evolution.
He was the Technical Director for the Center of Prokaryotic Genome Analysis at the University of Illinois from 1988-1990 under the direction of Carl Woese (Crawfoord Laureate) where he worked on the Thermoccocus celer genome that was one of the first microbial genome projects.
From 1990-1993 he was Director of the Harvard Genome Laboratory at Harvard University under the direction of Wally Gilbert (Nobel Laureate) where he worked on the Mycoplasma capriclum genome.
From 1993-1996. He directed the Core Sequencing Facility at the National Center for Human Genome Research under Francis Collins .
He is currently Professor in the Department of Biology and is the Director of the Microbiome Analysis Center at George Mason University which is dedicated to scientific research in Molecular Ecology of the Human Microbiome, Phylogenomics, HIV infection, and human disease. He developed a Multitag sequencing methodology that allows us to profile hundreds of samples at one time. He is using this technology and supporting Bioinformatics analysis to investigate various diseases associated with the human microbiome and human disease.