Harnessing Our Inner Ecology To Track and Treat Disease

On October 15 and 16, ISB hosts a virtual course and symposium on the microbiome and its future role in precision medicine.

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When a new scientific discipline is born, there is an initial natural history phase, where explorers map out the contours of the unknown. For the past couple of decades we have characterized the form and function of microbial ecosystems in and on the human body. Now, with this wealth of information collected on the human microbiome serving as a foundation, we have entered into a new phase of testing targeted, mechanistic hypotheses for how our microbiota contribute to the etiologies of diseases. ISB is hosting a series of events in October that highlight recent in silico, in vitro, and in vivo advances towards engineering the gut microbiome to resolve complex diseases.

microbiome drawing


Two Events, Two Days

ISB will host a one-day course on October 15, followed by a symposium on October 16. Both events will be virtual and free. The intended audience for these events are graduate students, postdocs, principal investigators, industry scientists, educators, and clinicians from across the globe.

Day One: Course

On October 15 at 9:15 a.m., we will provide a one-day, intensive course designed to enable novice microbiome researchers to get up-to-speed with amplicon sequencing data processing and analyses and we will introduce a powerful metagenome-scale metabolic modeling approach recently developed at ISB.

Day Two: Symposium

On October 16 at 9 a.m., we will host a symposium, featuring six researchers working in different parts of the world to build computational and experimental tools for manipulating the gut microbiome to track and treat disease.

Meet the Instructors

Sean Gibbons, PhD
Washington Research Foundation Distinguished Investigator & Assistant Professor, ISB
Christian Diener, PhD
Washington Research Foundation Distinguished Research Scientist, ISB
Tomasz Wilmanski, MPH, PhD
K. Carole Ellison Fellow in Bioinformatics, ISB
Noa Rappaport, PhD
Senior Research Scientist, ISB
Alex Carr
PhD Student, ISB
Priyanka Baloni, PhD
Research Scientist, ISB
Nathan Price, PhD
Associate Director and Professor, ISB

Course Requirements

Course participants will need to register below in order to receive a Zoom link and an invitation to the course's Slack account. Lectures will be given in Zoom and real-time tutorials will be monitored by teaching assistants via Slack. Thus, participants will need to install both Zoom and Slack prior to the start of the course. Presentations and course materials can be accessed on the course's GitHub repository. Course presentations can be viewed on a web browser (smartphone compatible). Course tutorials will be run in ipython notebooks within Google Colab, which provides all participants with free computational resources, but will also require everyone to sign up for a Google account (if they do not already have one). The first half of the course will be run using Quantitative Insights Into Microbial Ecology 2 (QIIME2). The second half of the course will involve using a new metabolic modeling tool called MICOM to infer gut microbial community function. Participants are encouraged to develop a basic familiarity with Zoom, Slack, and ipython notebooks prior to the course.

Course Syllabus – October 15

All times are in Pacific Daylight Time (GMT-7)
Time Talk Info Additional Materials
09:15 - 09:30 Introductory remarks - Sean Gibbons Webinar via Zoom
09:30 - 11:00 Analyzing amplicon sequencing data with Qiime 2 - Christian Diener Webinar via Zoom Slides Open Colab
11:00 - 11:45 Apply what you’ve learned Live chat and Q&A via Slack
11:45 - 12:00 Look at results and discuss Webinar via Zoom
12:30 - 14:00 Modeling microbiota-wide metabolism with MICOM - Christian Diener Webinar via Zoom Slides Open Colab
14:00 - 14:30 Apply what you’ve learned Live chat and Q&A via Slack
15:00 - 16:00 Presentation by Tom Wilmanski and Noa Rappaport Webinar via Zoom
16:00 - 16:30 Closing remarks - Nathan Price Webinar via Zoom

Symposium Speakers

Jason Papin, PhD
Professor, University of Virginia
Ines Thiele, PhD
Professor, National University of Ireland, Galway
Thomas Gurry, PhD
Founder, Vesta Biosciences; Senior Research Scientist, University of Geneva
Julie McDonald, PhD
Lecturer, MRC Centre for Molecular Bacteriology and Infection, Imperial College London
Gautam Dantas, PhD
Professor, Washington University School of Medicine
Johanna Lampe, PhD
Professor and Associate Director, Public Health Sciences Division, Fred Hutch

Symposium Schedule – October 16

All times are in Pacific Daylight Time (GMT-7)
Time Talk/Session Info
09:00 – 09:15 Welcoming remarks by Sean Gibbons Webinar via Zoom
09:15 – 11:00 Session One: Mechanistic Models
09:15 – 09:45 Jason Papin, PhD, Talk title: Metabolic mechanisms of interaction in microbial communities Webinar via Zoom
09:45 – 10:15 Ines Thiele, PhD, Talk title: Large-scale modelling of the human microbiome accounts for strain-specific drug metabolism Webinar via Zoom
10:15 – 10:45 Panel Discussion: Chaired by Priyanka Baloni Webinar via Zoom
11:00 – 12:30 Session Two: in vitro Approaches
11:00 – 11:30 Thomas Gurry, PhD, Talk title: Exploiting in vitro measurements of gut microbial fermentation capability towards disease prevention Webinar via Zoom
11:30 – 12:00 Julie McDonald, PhD, Talk title: Using artificial gut models to study how the gut microbiota protects against intestinal infections Webinar via Zoom
12:00 – 12:30 Panel Discussion: Chaired by Noa Rappaport Webinar via Zoom
12:45 – 14:15 Session Three: in vivo Interventions
12:45 – 13:15 Gautam Dantas, PhD, Talk title: Predicting and Combating Pathogenic and Abiotic Disruptions to Diverse Microbiomes Webinar via Zoom
13:15 – 13:45 Johanna Lampe, PhD, Talk title: Diet-Gut Microbiome Interactions: Controlled Feeding Studies and Metabolic Phenotypes Webinar via Zoom
13:45 – 14:15 Panel Discussion: Chaired by Tomasz Wilmanski Webinar via Zoom
14:15 – 14:30 Closing remarks by Nathan Price Webinar via Zoom

ISB-Town Hall Livestream

On October 6, ISB partnered with Town Hall Seattle for a livestreamed event on population-scale COVID-19 tracking using data collected from sewage. Dr. Eric Alm, microbiome researcher and professor in the Department of Biological Engineering at MIT and the Broad Institute, presented on low-cost pandemic tracking efforts in hundreds of cities across the U.S. Dr. Alm's presentation was followed by a discussion with Dr. Sean Gibbons (ISB faculty and microbiome researcher) and an audience Q&A.

Watch the event

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