2020 ISB Virtual Microbiome Series

Harnessing Our Inner Ecology To Track and Treat Disease

On October 15 and 16, 2020, ISB hosted 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 hosted a series of events in October of 2020 that highlight recent in silico, in vitro, and in vivo advances towards engineering the gut microbiome to resolve complex diseases.

microbiome drawing

About

Two Events, Two Days

ISB hosted a one-day course on October 15, 2020, followed by a symposium on October 16, 2020. Both events were 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, 2020 at 9:15 a.m., we provided 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, 2020 at 9 a.m., we hosted 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

Gibbons
Sean Gibbons, PhD
Washington Research Foundation Distinguished Investigator & Assistant Professor, ISB
Diener
Christian Diener, PhD
Washington Research Foundation Distinguished Research Scientist, ISB
Wilmanski
Tomasz Wilmanski, MPH, PhD
K. Carole Ellison Fellow in Bioinformatics, ISB
Rappaport
Noa Rappaport, PhD
Senior Research Scientist, ISB
Carr
Alex Carr
PhD Student, ISB
Baloni
Priyanka Baloni, PhD
Research Scientist, ISB
Price
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, 2020

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

Course Videos

Introductory Remarks
 
Analyzing amplicon sequencing data with Qiime 2 - Pt. 1
Analyzing amplicon sequencing data with Qiime 2 - Pt. 2
Modeling microbiota-wide metabolism with MICOM - Pt. 1
Modeling microbiota-wide metabolism with MICOM - Pt. 2
Defining A Healthy Gut Microbiome: Insights from Phenotyped Cohorts
Closing Remarks

Symposium Speakers

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

Symposium Schedule – October 16, 2020

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

Symposium Videos

Welcoming Remarks
 
Session 1: Mechanistic Models - Jason Papin, PhD
Session 1: Mechanistic Models - Ines Thiele, PhD
Session 1: Mechanistic Models - Panel Discussion
Session 2: in vitro Approaches - Thomas Gurry, PhD
Session 2: in vitro Approaches - Julie McDonald, PhD
Session 2: in vitro Approaches - Panel Discussion
Session 3: in vivo Interventions - Gautam Dantas, PhD
Session 3: in vivo Interventions - Johanna Lampe, PhD
Session 3: in vivo Interventions - Panel Discussion
Closing Remarks
 

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