2022 Microbiome Course and Symposium by ISB

On October 12 - 14, 2022, ISB will host a virtual course and symposium on global perspectives in microbiome research.

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The vast majority of biomedical research is focused on affluent populations in highly developed countries, and the microbiome field is no exception.

We know that variation in the composition and function of the gut microbiome is intimately tied to diet, lifestyle, socioeconomic factors, environmental exposures, behavior, and health status. We also know that the ways in which the microbiome can mediate differential responses to environmental exposures and clinical interventions is dependent upon this variation. Statistical models trained on populations in the U.S. and Europe may not apply to populations in other parts of the world.

Furthermore, mechanistic models, like community-scale metabolic modeling, focus on functional outputs that may be more convergent across populations and do not require training data, but they rely upon limited strain-level diversity from diverse human cohorts in genome-scale metabolic model databases.

Thus, it is critical that we capture the full span of human and commensal microbial phenotypic diversity if we wish to equitably translate microbiome science into medical advances that benefit all of humanity. 

ISB is hosting a series of events in October of 2022 that leverage data sets from a more representative set of global populations and highlight leading microbiome researchers who work with underrepresented groups from around the planet. 


Two Events, Three Days

ISB is hosting a two-day course on October 12 & 13, 2022, followed by a symposium on October 14, 2022. Both events are virtual and free. The intended audience for these events are graduate students, postdocs, principal investigators, industry scientists, educators, clinicians, or any other variety of microbiome-curious people from across the globe.

Days One and Two: Course

On October 12 & 13, 2022 starting at 9:00 a.m. PT, we will provide an 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 for mapping commensal genomic variation and dietary variation into metabolic niche space.

Day Three: Symposium

On October 14, 2022 at 9 a.m. PT, we will host a symposium, featuring six prominent microbiome researchers working to broaden the scope of microbiome research by focusing on underrepresented human populations, diets, and lifestyles from across the world.

Meet the Organizers

Christian Diener, PhD
Instructor and Session Chair
Washington Research Foundation Distinguished Research Scientist, ISB
Nick Bohmann
Graduate Student, ISB
Alex Carr
Instructor and Teaching Assistant
PhD Student, ISB
Noa Rappaport, PhD
Teaching Assistant and Session Chair
Senior Research Scientist, ISB
James Johnson
Teaching Assistant
PhD Student, ISB
Samantha Piekos, PhD
Teaching Assistant
K. Carole Ellison Fellow in Bioinformatics, ISB
Sean Gibbons, PhD
Director and Teaching Assistant
Washington Research Foundation Distinguished Investigator & Assistant Professor, ISB
Kathryn Stephenson, MD
Session Chair
Clinical Fellow, Seattle Children’s Hospital
Sue Ishaq, PhD
DEI Consultant
Assistant Professor of Animal and Veterinary Sciences, The University of Maine
Emily Wissel
DEI Consultant
PhD Candidate, Emory University

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 were run in ipython notebooks within Google Colab, which provided all participants with free computational resources, but also required 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 metabolic modeling tool called MICOM to infer gut microbial community function. Participants are encouraged to develop a basic familiarity with Zoom, Slack, and Jupyter notebooks prior to the course.

Course Syllabus – October 12 & 13, 2022

All times are in Pacific Daylight Time (GMT-7)

Day One: Analyzing microbiome data: from amplicon sequences to ecological insights

Time Talk Info Additional Materials
09:00 Introductory remarks by Sean Gibbons, PhD Webinar via Zoom
09:30 - 11:00 Analyzing amplicon sequencing data with Qiime 2, Part 1
Instructor: Christian Diener, PhD
Webinar via Zoom Presentation

11:00 - 11:20 Break Live chat and Q&A via Slack
11:20 - 12:20 Analyzing amplicon sequencing data with Qiime 2, Part 2
Instructor: Christian Diener, PhD
Webinar via Zoom
12:20 - 12:45 Break Live chat and Q&A via Slack
12:45 - 1:30 Presenter: Aashish Jha, PhD
Talk title: Scaling up multi-omics studies to identify functional contributions of microbiomes on health of underrepresented populations
Webinar via Zoom
1:30 - 1:40 Closing remarks by Sean Gibbons, PhD Webinar in Zoom

Day Two: Predicting personalized microbiome-mediated responses to dietary variation

Time Talk Info Additional Materials
09:00 Introductory remarks by Sean Gibbons, PhD Webinar via Zoom
09:30 - 11:00 Building community-scale gut microbiome metabolic models for a diverse human cohort
Instructor: Nick Bohmann
Webinar via Zoom Presentation

11:00 - 11:20 Break Live chat and Q&A via Slack
11:20 - 12:20 Exploring the impact of dietary variation on gut microbiome metabolic outputs
Instructor: Nick Bohmann
Webinar via Zoom
12:20 - 12:45 Break Live chat and Q&A via Slack
12:45 - 1:15 Presenter: Alex Carr
Talk title: Leveraging community metabolic models to predict C. diff colonization
Webinar via Zoom
1:15 - 1:25 Closing remarks by Sean Gibbons, PhD Webinar via Zoom

Meet the Speakers

Aashish Jha, PhD
Assistant Professor of Biology, NYU Abu Dhabi
Mathilde Poyet, PhD
Co-founder Global Microbiome Conservancy
Gregorio Iraola, PhD
Head of the Microbial Genomics Laboratory at the Institut Pasteur Montevideo in Uruguay
Catherine Lozupone, PhD
Associate Professor, Department of Biomedical Informatics at University of Colorado Anschutz
Cecilia Ximenez, MD, PhD
Universidad Nacional Autónoma de México (UNAM) Faculty of Medicine; Experimental Medicine Department
Katherine Amato, PhD
Assistant Professor, Northwestern University
Amber Benezra, PhD
Assistant Professor, Stevens Institute of Technology

Symposium Schedule – October 14, 2022

All times are in Pacific Daylight Time (GMT-7)
Time Talk/Session Info
09:00 – 09:15 Welcoming remarks by Sean Gibbons, PhD Webinar via Zoom
09:15 – 11:00 Session One: Diet, Lifestyle, and the Global Gut
09:15 – 09:45 Mathilde Poyet, PhD
Talk title: Impact of lifestyle on human gut microbiome function
Webinar via Zoom
09:45 – 10:15 Gregorio Iraola, PhD
Talk title: Unlocking the gut microbiome from underrepresented human populations
Webinar via Zoom
10:15 – 10:45 Panel Discussion: Chaired by Christian Diener, PhD Webinar via Zoom
10:45 – 11:00 Break
11:00 – 12:30 Session Two: The Curious Case of Prevotella
11:00 – 11:30 Catherine Lozupone, PhD
Talk title: Immune modulation by Prevotella-rich microbiomes in men who have sex with men and potential implications for transmission of HIV
Webinar via Zoom
11:30 – 12:00 Cecilia Ximenez, MD, PhD
Talk title: Immune regulation in mice transplanted with parasite-associated human fecal microbiota
Webinar via Zoom
12:00 – 12:30 Panel Discussion: Chaired by Noa Rappaport, PhD Webinar via Zoom
12:30 – 12:45 Break
12:45 – 2:15 Session Three: Social Determinants of a Healthy Gut
12:45 – 1:15 Katherine Amato, PhD
Talk title: The human gut microbiome and health inequities
Webinar via Zoom
1:15 – 1:45 Amber Benezra, PhD
Talk title: Who Decides What Healthy Is? Studying Microbiomes Across Disciplines
Webinar via Zoom
1:45 – 2:15 Panel Discussion: Chaired by Kathyrn Stephenson, MD Webinar via Zoom
2:15 – 2:30 Closing remarks by Sean Gibbons, PhD Webinar via Zoom

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