2021 ISB Virtual Microbiome Series

On October 13 - 15, 2021, ISB will host a virtual course and symposium on the latest cutting edge microbiome research.

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We are island ecosystems, rapidly colonized at birth by a diverse array of microorganisms. Many of these commensal microbial populations persist in and on our bodies for years, decades, perhaps as long as a century. For our microbes, these human timescales are equivalent to tens of thousands of generations, which in turn is equivalent to hundreds of thousands or even millions of years of evolution in a vertebrate — such as ourselves. While we are beginning to understand how disruptions to the ecological structure of commensal microbial communities can impact host health, less is known about how rapid evolutionary dynamics within individual commensal populations over the course of a host’s lifespan can influence ecosystem function.

ISB is hosting a series of events in October of 2021 that highlight recent advances toward understanding general patterns of commensal population genomic variation within the human gut, how fine-scale commensal genomic variation is influenced by host phenotypic variation, and whether or not commensal genomic variation has an impact on human health and disease.

microbiome drawing

About

Two Events, Three Days

ISB hosting a two-day course on October 13 & 14, 2021, followed by a symposium on October 15, 2021. 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 person from across the globe.

Days One and Two: Course

On October 13 & 14, 2021 at 9 a.m. PT, we will provide a two-day, intensive course designed to enable novice microbiome researchers to get up-to-speed with amplicon sequencing data processing and analyses, construct metabolic models from bacterial isolate sequencing data, and use those models to map commensal genomic variation to metabolic niche space.

Day Three: Symposium

On October 15, 2021 at 9 a.m. PT, we will host a symposium featuring six prominent microbiome researchers who are working to build computational and experimental tools for exploring rapid within-host bacterial evolution, and how these population genomic signatures may be related to ecosystem function, human phenotypic variation, or disease pathologies.

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
Research Scientist, ISB
Rappaport
Noa Rappaport, PhD
Senior Research Scientist, ISB
Carr
Alex Carr
PhD Student, ISB
Baloni
Priyanka Baloni, PhD
Senior Research Scientist, 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 building genome-scale metabolic models for individual bacterial isolates to map genomic variation onto ecological niche space.

Course Syllabus – October 13 & 14, 2021

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

Notebook
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 Introduction to the project challenge Webinar via Zoom
12:45 Open time to work on project Live chat and Q&A via Slack

Day Two: Reverse ecology of bacterial isolates - from genomes to metabolic models

Time Talk Info Additional Materials
09:00 Introductory remarks by Sean Gibbons, PhD Webinar via Zoom
09:30 - 11:00 Building metabolic models of bacterial isolates
Instructor: Christian Diener, PhD
Webinar via Zoom Presentation

Notebook
11:00 - 11:20 Break Live chat and Q&A via Slack
11:20 - 12:20 Reverse ecology: inferring environmental interactions with metabolic models
Instructor: Christian Diener, PhD
Webinar via Zoom
12:20 - 12:45 Introduction to the project challenge Webinar via Zoom
12:45 - 13:00 Break Live chat and Q&A via Slack
13:00 - 13:50 Presentation by Priyanka Baloni, PhD Webinar via Zoom
13:50 - 14:00 Break Live chat and Q&A via Slack
14:00 - 14:30 Closing remarks by Sean Gibbons, PhD Webinar via Zoom
14:30 Open time to work on project Live chat and Q&A via Slack

Symposium Speakers

Shapiro
Jesse Shapiro, PhD
Associate Professor, Department of Microbiology & Immunology, McGill University
Good
Benjamin Good, PhD
Assistant Professor of Applied Physics, Stanford University
Garud
Nandita Garud, PhD
Assistant Professor, Department of Ecology and Evolutionary Biology, UCLA
Groussin
Mathieu Groussin, PhD
Post-Doctoral Associate - Eric Alm Lab, MIT, Department of Biological Engineering, The Broad Institute
Lieberman
Tami Lieberman, PhD
Assistant Professor of Civil and Environmental Engineering, Assistant Professor of Institute for Medical Engineering and Science, MIT
Suzuki
Taichi Suzuki, PhD
Postdoctoral Researcher, Department of Microbiome Science, Max Planck Institute for Developmental Biology

Symposium Schedule – October 15, 2021

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 (Theory): Population genomics of commensal bacteria
09:15 – 09:45 Jesse Shapiro, PhD, Talk title: Does diversity beget diversity in the human gut microbiome? Webinar via Zoom
09:45 – 10:15 Benjamin Good, PhD, Talk title: Eco-evolutionary feedbacks in the gut microbiome Webinar via Zoom
10:15 – 10:45 Panel Discussion: Chaired by Christian Diener, PhD Webinar via Zoom
10:45 – 11 Break
11:00 – 12:30 Session Two (Natural History): Identifying signatures of within-host adaptation
11:00 – 11:30 Nandita Garud, PhD, Talk title: Evolutionary and ecological dynamics in the human gut microbiome from birth through adulthood Webinar via Zoom
11:30 – 12:00 Mathieu Groussin, PhD, Talk title: Evolution of host-microbiome systems in humans Webinar via Zoom
12:00 – 12:30 Panel Discussion: Chaired by Tomasz Wilmanski, MPH, PhD Webinar via Zoom
12:30 – 12:45 Break
12:45 – 14:15 Session Three (Clincial Relevance): Functional consequences of evolution in host-microbe systems
12:45 – 13:15 Tami Lieberman, PhD, Talk title: Tracking de novo mutations to understand microbial ecology on the skin Webinar via Zoom
13:15 – 13:45 Taichi Suzuki, PhD, Talk title: Codiversification of gut microbiota with humans Webinar via Zoom
13:45 – 14:15 Panel Discussion: Chaired by Noa Rappaport, PhD Webinar via Zoom
14:15 – 14:30 Closing remarks by Sean Gibbons, PhD Webinar via Zoom

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