2024 Microbiome Course and Symposium by ISB

A gut feeling: Microbes and their impacts on our minds

On October 16 - 18, 2024, ISB will host a virtual course and symposium on the gut-brain axis.

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The trillions of commensal (non-harmful) microbes that live in and on our bodies contain a hundred fold more unique genes than we harbor within our own genomes. Recent work has shown that many of these microbial genes are essential to the proper functioning of our bodies, with almost half of all metabolites in human blood significantly associated with variation in the ecology of the gut. This metabolic cross-talk between our microbes and our bodies extends to all organ systems, including the central nervous system. There has been an explosion of research into the two-way communication between the gut microbiota and the brain, which has helped us to understand complex behavioral and neurophysiological phenotypes in many animal species. This year’s course and symposium are dedicated to exploring the gut-brain axis.

ISB is hosting a series of events in October of 2024 that leverage data sets from neuropsychiatric cohorts to better understand the metabolic interplay between the human gut microbiome and the central nervous system in health and disease.

About

Two Events, Three Days

ISB is hosting a two-day course on October 16 & 17, 2024, followed by a symposium on October 18, 2024. 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 16 & 17, 2024 at 9 a.m., 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. We will introduce a powerful microbial community-scale metabolic modeling approach developed at ISB.

Day Three: Symposium

On October 18, 2024 at 9 a.m., we will host a symposium, featuring six prominent microbiome researchers working to broaden the scope of microbiome research by focusing on the gut-brain axis.

Free Membership: Applied Microbiology International

This year our sponsor, Applied Microbiology International, offered free memberships to anyone that registers and attends the event. Explore their website and make sure to check the box to opt in when you register.

Meet the Organizers

Easton
Alyssa Easton
Instructor
PhD Student, ISB
Carr
Alex Carr, PhD
Instructor
Postdoctoral Fellow, ISB
Rappaport
Noa Rappaport, PhD
Teaching Assistant and Session Chair
Principal Scientist, ISB
Cavon
Jacob Cavon
Teaching Assistant, Presenter and Session Chair
PhD Student, ISB
Perez
Crystal Perez
Teaching Assistant and Session Chair
MD/PhD Student, ISB
Bohmann
Nick Quinn-Bohmann, PhD
Teaching Assistant
Postdoctoral Fellow, ISB
Gaisser
Karl Gaisser
Teaching Assistant
Research Associate, ISB
Gibbons
Sean Gibbons, PhD
Director and Teaching Assistant
Associate Professor, ISB

Course Requirements

Course participants will need to register 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 (coming soon). Course presentations can be viewed on a web browser (smartphone compatible). Course tutorials will be run in Jupyter 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 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 16 & 17, 2024

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: Alyssa Easton
Webinar via Zoom
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: Alyssa Easton
Webinar via Zoom
12:20 - 12:45 Break Webinar via Zoom
12:45 - 1:30 Presenter: Jacob Cavon
Talk title: Using wearables data to look at the relationship between the gut microbiome and sleep.
Webinar via Zoom
1:30 - 1:40 Closing remarks by Sean Gibbons, PhD Webinar in Zoom
1:40 Work on project (get help on Slack) Live chat and Q&A via Slack

Day Two: Investigating the metabolic determinants of the gut-brain axis.

Time Talk Info Additional Materials
09:00 Introductory remarks by Sean Gibbons, PhD Webinar via Zoom
09:30 - 11:00 Microbial community-scale metabolic models.
Instructor: Alex Carr
Webinar via Zoom
11:00 - 11:20 Break Live chat and Q&A via Slack
11:20 - 12:20 Metabolic models and the gut-brain axis.
Instructor: Alex Carr
Webinar via Zoom
12:20 - 12:30 Closing remarks by Sean Gibbons, PhD Webinar via Zoom
12:40 Work on project (get help on Slack) Live chat and Q&A via Slack

Meet the Speakers

Coley-O'Rourke
Elena Coley-O'Rourke, PhD
Postdoctoral Fellow, UCSF
Venkatesh
Sid Venkatesh, PhD
Assistant Professor, ISB
Ritz
Nathaniel Ritz, PhD
Postdoctoral Fellow, ISB
Holscher
Hannah Holscher, PhD
Associate Professor, University of Illinois
Baloni
Priyanka Baloni, PhD
Assistant Professor, Purdue University
Qiu
Yunguang Qiu, PhD
Postdoctoral Fellow, Cleveland Clinic

A gut feeling: Microbes and their impact on our minds
Symposium Schedule: October 18, 2024
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: Early Life: Nutrition and the Developing Brain
09:15 – 09:45 Elena Coley-O'Rourke, PhD
Talk title: Malnutrition and the developmental gut-brain axis
Webinar via Zoom
09:45 – 10:15 Sid Venkatesh, PhD
Talk title: Regulation of gut luminal endocannabinoids by a human gut microbial amidase
Webinar via Zoom
10:15 – 10:45 Panel Discussion: Chaired by Crystal Perez Webinar via Zoom
10:45 – 11:00 Break
11:00 – 12:30 Session Two: Stress, Anxiety, and Depression
11:00 – 11:30 Nathaniel Ritz, PhD
Talk title: Stress gone viral: gut bugs that can impact behavior in preclinical models
Webinar via Zoom
11:30 – 12:00 Hannah Holscher, PhD
Talk title: Dietary and microbial connections to mood and cognition
Webinar via Zoom
12:00 – 12:30 Panel Discussion: Chaired by Jacob Cavon Webinar via Zoom
12:30 – 12:45 Break
12:45 – 2:15 Session Three: Neurodegeneration
12:45 – 1:15 Priyanka Baloni, PhD
Talk title: Identifying host and microbiome derived metabolic signatures associated with Alzheimer’s disease
Webinar via Zoom
1:15 – 1:45 Yunguang Qiu, PhD
Talk title: Systematic multi-omics landscape between gut microbial metabolites and GPCRome in Alzheimer’s disease
Webinar via Zoom
1:45 – 2:15 Panel Discussion: Chaired by Noa Rappaport, PhD Webinar via Zoom
2:15 – 2:30 Closing remarks by Sean Gibbons, PhD Webinar via Zoom

Thank you to our sponsors