On October 12 - 14, 2022, ISB hosted a virtual course and symposium on global perspectives in microbiome research.
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 hosted 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.
ISB hosted a two-day course on October 12 & 13, 2022, followed by a symposium on October 14, 2022. Both events were virtual and free. The intended audience for these events were graduate students, postdocs, principal investigators, industry scientists, educators, clinicians, or any other variety of microbiome-curious people from across the globe.
On October 12 & 13, 2022 starting at 9:00 a.m. PT, ISB provided an intensive course designed to enable novice microbiome researchers to get up-to-speed with amplicon sequencing data processing and analyses, and we introduced a powerful metagenome-scale metabolic modeling approach recently developed at ISB for mapping commensal genomic variation and dietary variation into metabolic niche space.
On October 14, 2022 at 9 a.m. PT, we hosted 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.
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.
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 | 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 |
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 Notebook |
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 |
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 | Sean Gibbons, PhD Talk title: How microbiomes shape our responses to statins |
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 |