On October 13 - 15, 2021, ISB hosted a virtual course and symposium on the latest cutting edge microbiome research.
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 hosted 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.
ISB hosted a two-day course on October 13 & 14, 2021, followed by a symposium on October 15, 2021. Both events were 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.
On October 13 & 14, 2021 at 9 a.m. PT, we provided 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.
On October 15, 2021 at 9 a.m. PT, we hosted 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.
Course participants needed to register in order to receive a Zoom link and an invitation to the course's Slack account. Lectures were given in Zoom and real-time tutorials were 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 was run using Quantitative Insights Into Microbial Ecology 2 (QIIME2). The second half of the course involved building genome-scale metabolic models for individual bacterial isolates to map genomic variation onto ecological niche space.
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 |
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 |
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 |