The study of microbiomes has skyrocketed in recent years. Advances in DNA sequencing and analysis technologies have made microbiome research projects increasingly accessible to undergraduate students. Microbiome projects allow students to explore the diversity and complexity of their local environmental microbiomes. The projects are flexible and can address core learning goals in a wide range of courses, including microbiology courses, introductory biology, ecology, genetics, environmental studies and others.
This webinar series will focus on the excitement of microbiomes and the potential for faculty to provide training in the scientific process to their students through engagement in data analysis. The tools and resources for microbiome analyses are extensive, and the rapid pace of change can make navigating the best pathway forward a significant challenge. This webinar will provide examples in how to embark on microbiome data analysis projects using resources that do not require coding or advanced bioinformatics skills.
People who complete the series will:
• Receive a certificate of completion.
• Have the opportunity to participate further with the REMNet network.
• Be featured on the REMNet website as an ambassador of the program.
Thursday, Sept. 26, 12-1 p.m. ET | You Have Thousands of Sequence Reads—Now What!?
The first session will follow the step-by-step process of taking FASTQ files, creating metadata and mapping files and uploading the data for analysis to the Nephele pipeline. We will cover what elements to include in the metadata file and how to screen for formatting errors using Keemei. The pre-processing and workflow parameters for Nephele will be described. The webinar will go over output files and data quality and filtering, so that you can determine if your data is ready for downstream analyses. The webinar will use freely available microbiome data analysis tools that can be used in a classroom setting.
Thursday, Oct. 17, 1-2 p.m. ET | Data Mining—Making the Most of the Diversity in Your Data
The second session will use rarefaction curves to determine how thoroughly a sample has been sequenced. We will cover how to create relative abundance bar plots using QIIME2 View, as well as using CSV files to create custom bar plots. The webinar will discuss several alpha-diversity metrics and interpreting the results in an ecological context. The diversity across samples will be introduced using beta-diversity PCoA plots generated in Nephele and other visualization tools. We will discuss how students can use their data to explore microbial communities, ask questions about resilience and responses to environmental stresses, as well as how their data can lead to novel, testable hypotheses.
Thursday, Oct. 31, 12-1 p.m. ET | Tools for Further Exploration—Digging Deeper Into the Data
The third session will focus on narrowing in on specific groups of bacteria and using sequence data to generate phylogenetic trees. Additional methods to visual diversity and similarity across samples will be explored with heatmaps, Venn diagrams and linear discriminant analysis effect size. We will examine how these tools and visualizations can be aligned with curriculum content and student learning objectives.
Thursday, Nov. 7, 1-2 p.m. ET | Microbiome Projects Using the Oxford Nanopore System
The low cost, portability and relative ease of use of the Nanopore sequencing systems have made this an increasingly popular tool for microbiome analyses. This session will introduce the basics of using the Oxford Nanopore system for microbiome analyses and the use of resources for analyzing sequence data from Nanopore-based projects.
Course Learning Goals
Having completed the sessions and the associated assignments, participants will be able to:- Create a metadata file to support the processing of data from FASTQ files using Nephele and other downstream microbiome analysis tools.
- Generate and interpret data for alpha-diversity and beta-diversity metrics, beta-diversity, relative abundance bar-charts and rarefaction curves from microbiome data projects.
- Construct heatmaps and Venn diagrams and interpret data using linear discriminant analysis for effect size and phylogenetic trees.
- Align microbiome research tools with curriculum guidelines and student learning objectives.
Format
- Attendance at the live events is required. The facilitators will be working in real-time during the webinar sessions.
- During the live events, there will be interactive lecture and guided small group hands-on practice.
- Attendees will receive a link to the recording after the live event. The recording will be available until Jan. 31, 2025.
- Attendees will be asked to complete additional synergistic work outside of the live events, approximately 1-2 hours per week.
Eligibility
To participate in the series, you must:
- Reside in the U.S. (requirement due to the NSF-RCN funding regulations).
- Be an undergraduate educator at any career level and at any type of institution, who wants to teach microbiome analysis in their classes or be a high school educator.
Registration Details
This series is being subsized by REMnet, which is a funded an NSF RCN-UBE grant (#1827035). People interested in enrolling must complete an application on or before Friday, Sept. 20, 2024. If your application is accepted, you will receive an email from education@asmusa.org with information about how to register and pay.- ASM members (all categories except supporting members): $50 for the 4-part course.
- Non-members (non-members or ASM supporting members): $150 for the 4-part course.
- No refunds will be given. All registrants will receive a link to the recording after the live event and will have access until Jan. 31, 2025.
