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 various courses, including microbiology courses, introductory biology, ecology, genetics and environmental studies.
This course 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. Explore examples of microbiome data analysis projects using resources that do not require coding or advanced bioinformatics skills.
This 3-part course will be hosted by ASM and co-sponsored by Research Experiences in Microbiomes Network (REMNet), a funded NSF RCN-UBE grant (#1827035).
Participants who complete the course will receive the following:
- A certificate of completion.
- The opportunity to participate further with the REMNet network.
- A feature on the REMNet website as ambassadors of the program.
Wednesday, Sept. 29 | 12-1 p.m. EDT
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. We will describe the pre-processing and workflow parameters for Nephele. The webinar will review 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 educators can use in a classroom setting.
Wednesday, Oct. 6 | 12-1 p.m. EDT
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 and use .csv files to create custom bar plots. The webinar will discuss several alpha-diversity metrics and interpreting the results in an ecological context. We will introduce the diversity across samples 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 and how their data can lead to novel, testable hypotheses.
Wednesday, Oct. 13 | 12-1 p.m. EDT
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. We will explore methods to visual diversity and similarity across samples 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.
EligibilityTo enroll in the course, you must meet the following requirements:
- Be an undergraduate educator at any career level and at any institution who wants to teach microbiome analysis in their classes OR be a high school educator.
- Reside in the United States (requirement due to the NSF-RCN funding regulations).
- Submit an application no later than Friday, Sept. 24, 2021.
Application and EnrollmentThis series is subsidized by REMnet and funded by an NSF RCN-UBE grant (#1827035). If you are interested in enrolling, you must complete an application by Friday, Sept. 24, 2021.
- If your application is accepted, you will receive an email from firstname.lastname@example.org with information about registering and payment.
- ASM members (all categories except Supporting members): $25 for the 3-part course.
- Non-members (non-members or ASM supporting members): $125 for the 3-part course.
- No refunds will be granted. All registrants will receive a link to the recording after the live event and have access for 30 days.