Microbiome data analysis using QIIME2

This course introduces students to the principles of microbiome research and microbial community analysis using next-generation sequencing (NGS) data and the QIIME 2 bioinformatics platform. The course begins with an overview of the microbiome, its biological importance, and its role in human health and disease. Students will also be introduced to key experimental considerations in microbiome studies, including sample collection, sample preservation, DNA isolation, and PCR amplification of microbial marker genes. The concept of barcoded sequencing and sequencing strategies used in microbiome studies will be discussed to provide the experimental context for downstream bioinformatics analysis.

The practical component focuses on microbiome data analysis using QIIME 2, one of the most widely used tools for microbial community analysis. Students will work with the widely used QIIME 2 “Moving Pictures” example dataset, which contains human microbiome samples collected over time from multiple body sites. This dataset allows students to explore how microbial communities vary across body sites and change over time.

Through guided exercises, participants will learn the core steps involved in microbiome sequence analysis, including:

• Importing sequencing data into QIIME 2
• Sequence quality control and filtering
• Denoising and generation of feature tables
• Microbial diversity analysis using alpha and beta diversity metrics
• Taxonomic classification of microbial sequences
• Visualization and interpretation of microbial community composition and relative abundance

By the end of the course, students will understand the full workflow of microbiome studies, from sample handling and DNA extraction to computational analysis and interpretation of microbial community data.

Credits: 1 ECTS

Learning Outcomes

After completing the course, students will be able to:

1. Describe the biological importance of the microbiome and its relevance to human health and disease.
2. Explain the key experimental steps involved in microbiome studies, including sample collection, preservation, DNA isolation, and PCR amplification.
3. Understand the principles of barcoded sequencing and next-generation sequencing workflows used in microbiome research.
4. Import and manage microbiome sequencing datasets in the QIIME 2 environment.
5. Conduct microbial diversity analyses using common alpha and beta diversity measures.
6. Visualize and interpret microbiome data generated using QIIME 2.

Prerequisites for QIIME 2 data analysis, which begins in April, 2026. If you want assistance with installation, please let me know so that we can plan a separate day.

Course Delivery

The course will be conducted online via Zoom. The same Zoom link will be used for all course sessions. If you experience any technical issues accessing the course, please contact the instructor.