12-16 June 2023

To foster international participation, this course will be held online

This course will provide a thorough introduction to microbial community data analysis (metagenomics, metatranscriptomics, and other culture-independent molecular data) through a balanced approach of lectures and hands-on lab sessions. Course participants will learn how to process data from raw meta’omic sequencing files through appropriate bioinformatic methods and approaches for subsequent integrative statistical analyses. Participants are invited to bring their own data to the practical session on the final day or can use publicly available data from the Integrative Human Microbiome Project (HMP2).

This course is designed for researchers and students with interest in using culture-independent molecular data (particularly DNA and RNA sequencing technologies) to study microbial communities. This includes both the human microbiome in population studies and techniques generalizable to any microbial communities. The course will mainly focus on the analysis of meta’omic sequencing, including workflows for processing raw sequencing data, multivariate analysis of microbial profiles, and visualization techniques.

• Familiarity with the goals of typical microbial community studies and common culture-independent molecular technologies used to assay them.

• Metagenomic and metatranscriptomic data analysis for taxonomic, functional, and strain-level characterization of communities using reproducible workflows.

• Learning how to perform multivariate statistical analyses, combine multiple measurement types in microbial communities, and how to visualize associated results.

• Experience in integrative multi’omics analysis for large sets of human microbiome or environmental microbial community populations.

Monday – Classes from 2-9 pm BERLIN TIME


Lecture 1: Introduction to metagenomics


Lab 1: Lab setup (Google Cloud)

Lecture 2: Introduction to meta'omic population studies


Lab 2: Introduction to command line (UNIX commands and the shell)


Lecture 3: Taxonomic profiling (MetaPhlAn)


Lab 3: MetaPhlAn

Dr. Curtis Huttenhower (Harvard Chan Center for the Microbiome in Public Health)

Dr. Amrisha Bhosle (Harvard Chan Center for the Microbiome in Public Health)

Dr. Kelsey N Thompson (Harvard Chan Center for the Microbiome in Public Health)

Dr. Eric Franzosa (Harvard Chan Center for the Microbiome in Public Health)

Dr. Meg Short (Harvard Chan Center for the Microbiome in Public Health)