We are now accepting applications!

Application forms are available here! The application deadline is 1-May, 2024.

The 2024 Workshop on Microbial Community Multi-omics is being held 3-7th of June2024 in Český Krumlov, Czech Republic. This is the 1st time the Workshop of Microbial Community Multi-omics will be held in the Czech Republic. We have held similar courses through different venues for the previous five years but are really excited about teaming up with Evomics courses to host our course this year!

Our philosophy is to train participants in the most relevant topics in microbial community analysis in a vibrant, immersive, and inclusive environment. In this week-long workshop, members of the Huttenhower Lab and Harvard Chan Microbiome in Public Health Center (HCMPH) will provide an overview of bioinformatics methods for profiling the taxonomic structure (microbes and viruses) and function of microbial communities from high throughput ‘omics data, alongside statistical methods for associating those profiles with community metadata (e.g., host phenotypes). This course will focus on analyzing shotgun metagenomes, metatranscriptomes, and untargeted metabolomic data using the bioBakery: a computing environment containing reproducible methods for microbial community analysis. Participants will be expected to bring a laptop-style computer and have some basic familiarity with working at the command line.

The Workshop on Microbial Community Multi-omics 2024 is organized by:

The Huttenhower group, T.H. Chan School of Public Health, US

Daniel Kintzl, Český Krumlov Coordinator

Scott Handley, Evomics Director, Washington University, US

We also have a talented group of teacher assistants who help with the organization and preparation of the computer practicals.

Workshop Information

The Workshop registration fee is $850. We provide approximately 40 hours of teaching during the two-week workshop, so our price is approximately $22 an hour. Note that this amount does not cover travel, lodging, or boarding.

Other important details can be read on our FAQ page.

If you do not manage to attend the workshop on Microbial Community Multi-omics 2024, stay tuned for June 2025!

 3-7 June, 2024

Note: This is the list of topics we plan to cover, timing and presenter may change closer to the date of the course.

3rd Jun Monday 9-12 Everyone

Curtis Huttenhower

Jacob Nearing


Welcome and introductions

Introduction in microbial community analysis

Experimental considerations in microbiome sequencing

Tutorial: KneadData sequence QC

3rd Jun Monday 2-5 Kelsey Thompson


Curtis Huttenhower

Taxonomic profiling in microbial communities

Tutorial: Taxonomic profiling with MetaPhlAn 4

The human microbiome Projects (HMP1&II)

3rd Jun Monday 7-9 Everyone Reception and networking
4th Jun Tuesday 9-12 Kelsey Thompson



Identifying strain in community data

Tutorial: Tree visualization with GraPhlAn

Tutorial: Strain profiling with StrainPhlAn 4

4th Jun Tuesday 2-5 Curtis Huttenhower

Eric Franzosa


Study design for microbial multi-comic studies

Functional profiling in microbial communities

Tutorial: Functional profiling with HUMAnN 4

4th Jun Tuesday 7-9 Everyone Lighting talks and networking
5th Jun Wednesday 9-12 Kelsey Thompson



Metagenomic assembly and applications

Tutorial: Prioritizing bioactive genes with MetaWIBELE

Tutorial: Detecting LGT with WAAFLE

5th Jun Wednesday 2-5 Curtis Huttenhower


Eric Franzosa

SGBs and microbial phylogenetics

Tutorial: Assembly and SGB creation tutorial

Meta’omic visualization

5th Jun Wednesday 7-9 Everyone Lighting talks and networking
6th Jun Thursday 9-12 Jacob Nearing



Statistics for microbial multi’omics

Tutorial: Microbiome association testing with MaAsLin and Anpan

Tutorial: Meta’omic visualization

6th Jun Thursday 2-5 Kelsey Thompson


Eric Franzosa

Metatranscriptomics (MTX)

Tutorial: Statistics for MTX with MaAsLin

Viral profiling in microbial communities

6th Jun Thursday 7-9 Eric Franzosa


Microbiome metabolomics

Tutorial: Prioritizing bioactive metabolites with MACARRoN

7th Jun Friday 9-12 Jacob Nearing


Methods for multi’omic data integration

Tutorial: Data integration with HAllA

7th Jun Friday 2-5 Curtis Huttenhower


Reproducible microbial community analysis

Open time/QA

Important information:

  • Group photo! (We will add in person!)
  • Online booking of your free time activities! (also available at the Info-Centre)
  • Český Krumlov town information
  • Map of 2024 Český Krumlov – Check before arrival to choose the bus stop closest to your accomodation!!
  • Map of the main locations in the schedule (Save to your Google Maps!)
  • Map of some of the main Český Krumlov restaurants (Save to your Google Maps!)
  • Map of some of the main Český Krumlov bars (Save to your Google Maps!)
  • Map of Český Krumlov service points: shops, pharmacy, ATM, hospital (Save to your Google Maps!)
  • Map of the historic City Centre of Český Krumlov
  • As a tradition we have a T-shirt design competition! Best T-shirt design will feature on the Workshop on Microbial Community Multi-omics 2024 T-shirts! Submit your design by EOD June 4th at the latest! (For inspiration, check out previous designs here!)
  • BINGO!