We are excited to host the second annual week-long Workshop on Microbial Community Multi-omics using the bioBakery this summer in Boston (Cambridge, MA), July 20–24. While we have offered this course through various venues since 2018, last year was the first time we held it locally, and the experience was so positive that we are delighted to welcome participants back to our home base again this year. The course will provide attendees with both instruction and hands-on experience concerning computational methods for profiling the taxonomic structure (microbes and viruses) and function of microbial communities from high-throughput molecular data, alongside statistical methods for associating those profiles with host phenotypes or environmental properties. We will focus on analysis of shotgun metagenomes, metatranscriptomes, and untargeted metabolomic data using the bioBakery: a computing environment comprising reproducible methods for microbial community analysis. Participants will need to bring their own laptops and have some basic familiarity with working at the command line, but prior knowledge of our software or microbial community analysis is not needed.
The course will be hosted and delivered by members of the Huttenhower Lab and the Harvard Chan Microbiome in Public Health Center (HCMPH). Our philosophy is to train participants in the most relevant topics in microbial community analysis in a vibrant, immersive, and inclusive environment. We welcome all skill levels for this in-person course and look forward to hosting a productive and engaging workshop! See below for an overview of the course program, its details, and registration information. Please contact our team (biobakercourses@gmail.com) with any questions about the workshop.
When: July 20-24, 2026
Where: Broad Institute, 415 Main Street, Kendall Square, Cambridge, MA
Instructors: Drs. Curtis Huttenhower, Eric Franzosa, Kelsey Thompson, and
other members of the HCMPH.
Registration:
To express your interest in joining this course please fill out this google form. Once approved we will send you the link for registration.
Morning: 9am-12:30pm |
| Lecture: General introduction |
| Student introductions |
| Lecture: Intro. to microbial community multi'omics |
| Lecture: Experimental considerations in microbiome sequencing |
| Lab: Google Cloud setup |
12:30pm-2pm Lunch |
Afternoon: 2pm-6pm |
| Lab: Sequencing QC with KneadData |
| Lecture: Taxonomic profiling |
| Lab: Taxonomic profiling with MetaPhlAn |
| Lecture: The Human Microbiome Projects (HMP1+2) |
| Open discussion / questions / wrap-up |
| Course dinner - TBD |
Morning: 9am-12:30pm |
| BONUS Lab: Intro to command line |
| Lecture: Strain profiling |
| Lab: Strain profiling with StrainPhlAn |
| Lab: Tree viz with GraPhlAn |
12:30pm-2pm Lunch |
Afternoon: 2pm-6pm |
| Lecture: Viral profiling |
| Lab: Viral profiling with BAQLaVa |
| Lecture: Functional profiling |
| Lab: Functional profiling with HUMAnN |
| Open discussion / questions / wrap-up |
| End of day |
Morning: 9am-12:30pm |
| BONUS LAB: Intro to R |
| Lecture: Metagenomic assembly and applications |
| Lab: Assembly and SGB creation |
| Lecture: SGBs and microbial phylogenetics |
| Lab: Microbial phylogenetics with PhyloPhlAn |
12:30pm-2pm Lunch |
Afternoon: 2pm-6pm |
| Lab: Prioritizing bioactive genes with MetaWIBELE |
| Lecture: Gene transfer in microbial communities |
| Lab: Detecting LGT with WAAFLE |
| Lab: Lecture: Meta'omic visualization |
| Open discussion / questions / wrap-up |
| End of day |
Morning: 9am-12:30pm |
| BONUS LAB: Meta'omic viz in R |
| Lecture: Microbial community study design |
| Lecture: Statistics for microbial multi'omics |
| Lab: Strain epidemiologic testing with Anpan |
| Lecture: Metatranscriptomics (MTX) |
12:30pm-2pm Lunch |
Afternoon: 2pm-6pm |
| Lab: Microbial community statistics with MaAsLin |
| Lecture: Microbiome metabolomics |
| Lab: Prioritizing bioactive metabolites with MACARRoN |
| Open discussion / questions / wrap-up |
| End of day |
Morning: 9am-12:30pm |
| BONUS LAB: High-dim. testing in R |
| Lecture: Methods for multi'omic data integration |
| Lab: Multi'omic integration with HAllA |
| Lecture: Meta-analysis with microbial community data |
| Lab: Meta-analysis with MMUPHin |
12:30pm-2pm Lunch |
Afternoon: 2pm-6pm |
| Lecture: Intro. to AnADAMA and bioBakery workflows |
| Lab: bioBakery workflows |
| Lecture: Reproducibility in microbiome studies (MBQC) - People's choice |
| Open discussion / questions / wrap-up |
| End of day |
This course will be held at the new building for the Broad Institute in Cambridge, MA located at 415 Main Street in Kendall Square.
Tuition to attend: $450 which covers the full week of instruction, daily light breakfast food and beverages, and a course dinner.
Registration: To express your interest in joining this course please fill out this google form. Once approved we will send you the link for registration.
Nearby hotels list:
- Boston Marriott Cambridge
- The Kendall Hotel
- Residence Inn Boston Cambridge
- The Fairfield Inn and Suites Boston/Cambridge
- Hampton Inn by Hilton Boston/Cambridge