Sunagawa Lab Block Course Fall 2024: 551-1119-00L Microbial Community Genomics

General information

• Course location: HCI F441

• Course dates: 05.11.2024 - 27.11.2024

  • First day (Tue 05.11): 12:45 - 16:30

  • Rest:

    • Tue | 13:00 - 16:30 w/ 15’ break

    • Wed - Fri | 9:00 - 17:00 w/ 2x15’ break + 1h lunch break

• Presentations: 27.11.2023, 9:00 - 15:00

• Tutors:

  • Samuel Miravet Verde - smiravet@ethz.ch

  • Martin Sperfeld - martin.sperfeld@biol.ethz.ch

• Technichal Support:

  • Hans-Joachim Ruscheweyh

  • Urs Blumentritt

• Coordinator:

  • Shinichi Sunagawa - ssunagawa@ethz.ch

Useful resources

• RStudio-Workbench and Jupyter introductions

  • Jupyter: http://cousteau-jupyter.ethz.ch/

  • R-Studio: http://cousteau-rstudio.ethz.ch/

• Zoom room

• Slack group

• Drive folder

Student Projects

• Project 1 (Linda & Matija): Determinants of AMPs diversity in the global ocean microbiome

• Project 2 (Gian & Remi): Exploring the relation between smORFs and AMPs with BGCs

• Project 3 (Louis & Takumi): Extracellular contractile injection systems (eCIS) in Acidobacteriota

• Project 4 (Enea & Lisa): Complex sugar degradation in Acidobacteriota

• Project 5 (Lola & Maide): Eukaryote-like proteins (ELPs) in Acidobacteriota

Useful links:

• Find more details in the project presentation and examples for reports and presentations in the shared folder

Data availability

The data samples used during this course come partly from:

• Biosynthetic potential of the global ocean microbiome

Some studies to use as reference:

• Global marine microbial diversity and its potential in bioprospecting

• Genome-resolved diversity and biosynthetic potential of the coral reef microbiome

• A catalog of small proteins from the global microbiome

Main resources from where genomes come from:

• Ocean Microbiomics DB

• mOTUs-DB

Some of the tools used to obtain the working data:

• Macrel (v1.5) to identify AMPs from smORFs extracted by a custom ORF Finder.

• antiSMASH (v7) to identify BGCs.

• EggNOG (v5) to annotate genes for KEGG, PFAMs, etc.

• PFAM (v36) to annotate PFAMs.

Agenda

Week 1

W1.1	05.11	12:45 - 14:15	Introductory lecture
W1.2	05.11	14:30 - 16:30	Setup infrastructure and Using Bash/UNIX
W1.3	06.11	09:00 - 10:15	Lecture on genomics and genome mining
W1.4	06.11	10:30 - 12:00	Lecture on computational genomic mining
W1.5	06.11	13:00 - 14:30	Introduction to Python Programming, Data Analysis and Data Visualization
W1.6	06.11	14:45 - 17:00	Introduction to Python (continuation)
W1.7	07.11	09:00 - 10:15	Hands-on tutorial on genome mining methods
W1.8	07.11	10:30 - 12:00	Hands-on tutorial on genome mining methods (continuation)
W1.9	07.11	13:00 - 14:30	Hands-on tutorial on genome mining methods (continuation)
W1.10	09.11	14:45 - 17:00	Hands-on tutorial on genome mining methods (continuation)
W1.11	09.11	09:00 - 10:15	Introduction to the Ocean Microbiome Database (exercise)
W1.12	10.11	10:30 - 12:00	Introduction to the Ocean Microbiome Database (continuation)
W1.13	10.11	13:00 - 14:30	Introduction to the Ocean Microbiome Database (continuation)
W1.14	10.11	14:45 - 17:00	Introduction to group projects

Week 2

W2.1	14.11	13:00 - 14:30	Lecture on best practices for bioinformatic projects
W2.2	14.11	14:45 - 16:30	Explanation, selection and planning of projects
W2.3	15.11	09:00 - 10:15	Student projects
W2.5	15.11	10:30 - 12:00	Student projects
W2.4	15.11	13:00 - 14:30	Invited speaker lecture: Dr. Serina Robinson
W2.6	15.11	14:45 - 17:00	Student projects
W2.7	16.11	09:00 - 10:15	Student projects
W2.8	16.11	10:30 - 12:00	Student projects
W2.9	16.11	13:00 - 14:30	Invited speaker lecture: Prof. Dr. Shinichi Sunagawa
W2.10	16.11	14:45 - 17:00	Student projects
W2.11	17.11	09:00 - 10:15	Student projects - Prepare presentation
W2.12	17.11	10:30 - 12:00	Institute seminar: Dr. Martin Steinegger
W2.13	17.11	13:00 - 14:30	Present progress & Discussion
W2.14	17.11	15:30 - 17:00	Present progress & Discussion - Wrap-up and plan W3

Week 3

W3.1	21.11	13:00 - 14:30	Lecture on writing and presentations (check examples)
W3.2	21.11	14:45 - 16:30	Student projects
W3.3	22.11	09:00 - 10:15	Student projects
W3.5	22.11	10:30 - 12:00	Institute seminar: Fabienne Wiederkehr
W3.4	22.11	13:00 - 14:30	Student projects
W3.6	22.11	14:45 - 17:00	Student projects
W3.7	23.11	09:00 - 10:15	Student projects
W3.8	23.11	10:30 - 12:00	Student projects
W3.9	23.11	13:00 - 14:30	Student projects
W3.10	23.11	14:45 - 17:00	Student projects
W3.11	24.11	09:00 - 10:15	Student projects
W3.12	24.11	10:30 - 12:00	Prepare presentation
W3.13	24.11	13:00 - 14:30	Present progress & Discussion
W3.14	24.11	15:30 - 17:00	Present progress & Discussion - Wrap-up, data freeze and plan W4

Week 4

W4.1	28.11	13:00 - 14:30	Prepare presentation
W4.2	28.11	14:45 - 16:30	Prepare presentation
W4.3	29.11	09:00 - 10:15	Presentations (15 min. presentation + 5 min. questions)
W4.4	29.11	10:30 - 12:00	Presentations (continuation)
W4.5	29.11	13:00 - 14:30	Presentations (continuation)
W4.6	29.11	14:45 - 16:00	Discussion for writing the project
W4.7	29.11	16:00 - 16:30	Block Course wrap-up