Ctrl+K

Sunagawa Lab Block Course Fall 2021: 551-1119-00L Microbial Community Genomics

Sunagawa Lab Block Course Fall 2021: 551-1119-00L Microbial Community Genomics#

General information#

  • Course dates: 09.11.2021 - 01.12.2021

    • Week 1: Tue 1:30PM - 5PM, Wed - Fri 8:30AM - 5PM

    • Week 2: Tue 1:30PM - 5PM, Wed - Fri 8:30AM - 5PM

    • Week 3: Tue 1:30PM - 5PM, Wed - Fri 8:30AM - 5PM

    • Week 4: Tue 1:30PM - 5PM, Wed - Wed 8:30AM - 5PM

  • Exam: 30.11.2021, 13:30 - 15:30

  • Presentation: 01.12.2021, 13:30 - 16:00

  • Tutors:

Useful resources#

Student Projects#

  • Project 1 (Mads & Elina): Patient gut microbiome and patient response to intensive chemotherapy in AML

  • Project 2 (Gioia & Lena): Patient gut microbiome and patient risk of developing neutropenic enterocolitis as a consequence of intensive chemotherapy in AML

  • Project 3 (Dennis & Léa): Potential of AML patient gut microbiome to interact with chemotherapeutic drugs used during intensive induction chemotherapy

  • Project 4 (unassigned): Functional redundancy in AML patient gut microbiome

  • Project 5 (unassigned): Bacterial population structure in AML patients

  • Project 6 (Marius & Manuel): Investigate the uncharted diversity of the gut microbiome in AML patients

Find more details in the Project presentation

Data availability#

The following data is available for the development of the projects:

In general, DNA extracted from fecal samples collected from AML patients undergoing intensive chemotherapy have been sequenced using

  • 16S amplicon sequencing

  • metagenomic shotgun sequencing

All computed data can be found at /nfs/course/551-1119-00L_masterdata/projects with the following folder structure:

  • 16S

    • aml_metab_ASV_BC_HS21.txt: ASV table containing all samples that have been sequenced using 16S amplicon sequencing

    • aml_metab_tax_BC_HS21.txt: Taxonomy table containing the sequences of individual ASVs and their taxonomic annotation as derived using mTAGs

  • metaG:

    • gene_catalog:

      • AML_115_METAG_cdhit9590.functional_profile_insertcounts.lengthnorm.cellab.withKEGG.profile.gz: Functional profile of the gene catalog. Per cell abundance of each KO.

      • AML_115_METAG_cdhit9590.functional_profile_insertcounts.profile.gz: Functional profile of the gene catalog. Number of reads of each KO. This table is not normalized and is only intended to be used for rarefaction and downstream alpha diversity analyses.

      • AML_115_METAG_cdhit9590.gene_profile_insertcounts.lengthnorm.cellab.withKEGG.profile.gz: Gene profile of the gene catalog. Per cell abundance of each gene x 1000

    • MAGs:

      • gtdbtk.ar122.summary.tsv: Taxonomic information on the MAGs out of GTDB (Archaea)

      • gtdbtk.bac120.summary.tsv: Taxonomic information on the MAGs out of GTDB (Bacteria)

    • mOTUs:

      • aml_metag_motus_BC_HS21.txt: Microbial abundance profiles for all samples sequenced using shotgun metagenomic sequencing as derived using mOTUs

  • auxiliary_data:

    • clinical_data:

      • AML_metadata_BC_HS21.txt: File containing all available clinical metadata from patients enrolled within the AML study as of per OCT2021

      • AML_Antiinfectives.txt: File containing the usage scheme of all antiinfective drugs given to patients enrolled within the AML study as per AUG2021

      • AML_AntineoplasticAgents.txt: File containing the usage scheme of all antineoplastic drugs given to patients enrolled within the AML study as per AUG2021

    • DGIdb_KEGG:

      • interactions_withKO.tsv: Interaction table from DGIdb with the KO annotation for all genes.

Agenda#

Week 1#

W1.1

09.11

13:30 - 15:00

Introductory lecture

W1.2

09.11

15:30 - 17:00

Setup infrastructure

W1.3

10.11

08:30 - 10:00

Lecture on omics techniques & data

W1.4

10.11

10:30 - 12:00

Introduction to R

W1.5

10.11

13:30 - 15:00

Lecture on metagenome-assembled genomes (MAGs)

W1.6

10.11

15:30 - 17:00

Data transformation with R: tidyverse

W1.7

11.11

08:30 - 10:00

Data visualization with R: ggplot2

W1.8

11.11

10:30 - 12:00

16S rRNA gene amplicon pipeline (lecture)

W1.9

11.11

13:30 - 15:00

16S rRNA gene amplicon pipeline (tutorial)

W1.10

11.11

15:30 - 17:00

Describing microbial community structure (Concept Course lecture) and Introduction to alpha and beta-diversity

W1.11

12.11

08:30 - 10:00

Describing microbial community structure (Concept Course tutorial)

W1.12

12.11

10:30 - 12:00

Data wrangling (hands-on session)

W1.13

12.11

13:30 - 15:00

Data wrangling solutions

W1.14

12.11

15:30 - 17:00

Wrap-up and plan W2

Week 2#

W2.1

16.11

13:30 - 15:00

Plan group projects

W2.2

16.11

15:30 - 17:00

Group projects

W2.3

17.11

08:30 - 10:00

Lecture on best practices for data/project/software management

W2.4

17.11

10:30 - 12:00

Group projects

W2.5

17.11

13:30 - 15:00

Group projects

W2.6

17.11

15:30 - 17:00

Group projects

W2.7

18.11

08:30 - 10:00

Group projects

W2.8

18.11

10:30 - 12:00

Group projects

W2.9

18.11

13:30 - 15:00

Group projects

W2.10

18.11

15:30 - 17:00

Group projects

W2.11

19.11

08:30 - 10:00

Group projects

W2.12

19.11

10:30 - 12:00

Group projects

W2.13

19.11

13:30 - 15:00

Present progress by each group & Discussion

W2.14

19.11

15:30 - 17:00

Wrap-up and plan W3

Week 3#

W3.1

23.11

13:30 - 15:00

Lecture on report writing (check also the report example)

W3.2

23.11

15:30 - 17:00

ANOVA and DESeq2

W3.3

24.11

08:30 - 10:00

Group projects

W3.4

24.11

10:30 - 12:00

Group projects

W3.5

24.11

13:30 - 15:00

Group projects

W3.6

24.11

15:30 - 17:00

Group projects

W3.7

25.11

08:30 - 10:00

Group projects

W3.8

25.11

10:30 - 12:00

Group projects

W3.9

25.11

13:30 - 15:00

Group projects

W3.10

25.11

15:30 - 17:00

Present progress by each group & Discussion

W3.11

26.11

08:30 - 10:00

Group meeting

W3.12

26.11

10:30 - 12:00

Freeze results of group projects

W3.13

26.11

13:30 - 15:00

Freeze results of group projects

W3.14

26.11

15:30 - 17:00

Wrap-up and plan W4

Week 4#

W4.1

30.11

13:30 - 15:30

Exam

W4.2

30.11

16:00 - 17:00

Prepare presentation

W4.3

01.12

08:30 - 10:00

Prepare presentation

W4.4

01.12

10:30 - 12:00

Prepare presentation

W4.5

01.12

13:30 - 16:00

Presentations

W4.6

01.12

16:30 - 17:00

BlockCourse wrap-up
Contents