R Course on Metagenomics / Community Analysis
R practical + Seminar, Metagenomics, Community analysis. Practical Course and Seminar, together 6 ECTS
About
This course deals with the analysis of metagenomic (16S amplicon) sequencing data using R.
Biological background
Many multicellular organisms host other, microbial, organisms. These are collectively called the "microbiome" and it is becoming evident that the microbiome is dynamic, both spacially (e.g. body-parts and cavities for humans, or plant roots vs leaves) and temporally. For plants, the main driver of root microbiome composition is the soil, followed by plant species and genotype. This indicates that there is some co-dependency between host and microbiome. The microbiome carries out some important services for the host, the best understood services are related to nutrient acquisition. How, and to which degree hosts can control the microbiome remains elusive, although it appears some aspects of the microbiome are reproducible.
Course details
This course deals with the analysis of a large experiment. To understand the influence of plant secondary metabolites on the composition of bacterial communities, eight different synthetic bacterial communities were assembled, with 20-50 members each. Each community was grown in presence or absence of plant secondary metabolites, and sampled in a time-series (4 timepoints, 24hrs apart). This was replicated 5 times. Genomic DNA was extracted, 16S amplicon libraries were generated and sequenced using illumina technology.
If you participate in this course you will learn how to perform the full analysis of 16S metagenomic profiling experiments in R: The first week deals with getting the reads into R, performing quality control and preparing the reads for analysis. The second week you will learn how to perform analysis of these data, in the third week you will apply these skills and move towards interpretation. You will be asked to analyze one community and you are encouraged to discuss with the other participants and compare the results obtained for different communities.
This course is an advanced R course. A basic understanding of R (assignment, plotting, functions, data frames, tidyverse) is recommended for participants, introductions to R will be limited to the first day.
Some computations are heavy, to make sure your learning success does not depend on your personal hardware, you will be granted access to high-performance computing infrastructure for the duration of this course. You will work largely at your own pace, the course instructor will be available to troubleshoot.
The R course-scripts are available here:
https://github.com/nschan/16S_Metagenomics_Coursefiles
Goals
After this course, you should be able to:
- navigate R and the RStudio IDE
- work with short read data in R
- understand metagenomic sequencing
- carry out & interpret (multivariate) analysis of such datasets
ETCS
Grand total
Total hours:
| Breakdown of hours | ||
|---|---|---|
| Metagenomics course (19442) | ||
| Task1 | Time (h) | |
| Seminar / Presentation | ||
| Collecting information on the topic | 4 | |
| Preparations of presentation (own) | 5 | |
| Practicing presentation (own) | 5 | |
| Refinement of presentation (own) | 5 | |
| Feeback & reflection on own presentation (own, FT) | 2 | |
| Participation (10x Presentations; FT) | 5 | |
| Reflection of presentation (9x) | 5 | |
| Seminar / Paper Discussion | ||
| Paper reading (10x) | 40 | |
| Paper discussion (10x; FT) | 9 | |
| Reflection of manuscript discussion (10x) | 10 | |
| Course | ||
| Working through daily protocol (12 days) | 60 | |
| Assignments on Moodle (12 days) | 12 | |
| Daily reflection (12 days) | 6 | |
| Final Discussion and report | 12 | |
| Total | 180.00 | |
|
1 FT = Face Time |
||
With 1 ECTS equaling 30 hours, this is worth 6 ECTS.
Seminar
Seminar
The seminar is divided into presentation, and paper discussion. There will be 10 presentations, that generally introduce a topic, and 10 seminars, where a paper is discussed. The presentations and discussion of papers may take place on different days.
| Breakdown of hours for the Seminar | ||
|---|---|---|
| Metagenomics course (19442) | ||
| Task1 | Time (h) | |
| Seminar / Presentation | ||
| Collecting information on the topic | 4 | |
| Preparations of presentation (own) | 5 | |
| Practicing presentation (own) | 5 | |
| Refinement of presentation (own) | 5 | |
| Feeback & reflection on own presentation (own, FT) | 2 | |
| Participation (10x Presentations; FT) | 5 | |
| Reflection of presentation (9x) | 5 | |
| Seminar / Paper Discussion | ||
| Paper reading (10x) | 40 | |
| Paper discussion (10x; FT) | 9 | |
| Reflection of manuscript discussion (10x) | 10 | |
| Total | 90.00 | |
|
1 FT = Face Time |
||
With 1 ECTS equaling 30 hours, this is worth 3 ECTS.
Course
Tabulation of hours for the practical:
| Breakdown of hours for the Course | ||
|---|---|---|
| Metagenomics course (19442) | ||
| Task | Time (h) | |
| Course | ||
| Working through daily protocol (12 days) | 60 | |
| Assignments on Moodle (12 days) | 12 | |
| Daily reflection (12 days) | 6 | |
| Final Discussion and report | 12 | |
| Total | 90.00 | |
With 1 ECTS equaling 30 hours, this is worth 3 ECTS.