Metagenomics

Metagenomics#

Metagenomics is transforming biotechnology by allowing us to study entire microbial communities directly from environmental samples without the need of culturing bacteria. This powerful approach provides insights into microbial diversity, taxonomical composition, microbial functions, and microbial associations.

In this course, you’ll learn every step of the process, from experimental design and sample acquisition to data processing (nf-core/taxprofiler), downstream analysis (diversity, taxa overviews, groups comparison, microbial associations), and visualization (in R). You’ll also explore the significance and real-world applications of metagenomics, gaining all the skills you need to analyse complex microbial communities. The course is open to all levels! Whether you’re working with metagenomics data or looking to integrate it into your research, this course will provide essential knowledge and practical skills.

Objectives#

Theoretical#

  • Microbiome importance and application

  • Experimental design: from sample acquisition to abundance tables

  • Technology

    • 16S RNA amplification

    • Shotgun metagenomics

      • Reference-based

      • Metagenome assembled genomes (MAGs)

  • Diversity measuremets

  • Compositionality issues

  • Microbial gene catalogs

  • Functional analysis

Hands on#

  • Sample processing with nf-core/taxprofiler using Metaphlan database

  • Taxonomical overviews (stacked barplots)

  • Diversity measures

  • Sample distances

  • Principal coordinate analysis (PCoA) based on sample dissimilarity

  • Group comparison

    • Abundance comparison by Boxplots

    • Abundance comparison by Heatmap

  • Microbial Association Networks (MAN)

  • Reporting with vuegen

Contents