With the term “microbe” we describe many different forms of life, such as archaea, bacterial, fungi, and protists. They can live everywhere, including in and over the human body, where they impact human physiology. For instance, the human gut microbiome is helping food digestion, performing the synthesis of vitamins and other key compounds, and is involved in the development of the host immune system. It is also influencing drug action and it has been linked with multiple diseases, such as metabolic, autoimmune, neuropsychiatric disorders. Similarly, the vaginal microbiome has been linked to women’s and reproductive health, for instance, to inhibition or promotion of infections (e.g., bacterial vaginosis and sexually transmitted diseases), and it also differs between pregnant and non-pregnant women. Changes in the vaginal microbial composition are linked to the risk of pre-term births.
Studying the human microbiome allows us to determine:
Metagenomics is a rapidly developing discipline, which requires careful study design and high bioinformatics expertise. In this workshop, we will discuss best practices for the implementation of a metagenomics project and get a first-hand experience thanks to a series of live coding tutorials.
The workshop is aimed at individuals who have no previous knowledge of the tools that will be presented at the workshop. During this workshop, we will be using the Unix Shell and the R programming language/RStudio. These environments are covered in our Unix shell and programming in R workshop.
Lasting two days (12h in total), this workshop will cover the basics of 16S rRNA gene amplicon and whole-shotgun metagenomics sequencing data, and it is divided into two morning lectures, which will cover:
These lectures will be followed by two hands-on tutorials in the afternoon, which will cover basic concepts and tools for the analysis of 16S rRNA gene amplicon and whole-shotgun metagenomic and sequencing data, namely: