Microbial Genomics

Recommended Prerequisites

Basic knowledge in Microbiology and Bioinformatics.

Teaching Methods

Different teaching strategies are used: 1) lectures supported in the projection of images, schemes and videos, complemented with questionnaires for self-evaluation; 2) seminars (face-to-face or distance) followed by discussion of case studies; 3) team work to solve specific microbiological problems; 4) practical classes (face-to-face or distance) where microbial genomes will be analyzed. During and after classes will be encouraged the interactivity and participation of the students proposing topics of discussion. 

Learning Outcomes

The aim is to provide students a thorough knowledge on the structure, organization and plasticity of microbial genomes, as well as on the tools and methodologies of genome analysis. Emphasis will be given to current applications of microbial genomics in different areas such as human, animal and environmental health, agriculture and biotechnology. By the end of the course students will be able to understand the following important principles/methodologies:

1) Nucleic acids sequencing.

2) Databases of microbial genome sequences.

3) Bioinformatic tools to analyze second and third generation sequencing data for the purpose of assembling and annotating a genome.

4) Planification of microbial genomics experiments, predicting results.

5) Genome evolutionary principles and diversity.

6) Comparative and functional genomics.

7) Applications of microbial genomics.

8) Critically evaluate the ethical issues related to the use of genomics in different contexts.

Work Placement(s)

No

Syllabus

Thematic Units

A - Introduction: structure and diversity of microbial genomes; History of genomics

B - Sequencing of nucleic acids; Databases; genomes assembly and annotation; Algorithms and protocols

C - Functional genomics; Comparative genomics

D - Genomics for species typing and identification

E – Microbial genome and evolution

F - Population genomics and phylogeography

G - Genomics and epidemiology

H-The resistome and the mobilome

I - Genomic analysis of interactions with environment and hosts

J - Assembly and analysis of genomes from metagenomic data

The bacterial genome will be approached as a model for the exploration of methodologies and tools. The practical classes will consist of assembling and annotating a genome, exploring different analyzes such in silico strains identification and typing, point mutations, plasmids, genomic islands, CRISPR elements, resistance genes, virulence factors ( for humans, other animals or plants).

Assessment Methods

Assessment
Resolution Problems: 10.0%
Frequency: 30.0%
Project: 60.0%

Bibliography

Artigos científicos na área da genómica microbiana que serão fornecidos para cada unidade temática/Scientific papers in the area of microbial genomics that will be provided for each tematic unit.