Microbial metagenomics: a 360º approach

Overview

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Course overview

This course will provide a global overview of the different metagenomic approaches to study microbial communities, covering methods for the functional search of genes, sequencing of metagenomes using the most recent technologies and in silico methods for sequence analysis.

During the course, participants will receive an overview of state-of-the-art genomic technologies and bioinformatic tools. A balanced approach of lectures and practical sessions will provide a general background and the latest advancements in the field as well as its relationship with other disciplines.

The course will begin with experimental training in functional metagenomics by preparing metagenomic libraries for gene searching. Metagenomic DNA will be isolated from soil samples to analyze bacterial diversity in situ by third generation
sequencing (Nanopore). Cutting-edge single-cell microbial genomics using microfluidics will be addressed.

Additionally, students will learn bioinformatics analysis of metagenomic data
sets, from raw sequences to the application of algorithms. Follow-up practical exercises and sessions to discuss experimental design will allow students to learn and test their knowledge.

In summary, this course will allow participants to work through the entire workflow, from sample preparation to in silico data analysis.

Audience

This course is aimed at advanced PhD students and post-doctoral researchers who are doing or planning to start research in the field of metagenomics.

Modules/resources

• Experimental design
• Extraction of metagenomic DNA
• Construction of metagenomic libraries
• Single-cell microbial genomics
• 3rd generation sequencing (Nanopore)
• Bioinformatic analysis of metagenomic data: data standards and submission, processing of raw data, assembly, functional annotation, overview of databases, retrieval and analysis tools.

Learning outcomes

• Construct your own metagenomic library
• Analyse and organise your data
• Interpret results, explore different databases, use different retrieval and analysis tools
• Sequence analysis

What past participants say about the course

“This course gave me the opportunity to learn from my coursemates and understand the software used in metagenomics. The speakers were friendly and are always ready to answer our research questions, and provide us with valuable advice and comments.” – Lee Hwei Huih, The University of Hong Kong

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