Microbes in Focus

Erasmus Lyon Blended Intensive Program
June 29th to July 3rd, 2026

Microbes in Focus: Modern Tools for Understanding and Engineering Microorganisms

Unlock Your Potential in Microbiology: Join our Erasmus+ BIP in Lyon!

Dear Students (Bachelor 3rd year – L3, Master’s, and PhD),

Are you ready to take your skills in molecular microbiology to the next level while experiencing life in France? We are excited to invite you to the “Microbes in Focus” Blended Intensive Programme (BIP) scheduled for the 2025–2026 academic year.

What is the BIP Lyon 2026 "Microbes in focus"?

A Blended Intensive Programme (BIP) is a modern Erasmus+ format that gives you the best of both worlds. It will combine a flexible virtual component (online preparatory courses, around 5 hours in may/june 2026) with a short, immersive physical mobility experience in Lyon the fist week of July 2026. It allows you to gain 3 ECTS credits, work with international teams, and access high-level training without spending a full semester away.

The Science: Cutting-Edge Tools and Innovation

Hosted by the Université Claude Bernard Lyon 1 and local research centers (MAP, CIRI, LBTI, MMSB, IGFL), this program focuses on “Modern Tools for Understanding and Engineering Microorganisms”.

You will dive deep into:

• CRISPR and genetic engineering: strategies to investigate and modify microbial genomes, with examples focused on pathogenic bacteria.

• Artificial intelligence: hands-on workshops using computational tools such as AlphaFold for protein structure prediction and functional annotation.

• Diagnostics and molecular analysis: practical sessions introducing quantitative PCR and complementary approaches for detecting and characterizing microbial traits.

• Host–pathogen interactions and microbial ecology: tools to explore microbial physiology, diversity, and community structure in bacteria, yeasts, and filamentous fungi, spanning molecular mechanisms to ecological dynamics.

The Destination: Experience Lyon

Pack your bags for a vibrant stay in Lyon, France. The intensive on-site week is scheduled from June 29th to July 3rd.

Beyond the lab, you will discover the rich history of the French capital of gastronomy:

• Explore the ancient Roman Amphitheater and the Basilica of Fourvière.

• Wander through the secret passageways (“traboules”) of Old Lyon.

• Enjoy a traditional group dinner in the city.

The programme is coordinated by Erwan Gueguen (Associate Professor, Université Claude Bernard Lyon 1, MAP) and brings together recognized experts from leading French research institutions affiliated with the Université de Lyon:

MAP – Microbiology, Adaptation and Pathogenesis
MMSB – Molecular Microbiology and Structural Biochemistry
CIRI – International Center for Infectiology Research
IGFL – Institute of Functional Genomics of Lyon
LEM – Laboratory of Microbial Ecology
LBTI – Laboratory of Tissue Biology and Therapeutic Engineering

International collaborators from Erasmus+ partner universities (Technical University of Madrid, University of Granada, University of Minho, University of Gdańsk, Maynooth University) and industry partners (Evotec) also contribute their expertise.

If you are interested in participating, please contact the relevant teacher at your university:

- Eva Miedes, Technical University of Madrid, Spain.

- Matilde Fernandez, Grenada University, Spain .

- David Fitzpatrick, Maynooth University, Ireland.

- Maria João Sousa, Minho University, Portugal.

- Dorota Pomorska, Gdansk University, Poland.

The coordinator of the BIP "Microbes in Focus"

Associate Professor Erwan Gueguen, University Claude Bernard Lyon, Head of the Microbiology bachelor program.

On-Site Preliminary Component preliminary program: Intensive Week in Lyon (29 June – 3 July 2026)

Monday, 29 June: Focus on Yeasts

Keynotes: Essential gene studies in budding yeasts (Saccharomyces cerevisiae, Kluyveromyces lactis) using CRISPR/Cas and Auxin-Inducible Degron strategies; biotechnological exploitation of non-Saccharomyces yeasts
Practical Session: Introduction to qRT-PCR for analyzing differential gene expression in yeast
Cultural Activity: Visit to the Fourvière Basilica (Roman amphitheater and basilica)

Tuesday, 30 June: Focus on Filamentous Fungi

Continuation: Advanced qRT-PCR practical training
Keynotes: Cell painting in filamentous fungi ; cell wall remodeling, antifungal resistance, and vaccine targets in Aspergillus fumigatus and Candida albicans species complex
Cultural Activity: Guided tour of Old Lyon (historic traboules—secret passageways)

Wednesday, 1 July: Focus on Bacteria and Artificial Intelligence

Keynotes:
- Bacterial functional genetics: how to study bacterial gene expression at the transcriptional and post-transcriptional level (case study of phytopathogenic bacteria)
- Horizontal gene transfer by bacterial conjugation in live cells
- Innovative genetic engineering strategies for antimicrobial activity
Practical Session: Protein structure prediction with AlphaFold—theoretical principles and hands-on computational exercises

Thursday, 2 July: Bacterial Immunity and Pathogenesis

Keynotes:
- Bacterial anti-phage immune systems & the role of mobile genetic elements in spreading anti-phage systems
- Learning on the Fly: Molecular Tools to Study Probiotic-Host Interactions
- Proteomic interrogation of the lung-bacteria interface
Practical Session: Rapid detection of plant pathogenic bacteria using isothermal LAMP (Loop-mediated Isothermal Amplification) PCR
Social Event: Group dinner at a traditional Lyon restaurant

Friday, 3 July: Environmental Microbiology and Industrial Perspectives

Continuation: LAMP practical training (rapid pathogen identification in plant tissues)
Keynotes:
- How to study microorganisms when cultivation is not possible: the case of environmental studies
- Plant-microbiome functions: boosting plant health and ecosystem resilience
- Microbiology in industry: antibiotic drug discovery perspectives
Closing Ceremony

Microbes in Focus: Online Component Overview

Program Introduction

The online phase of the Microbes in Focus Blended Intensive Program (BIP) serves as the theoretical cornerstone for participants. It provides a deep dive into the molecular machinery of life, contrasting the streamlined efficiency of prokaryotes with the sophisticated complexity of eukaryotes, and concludes with the practical logic of genetic engineering.

This component is structured into three thematic modules designed to prepare students for advanced practical applications and research-driven discussions.

Module 1: Prokaryotic Transcription, Translation, and Regulation

Refresher: The Bacterial Central Dogma and its Control

This module explores the elegance of bacterial systems where speed and adaptability are paramount.

Key Topics:

• The Central Dogma: Detailed analysis of transcription and translation coupling.

• Transcription Machinery: The role of RNA polymerase and various sigma ($\sigma$) factors in environmental adaptation.

• Genetic Organization: The operon model and polycistronic mRNA.

• Regulatory Networks: From simple repressors/activators to complex Two-Component Systems (TCS) and sRNA-mediated regulation.

• Modern Transcriptomics: Evaluating tools like RT-qPCR, RNA-seq, and reporter fusions (GFP, Lux) to monitor gene expression.

Module 2: Eukaryotic Transcription, Translation, and Regulation

Refresher: Managing Complexity and Compartmentalization

Module 2 contrasts bacterial simplicity with the multi-layered regulatory architecture of eukaryotic cells, focusing on the implications of the nuclear envelope and chromatin.

Key Topics:

• Genome Architecture: Nucleosome structure, chromatin remodeling (euchromatin vs. heterochromatin), and the "histone code."

• Specialized Polymerases: The distinct roles of RNA Pol I, II, and III.

• RNA Maturation: The critical lifecycle of pre-mRNA involving 5' capping, splicing (alternative splicing), and 3' polyadenylation.

• Post-Transcriptional Control: Cap-dependent translation scanning, miRNA-mediated silencing via the RISC complex, and mRNA stability.

Module 3: Contribution of Cloning to Bacterial Gene Function

Applications: The Molecular Toolkit for Functional Genomics

The final module transitions from natural mechanisms to human-engineered tools, detailing how we isolate and study gene function in the lab.

Key Topics:

• The Cloning Toolkit: Anatomy of vectors (plasmids), selectable markers, and specialized shuttle/expression vectors.

• The Cloning Workflow: Precision techniques in PCR amplification, directional cloning, ligation, and transformation.

• Quality Control: Using blue/white screening and Sanger sequencing to verify recombinant constructs.

• Functional Analysis Strategies: Complementation: Proving gene necessity by restoring phenotypes.

• Overexpression: Studying gain-of-function effects.

• Site-Directed Mutagenesis: Dissecting protein domains at the amino acid level.

Learning Outcomes

Upon completion of these online modules, students will be able to:

1. Analyze the fundamental differences in gene expression between the three domains of life.

2. Predict the regulatory response of a microbe to specific environmental stimuli.

3. Design a complete molecular cloning strategy to investigate unknown gene functions.

4. Critique transcriptomic data and select appropriate methodologies for microbial research.

Microbes in Focus BIP Online Preparatory Phase

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