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Frontiers in Microbial systems

Biology Master, ENS
Year : M2
Semester : S1
Course code : BIO-M2-E18-S1
ECTS : 3

Coordinators : Olivier Espéli, Alice Lebreton, Lionel Navarro, & Guy Tran Van Nhieu.

Aims – Introduction to microbial systems and their diversity

The development of diverse and recent approaches (genome wide studies, single cell imaging, biophysics, modelling) has revealed key aspects of microbial biology and ecology, which will be illustrated throughout this course.

Themes 2018

This theme will focus on the functional complexity of microbial communities known as microbiomes, their structure, dynamics, and consequences on host physiology or environmental ecosystems. Relationship between the animal or plant microbiota and health will be drawn. Lectures will also emphasize how the thorough and functional analysis of microbial -–Omics (genomics, but also metagenomics, transcriptomics, proteomics, etc.) contribute to a better understanding of bacterial diversity and interactions.

Environmental microbes & phages

This theme will explore the interplay between bacteria and their viral predators, phages. Mechanisms of phage predation will be covered, alongside their use in infection diagnostic, treatment, or as genetic tools. Lectures will also discuss the role of phages in gene transfer mechanisms, with consequences on antibiotic resistance or transfer of virulence genes among bacterial populations.
Parts of the topics covered in this session will be shared with the microbiome session, the bacterial-phage ecosystem being considered as a whole in each environmental niche.

Regulating RNA & with RNA in bacteria

This theme will introduce mechanisms controlling bacterial gene expression, thus defining the ability of microbes to adapt to their niche and respond to environmental cues. The critical role played by RNA-mediated regulation of gene expression will be emphasized. Lectures will highlight the contribution of molecular biology, genetics and genomics to the understanding of complex regulatory networks .

Infectious bacteria

This theme will illustrate how pathogenic bacteria interact with their host during infection, thus leading to a perturbation of cell or tissue functions and causing disease. Processes involved in bacterial adherence, injection of effectors, invasion of host cells, intracellular trafficking and spread of bacteria will be covered, as well as strategies of bacterial persistence in response to host defences or treatments. The most recent approaches allowing high-resolution analysis of gene expression manipulation by pathogens will be highlighted.


Basic knowledge in molecular and cellular biology (gene regulation, organization of prokaryotic and eukaryotic cells, signalling, etc.).


This one-week course takes place during the first semester, in October. It is divided in four days of lectures and one day of article presentations and lab visits. Lectures are given in English. Slides in .pdf format of each lecture are provided on Intranet.


Groups of two or three students are proposed to analyse an article related to the course contents. The article is analysed by each group after classes. On Friday, each group presents their article, which is followed by questions from the audience ; another of the groups is acting as opponents. Evaluation is performed on the basis of the oral presentation, quality of article analysis, answers to specific questions, and on the student’s active participation (questions during lectures and presentations).

Keywords : Bacteria, modelling, bacterial networks and communities, microbiota, adjustment to environmental cues, infection, host-pathogen interactions, virulence, metagenomics, phages, RNA-mediated regulation, immunity.
Contact :
PNG - 1.6 ko