Quick peek at the 5th EBAME Workshop on Computational Microbial Ecogenomics

As many as 50 researchers, professors and students participated in the EBAME workshop organized by LM2E at IUEM during two weeks at the end of October.

Every year, the high level of scientific interdisciplinarity and the great international dimension is placed at the very heart of the project. This event, combining informatics and microbial ecogenomics, has firmly established itself as an essential meeting point at the tip of Brittany between experts of theses disciplines.

International participants during the EBAME workshop at IUEM.
© meren

Bioinformatics & Microbial Ecogenomics

In the human body, the genes and cells of the microbiome outnumber those of host organisms and are in constant metabolic interactions with them providing key environmental adaptations. 

Planktonic and benthic microorganisms are at the centre of cycles processing climate, the functioning of marine ecosystems and most other ecosystem services. The next generation DNA sequencing is the prefered approach in order to understand the diversity and the role of this invisible biosphere.  

However, on one hand, the volume and complexity of data generated by these approaches require ongoing development of new bioinformatic tools at the service of biologists. On the other hand, the needs of users in microbial ecogenomics is essential for the development of new better performing and adapted analysis methods. It is then critical to promote interactions between biologists and algorithms developers in order to produce and implement computer, statistical and visualization tools that are able to extract information from these massive databases. 

Workshop objectives

  • Scientific objectives

The EBAME workshop is an event gathering the best possible researchers in biology, allowing an interaction where will be defined bioinformatics analysis standards and best practices in microbial ecogenomics. The reached outcomes will then be directly applied to major projects in environmental genomics led by UBO (ANR Southern Ocean Microbiome) or IFREMER (Abyss) and supported by the national sequencing platform Genoscope.

EBAME aims at strengthening skills transfers between public research and the biotechnology and pharmaceutical industry by inviting major players from industrial groups in the field.

  • Pedagogical objectives
Hands-on computer sessions during EBAME
© meren

At the same time, it is crucial to teach theoretical foundations and the latest progress in this extremely dynamic scientific field to young researchers (master, phd and post-doc) involved in these data set analyses. Indeed, a significative part of these two weeks is dedicated to seminars but also hands-on computer sessions taught by invited speakers.

By establishing a forum for exchange between young researchers and experts, the workshop has also proved to be a successful place of recruitment. Thus, in 2018 a PhD student from UBO was recruited at the University of Chicago and five scientific job offers were released during the workshop.

EBAME, entirely conducted in English, is also a key event regarding international outreach through the high quality of participants hosted in Brest, coming from the best research centres in Europe and further afield.

Invited speakers:

•  A. Murat Eren (Meren) – Assistant Professor , Department of Medicine, University of Chicago (USA). 

 •  Antonio Fernández Guerra  – Researcher , Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology in Bremen (Germany). 

 •  Christopher Quince – Principal Research Fellow at Warwick Medical School, University of Warwick (UK). 

 •  Damien Eveillard – Associate Professor at the Department of Computer Science, Université de Nantes (France). 

 •  Jesse Sh apiro – Associate Professor of Biology at the Université de Montréal (Canada).

 •  Martial Marbouty  – CNRS researcher , « Spatial Regulation of Genomes », Institut Pasteur (Paris, France). 

 •  Julie Reveillaud  – Institut National de Recherche Agronomique , researcher (Montpellier France). 

 • Sheri Simmons – Bioinformatics Researcher, Johnson&Johnson (Cambridge, U.S.A.)

 •  Samuel Chaffron – CNRS researcher , Laboratoire des Sciences du Numérique (Nantes, France ) .

Home universities and institutes of participants: 

University of Brest, University of Rennes, University of Paris Sud, University of Copenhagen, Sorbonne University, Rutgers University, University of Surrey, University of Southampton, University of Montpellier, University of Hawaii, U.C. Berkley, University Medical Centre Groningen, Quadram Institute, University of the Basque Country, University Bremen, Alfred Wegener Institute, TU München, Marine Biological Laboratory Woods Hole, Norwegian University of Science and Technology, Max Planck Institute for Marine Microbiology, University of Concepción,  ETH Zurich, Kaust Saudi Arabia, Institute of Biomedical Sciences Abel Salazar, Wageningen University & Research Center, INRA, Dijon.

For more information on EBAME workshops, you can visit the EBAME site (https://pagesperso.univ-brest.fr/~maignien/ebame5.html) or contact Loïs Maignien: lois.maignien@univ-brest.fr