Microbial ecology lesson from re-use of open access metagenomic dataset: the case-study of fermented vegetables

Published: May 17, 2024 by FME Lab

Happy to share our last article published online last week 15th of May in Microbiology Spectrum¹.

This study being part of Romane Junker PhD (MaIAge/Micalis/CIRM-BIA laboratories). In this work, we show that the re-use of public 16S amplicon dataset can bring new understanding in the dynamic microbial ecology of fermented vegetables.

During the 1st Food System Conference in Torino last week, Romane also presented a poster pitch of the follow up of this study using new and public metagenomic shotgun data.

Junker R, Valence F, Mistou M, Chaillou S, Chiapello H.0. Integration of metataxonomic data sets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables. Microbiol Spectr0:e00312-24. ↩

Share

Latest Posts

A seed meeting between INRAE Micalis Institute and Imperial College London

Last week on October 3rd, scientists from Imperial College London (ICL) and from INRAE Micalis Institute were hosted by the French embassy in London for a seed meeting around synthetic biology and synthetic microbial ecology as scientific strategies for biotechnology and food production. A special thanks to the organizer: Ludovic Drouin (French Embassy), Young-Kyoung Park (Micalis) and Rodriguo Ledesma-Amaro (ICL). Our several groups with complementary research discussed about perspectives of future collaborations on the field together with Ferment du Futur or Bezos Centre.

School of Artificial Intelligence Applied to Microbiomes

Earlier this month, Julien had the pleasure of participating as a lecturer at the School of Artificial Intelligence Applied to Microbiomes, hosted at AgroParisTech and organized by Aristeidis Litos, Daniel Garza, and Ariane Bize. The event brought together an exceptional group of researchers and students exploring how AI, data science, and mathematical modeling are reshaping our understanding of microbial ecosystems.

Consumers at the core of fermented food innovation

Yesterday on September 23rd, about 100 participants from academia, industry, NGOs and policy makers across Europe had joined the second Stakeholder Forum of Horizon Europe #DominoEU project. Four speakers Pr. Jutta Roosen from the Technical Universty of Munich, Dr. Emmanuella Magriplis associate professor from the Agricultural University of Athens, Dr. Michail Syrpas associate professor at Kaunas University of Technology in Lithuania and Dr. Nikoletta Vidra Science Manager at Yakult Europe altogether spotlighted the central role of consumer research in advancing the field of fermented foods.