Metagenomic driven isolation of poorly culturable species in food

Published: Feb 4, 2025 by FME Lab

A new article entitled “Metagenomic driven isolation of poorly culturable species in food” from Caroline and Pierre has been published in Food microbiology journal¹.

This paper presents an easy-to-implement culturing strategy, supervised by metagenomic assemblies, that Caroline Kothe (PhD student in our lab at the time) initially developed to isolate all species present in food ecosystems, including as many subdominant and poorly culturable species as possible. We give here an example of application to cheese, but we have successfully used this approach in other food ecosystems such as water kefir, traditional Brazilian, Lebanese and African products, from which a number of undefined and/or poorly cultivable species have been isolated for further study (starters, safety…). This approach has been successfully transferred to teams around us, as well as in Africa and the Middle East, and we believe it could be useful more widely.

Highlights are:

Easy-to-implement culturomic strategy supervised by metagenomic assembly.
Proof of concept applied to two cheeses, targeting specific species.
Recovery of 10 species, including two not previously reported in food.

Kothe et al. *Metagenomic driven isolation of poorly culturable species in food. Food Microbiology. 2025 ↩

Focus on Microbial Ecology Modelling at the NEM days meeting in Rennes

The French NEM (Nutrition & Microbial Ecosystems) network hold its annual meeting this last two days (5th – 6th of May) in Rennes. Julien Tap, researcher from the FME lab presented the first results of his Ferment du Future SynthPlex project and how Engineering food microbial consortia can be performed using microfermentors to reveal strain epistasis. With the Support of Holoflux and Digit-Bio INRAE Metaprogram, He also co-organized with Guillaume Gautreau from the MaIAge Unit a specific workshop on modelling of microbial ecosystems.

Lovely second annual meeting of DOMINO project in Cork, Ireland

The DOMINO project held its second annual meeting from 26 to 28 March in the picturesque city of Cork, Ireland. It was an intense and warm moment thanks to the efficient and very friendly organisation of Teagasc and its incredible team coordinated by Orla O’Sullivan and John Kenny.

Health promoting effects of Fermented Foods was the highlight at 2nd Forum on Fermented Foods in Malaga

#DominoEU researchers participated significantly to this amazing conference organised by the COST Pimento. Paul Cotter, Orla O’Sullivan, Jekaterina Kansatseva, Bastien Renard, Isabelle Savary-Auzeloux, Luca Cocolin, Kelly Rantsiou and Tanja Kostic gave talks.