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 ↩

cFMD workshop in Trento

Last February 23-24th 2026, at University of Trento, a workshop was organized by the CIBIO (Nicola Segata’s lab) for #DominoEU partners. The workshop aimed at learning to query & analyse data from the Curated Food Microbiome Database (cFMD). Thanks to the very efficient and skilled teaching team (vitor Heidrich, Hrituraj Dey, Francesco aniscar, Sergio Andrés Castañeda Garzon) and for the incredible hospitality of Frederica Pinto and Nicola Segata.

From food spontaneous fermentations to food designed consortia

Our new article entitled “Microbiome metabolic modeling as a tool for innovation in fermented foods” has been published in in Current Opinion of Food Science¹.

Elham Karimi, Julien Tap, Marie-Christine Champomier-Vergès, Stéphane Chaillou. Microbiome metabolic modeling as a tool for innovation in fermented foods. Current Opinion of Food Science. 2025 ↩

The FME lab communicates about the links between the microbiome, nutrition and health.

On Thursday 27 November, the FME lab took part in the Food System Microbiomes Conference in Wageningen during the session dedicated to the connections between microbiomes, nutrition and health. The session was co-chaired by Stéphane Chaillou (INRAE, Micalis) and Prof. Christophe Courtin (KU Leuven), and provided an opportunity to showcase advances from two major European projects: DOMINO and HealthFerm.