Impact of farming practices and diet on chicken microbiomes

Published: May 17, 2024 by FME Lab

Last week, in the frame of the 1st Food System Conference in Torino, Stéphane was pleased to show for the first time the results of the Holoflux egg-to-meat project.

In this project, a consortium of 7 INRAE laboratories collaborated for a very ambitious experimental design aiming at studying the impact of farming practices (claustration versus open field), and therefore the impact of the diet on several chicken microbiomes (Fecal, Caecal …). The project revealed how the different microbiomes are changing (or not) with the diet and how the microbiomes maturate during the longitudinal (age) study from egg-to-meat. During the rest of the conference, Stéphane received a lot of positive feedback from the participants with strong encouragements for publishing the outcome of this study.

FME at Bioket 2026 advancing synthetic microbial ecology for sustainable food

At the BIOKET (Bioeconomy Key Enabling Technologies) conference in Fribourg, Julien presented recent advances from the SynthPlex project, positioning synthetic microbial ecology as a core tool for next-generation fermented foods.

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 ↩