Effect of growth conditions on the development of Faecalibacterium duncaniae

PAM (Food and Wine Science & Technology Laboratory) focuses on understanding the physical, chemical, and biological processes that influence the quality of food and wine, with the goal of developing innovative food products and processes. One of the main subjects is the study of ferments and food microbial flora (microbiomes - metabolomes) and control their production.

UTINAM (Functionalized Materials and Surfaces), the team's expertise in monomer synthesis and electrochemical polymerization enables the design of new sensors for the detection of molecules or microorganisms in water or air. Our main achievements are ammoniac sensors, COV sensors, pH sensors, glyphosate sensor, immunosensors, enzymatic sensors (urea, creatinine).

Project Context

The study of fermentations in complex environments, such as solid-state fermentation or anaerobic conditions, is gaining increasing interest for the production of biomass, molecules of interest, or fermented foods. However, the difficulty in controlling these types of fermentations hinders progress in understanding of the bacteria and their large-scale production.

The production of extremely oxygen sensitive (EOS) bacteria has awaken interest of researchers and industrials since several strains are currently being explored as next-generation probiotics (NGPs). F. duncaniae is a commensal bacterium which has shown promising results in murine models against inflammation, colitis, diabetes and obesity (De Filippis et al., 2022; Miquel et al., 2013). These effects seem to be partially related to the production of butyrate (Miquel et al., 2013). However, cultivating Faecalibacterium spp. is still challenging due to its extreme oxygen sensitivity and complex growth media (Andrade et al., 2020).

The production of Faecalibacterium has been a major challenge over the last decade. The achievements of the studies open some questions about how to mimic the natural environment of Faecalibacterium spp. in the gastrointestinal track, in terms of composition, and physical characteristics such as turbidity, viscosity, or agitation. In the gastrointestinal track, Faecalibacterium spp. grows in a anaerobic semi-solid media.

In this environment turbidimetric or optical probes, which are usually used in the assessment of bacterial growth in laboratories and industries, would not permit biomass determination. Furthermore, the anaerobic conditions result in very low redox levels, what may reduce sensor sensitivity or cause inaccurate readings. The presence of secondary metabolites produced during fermentation is normally determined by analytical methods such as gas chromatography and HPLC. These methods are expensive and time-consuming. That is why, it seems necessary to develop new sensors adapted to these conditions, such as conductimetric methods (Ben Halima et al, 2024).

Objective

As part of the project HARMI Starters MICMET, the objectif of this internship is double:

1. Determine the effect growth media characteristics (composition, viscosity, turbidity, agitation) on the production of Faecalibacterium duncaniae biomass and secondary metabolites

2. Analyse the potential of real-time conductimetric sensors in assessing production of Faecalibacterium duncaniae biomass and secondary metabolites

Internship:

6-month internship starting in January/February 2026. The laboratory work will be at PMB laboratories (UMR PAM) Dijon.

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