Building the Future of Fermentation Modeling: From Microbial Metabolism to Digital Twins

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INRAE presentation

The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.

Work environment, missions and activities

About INRAE-LBE

The Laboratory of Environmental Biotechnology (LBE) at INRAE is a world-leading research institute dedicated to innovative environmental technologies. We focus on developing sustainable solutions to address pressing global environmental challenges. Our interdisciplinary team of scientists and engineers works collaboratively to advance the field of environmental biotechnology, with a particular emphasis on resource recovery, wastewater treatment, and bioenergy production. More information is available at: https://narbonne.montpellier.hub.inrae.fr/

You will also join an exceptional research environment and collaborate in a project with experts from six additional INRAE research units:

• IATE in Montpellier (https://iate-montpellier.fr/)
• Pech Rouge in Gruissan (https://pechrouge.montpellier.hub.inrae.fr/)
• SayFood in Palaiseau (https://eng-umr-sayfood.versailles-saclay.hub.inrae.fr/)
• SPO in Montpellier (https://spo.montpellier.hub.inrae.fr/)
• STLO in Rennes (https://eng-stlo.rennes.hub.inrae.fr/)
• TBI in Toulouse (https://www.toulouse-biotechnology-institute.fr/en/)

Job description and scientific context

How can we predict and optimize any fermentation process – from cheese and wine production to hydrogen generation, biorefineries, and next-generation industrial biotechnology?

A consortium of seven leading INRAE laboratories is launching ModelFerm, an ambitious project to develop the first generic mathematical model of fermentation processes. Inspired by landmark models such as the IWA-ADM1 for anaerobic digestion, ModelFerm aims to become a scientific and industrial reference framework for understanding, simulating, and controlling microbial fermentations.

We are seeking an outstanding and highly motivated Postdoctoral Researcher to play a central role in this pioneering initiative.

The scientific challenge

Fermentation processes are used worldwide to produce foods, beverages, bio-based chemicals, fuels, and biomaterials. Despite their diversity, they share common metabolic mechanisms, thermodynamic constraints, and microbial interactions. The successful candidate will contribute to the development of a novel modeling framework integrating metabolic and biochemical pathways, mass balances and reactor dynamics, thermodynamic constraints, microbial ecology together with data science and hybrid AI approaches. The ultimate goal is to create an open, extensible platform capable of simulating a wide range of fermentation systems and supporting future developments in biotechnology and sustainable bioeconomy.

Specific tasks 

Your main missions will include:

• Visiting the different laboratories involved in ModelFerm and discussing with scientists from other disciplines, particularly in the field of fermentation (to validate certain hypotheses of the model and develop a common vocabulary)
• Harmonizing datasets from multiple fermentation applications 
• Developing mechanistic and thermodynamics-based models 
• Integrating heterogeneous biological and process data 
• Calibrating and validating models using experimental datasets 
• Exploring hybrid modeling approaches combining mechanistic knowledge and AI 
• Publishing in leading international journals 
• Contributing to open-source software and scientific dissemination  

 

Training and skills

• Strong candidates will have experience in several of the following: dynamic modeling and simulation, mass balances and process engineering, microbial systems, data analysis and statistics, Python, Matlab, R, Julia, or similar scientific programming languages, machine learning and AI.
• Attributes: self-motivated, able to work both independently and as part of a team, and enjoys supervising students.
• Language: fluent use of English; knowledge of French is an advantage but not required.
• Motivation: We are particularly looking for candidates who enjoy working across disciplines and collaborating within large research networks. The candidate should aim for scientific output in top conferences and high impact scientific journals.

INRAE's life quality

• Cutting-edge research environment: work in a state-of-the-art laboratory equipped with the latest technologies in environmental biotechnology. The equipment is fully shared, so you will have access to all the facilities.
• Mentorship and training: receive guidance from leading experts in the field and access to a comprehensive training program.
• Collaborative network: engage with a dynamic team of researchers and industry partners, both nationally and internationally.
• Funding and resources: competitive stipend and funding for research-related expenses, including conference travel and publications.
• Career development: opportunities for professional development, including workshops, seminars, and networking events.
• Work atmosphere: You will be part of a team that takes their work very seriously. We pride ourselves on fostering a collaborative and supportive atmosphere where researchers and interns work together in a dynamic and friendly environment to drive innovative solutions for environmental sustainability.
• Great working conditions: 30 days of holidays per year (+ 15 days if time recovery is affected); support for parenting; access to inexpensive collective restaurants; flexible schedule; access to on-site sports facilities; sunny weather.

How to apply

I send my CV and my motivation letter