Mots-Clés
metabolic modelling
systems biology
microbiome
computational biology
ODE
Description
Project description
Ruminants play a significant role in human nutrition and food security. Ruminants can harvest
nutrients from forage diets rich in fibres and transform them into human-edible products with high-quality proteins.
Feed transformation occurs mainly in the rumen through a metabolic cascade of hydrolytic and fermentative reactions
carried out by a complex microbial community (rumen microbiota) constituted by hundreds of species that include
bacteria, archaea and eukaryotes. During rumen fermentation, methane (CH4) is produced and eructed by the animal.
This CH4 contributes to 44% of greenhouse gas emissions from the livestock sector.
The postdoc project aims at developing metabolic models of rumen microbiota with capabilities for designing
microbial strategies for reducing methane emissions and improving rumen fermentation. It will contribute to fill the
existing gap on how to integrate microbial genomic information into rumen fermentation models [1].
The postdoc fellow will be part of the project H2Rumen funded by the French National Agency for Research (ANR).
The specific objectives are
(i) To obtain metabolic models of the species constituting a rumen microbial mini-consortium.
(ii) To derive a bag-of-genome model of a complex rumen consortium.
(iii) To develop a community-scale kinetic models of mini and complex consortia accounting for H2 transactions and thermodynamic control.
The postdoc fellow will collaborate with Clémence Frioux, Simon Labarthe and David James Sherman from the PLEIADE
team (Inria, INRAE, Bordeaux) and with Rafael Muñoz-Tamayo from the MoSAR team (INRAE, AgroParisTech,
Université Paris-Saclay). The work is organized in two parts. 18 months in PLEIADE to work on the objectives (i,ii) and
14 months at MoSAR to work on the objective (iii).
Genome-scale network reconstructions will be done with state-of-the-art methods and pipelines developed in
PLEIADE. Metabolic capabilities of rumen microbial communities will be explored using Metage2Metabo [2]. Kinetic
models will be built on the basis of existing models developed at MoSAR [3,4]. Models will be constructed using
experimental data produced by our partners at UMRH and MoSAR.
Background and skills required
- PhD in applied mathematics or computational biology or process engineering.
- Experience in metabolic modelling with willingness to learn dynamic modellingor viceversa. Expertise in
dedicated software: Python, R or Scilab/Matlab.
- Experience on modelling the metabolism of microbial ecosystems and/or systems biology is a plus.
- Excellent communications skills, willing to discuss with scientists with different backgrounds.
Contract information
Location: Bordeaux (18 months contract with Inria), Palaiseau (14 months contract with INRAE), France
Start date: October 1st 2025/position immediately available
Job conditions
Gross monthly salary ranging from 2,788€ to 3,405€, depending on profile and previous experience.
Benefits
- Subsidized meals
- Partial reimbursement of public transport costs
- Leave: 7 weeks of annual leave + 10 extra days off due to RTT (statutory reduction in working hours) + possibility of exceptional leave (sick children, moving home, etc.)
- Possibility of teleworking and flexible organization of working hours
- Professional equipment available (videoconferencing, loan of computer equipment, etc.)
- Social, cultural and sports events and activities
- Access to vocational training
- Social security coverage
Application
Candidates should apply online https://recrutement.inria.fr/public/classic/en/offres/2025-08790
More details about the offer.