Postdoc fellowship - Metabolic modelling of the rumen microbiome

euraxess.ec.europa.eu - Jobboard; France; Sur place; EUR 20 000 - 40 000; Plein temps

Résumé du poste

Une institution de recherche réputée recherche un chercheur postdoctoral pour travailler sur un projet innovant axé sur la modélisation métabolique du microbiote du rumen, visant à réduire les émissions de méthane. Le candidat idéal aura un doctorat en mathématiques appliquées ou en biologie computationnelle, avec expérience ou intérêt pour la modélisation dynamique, et travaillera dans une équipe interdisciplinaire à Bordeaux et Palaiseau.

Prestations

Remboursement partiel des frais de transport public

7 semaines de congés annuels

Possibilité de télétravail

Équipement professionnel disponible

Formation professionnelle accessible

Couverture de sécurité sociale

Qualifications

• PhD requis dans le domaine pertinent.
• Expérience en modélisation métabolique souhaitée.
• Compétences en communication excellentes.

Responsabilités

• Développer des modèles métaboliques du microbiote du rumen.
• Collaborer avec d'autres chercheurs sur les objectifs du projet.
• Utiliser des méthodes de pointe pour l'analyse des données.

Connaissances

Modélisation métabolique

Python

R

Scilab/Matlab

Communication

Formation

PhD en mathématiques appliquées ou biologie computationnelle

Description du poste

Organisation/Company Inria Research Field Computer science Researcher Profile Recognised Researcher (R2) Country France Application Deadline 30 Sep 2025 - 23:00 (UTC) Type of Contract To be defined Job Status Full-time Hours Per Week To be defined Is the job funded through the EU Research Framework Programme? Not funded by a EU programme Is the Job related to staff position within a Research Infrastructure? No

Offer Description

Ruminants play a significant role in human nutrition and food security. Ruminants can harvestnutrients 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 reactionscarried out by a complex microbial community (rumen microbiota) constituted by hundreds of species that includebacteria, archaea and eukaryotes. During rumen fermentation, methane (CH 4 ) is produced and eructed by the animal.This CH 4 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 designingmicrobial strategies for reducing methane emissions and improving rumen fermentation. It will contribute to fill theexisting 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 PLEIADEteam (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) and14 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 inPLEIADE. Metabolic capabilities of rumen microbial communities will be explored using Metage2Metabo [2]. Kineticmodels 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 .

References

1. Muñoz-Tamayo R, Davoudkhani M, Fakih I, Robles-Rodriguez CE, Rubino F, Creevey CJ, et al. Review: Towards the next-generation models of the rumen microbiome for enhancing predictive power and guiding sustainable production strategies. animal. 2023;17: 100984. doi:10.1016/J.ANIMAL.2023.100984

2. Belcour A, Frioux C, Aite M, Bretaudeau A, Hildebrand F, Siegel A. Metage2metabo, microbiota-scale metaboliccomplementarity for the identification of key species. Elife. 2020;9: e61968. doi:10.7554/eLife.619683.

3. Muñoz-Tamayo R, Chagas JC, Ramin M, Krizsan SJ. Modelling the impact of the macroalgae Asparagopsis taxiformis on rumen microbial fermentation and methane production. Peer Community J. 2021;1: e7. doi:10.24072/PCJOURNAL.11

4. Fakih I, Got J, Robles-Rodriguez CE, Siegel A, Forano E, Muñoz-Tamayo R. Dynamic genome-based metabolic modeling of thepredominant cellulolytic rumen bacterium Fibrobacter succinogenes S85. mSystems. 2023;8: e01027-22.doi:10.1128/msystems.01027-22

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 indedicated 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 1s 2025/position immediately available

Salary: 2,788€ to 3,405€ gross/month based on experience

To postulate, apply with your motivation letter, CV and the name of two scientists (references) online Only online applications will be considered.

• 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

Remuneration

The gross monthly salary will be from 2788€ to 3405€ (before social security contributions and monthly witholding tax).