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PhD position: effects of mycotoxins exposure on the metabolism and immunity of ruminants
Deadline for applications
Date of publication


Details on the type of contract
PhD contract
Duration of contract
3 years



Name of unit of assignment
UMR1213 UMRH Unité Mixte de Recherche sur les Herbivores
Address of unit of assignment
Region of assignment
Auvergne Rhône-Alpes


Working environment

Context :

Mycotoxins are toxic metabolites that are commonly found in feeds. They have been shown to cause a wide variety of toxic responses in animals including carcinogenic, mutagenic, immunosuppressive, neurotoxic and teratogenic effects. Several studies on monogastric animals have shown that major mycotoxins have a negative effect on immunity increasing susceptibility to infectious disease and reducing vaccine efficacy. Despite their recognized effects on the immune system of monogastric animals, information on ruminants is scarce particularly in young animals.  

The aim of this PhD project will be to evaluate the effect of mycotoxins on dairy calves during the passage from milk to solid feed ingestion.  The transition from the pre- to ruminant phase is a stressful period that is accompanied by profound changes in the development of the gastrointestinal tract that might affect the susceptibility to mycotoxins.  The effect of mycotoxins will be mainly assessed on immunity parameters.  Effects on the overall metabolic status will the assessed by a metabolomic approach and the gastrointestinal microbiota will be monitored by metataxonomics.  Microbial strategies to reduce the toxic effect of mycotoxins, improve the immunological status of calves or both will be tested.


This is a CIFRE (industrial agreement on training through research) PhD program involving Lallemand SAS and INRA UMR1213 Herbivores.

The successful candidate will work at the Herbivores research Unit (http://www1.clermont.inra.fr/urh/) based in Theix, Auvergne-Rhône-Alpes Centre. Before starting animal experiment(s), she/he will do a complete literature review of known parameters involved in the immunity.  

During his/her thesis, the PhD student will supervise the animal experiment(s) planned in this project. She/he will be responsible for sample collection and preparation for analysis. She/he will have to develop the main analytical tools to assess immune status in ruminants. The successful applicant will work in close collaboration with researchers from other teams involved in the project.  To exchange with these partners some travel may be required.

The successful candidate will be engaged in analysis of samples, data processing including statistical analysis, data interpretation. He/she will publish the results.


Keywords: Immunity, transcriptomics, metabolomics, mycotoxins, ruminants

Training and skills required

Qualifications and skills



  • The successful candidatewill have an MSc or equivalent academic degree in analytical chemistry and/or biological sciences.
  • A background in animal physiology, immunity and/or biochemistry is desirable.



  • Proficiency in scientific writing in English;
  • Excellent communication and proactive attitude are expected.
  • Knowledge in statistics, including statistical analysis of large data sets (multivariate, regression)


Please send an up-to-date CV focusing on relevant experiences for this position, a  motivation letter, a list of publications, and  recommendation letter(s) from at least 2 referees  details to : Hamid Boudra (INRA, Theix), Diego Morgavi (INRA, Theix), Imourana Alassane-Kpembi and Frédérique Chaucheyras-Durand


Hamid Boudra / Diego Morgavi / Imourana Alassane-Kpembi / Frédérique Chaucheyras-Durand