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Adaptation and resilience of cyathotomin communities in face of environmental perturbations
Deadline for applications
Date of publication


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

1770 euros brut/month


Name of unit of assignment
UMR1282 ISP Infectiologie et Santé Publique
Address of unit of assignment
Region of assignment
Central France-Loire Valley


Working environment

Context : 

Grazing horses are infected by a wide variety of gastro-intestinal strongyles, encompassing large strongyles (Strongylus vulgaris) or small strongyles (cyathostomins).S. vulgarisis the most pathogenic species and a frequent cause of colic but has been maintained under low prevalence thanks to anthelmintics. On the contrary, cyathostomin can infect up to 100% of horses and are responsible for growth retardation, weight loss, and a so-called larval cyathostominosis due to the emergence “en-masse” of encysted larvae from the colic mucosa where they reside. Without treatment such condition can lead to the death of infected horses in at least 30% of cases. Parasite control is therefore required but prevalence of anthelmintic-resistant populations threatens the sustainability of this approach. A recent survey in French farms and riding-schools demonstrated the generalized failure of fenbendazole but the high efficacy of ivermectin treatment. Pyrantel had an in-between status with lowering efficacy being reported. Three different strategies can be proposed to maintain the sustainability of anthelmintics in horses.

First, it is of primary importance to understand the genetic architecture underpinning pyrantel resistance in worm populations, to monitor and foresee drug resistance emergence. This requires the building of genomic resources for most prevalent and most abundant cyathostomin species.

Second, a better understanding of the interactions between digestive microbia and nematode community (10 to 20 species within a single horse) is required for both diagnostic purpose and the identification of putative bacterial compounds with anthelmintic activity.


Project outline : 

The student will first lead a meta-analysis study about the resilience of cyathostomin communities.

Following this initial work, he/she will be in charge of characterizing community evolution in face of environmental perturbations using a metabarcoding approach. A first objective will be dedicated to the study of community interactions between gut microbiota (16S metagenomic) and cyathostomins with or without perturbations by an anthelmintic treatment. Second, drug-resistant and drug-susceptible communities will be compared to identify the species associated with lower drug efficacy.

Last, the genetic architecture of pyrantel resistance will be mined by comparing drug-resistant and drug-susceptible isolates from Normandy. This work will be run in parallel to the building of three reference genomes for three major species, namelyCylicocyclus nassatus, Cylicostephanus longibursatus et Cyathostomuum catinatum.

Training and skills required

Essential skills :

  • • Msc in quantitative genetics, population genetics, biostatistics or bioinformatics
  • • Proficiency in shell, python/perl under a unix environment
  • • Fluent spoken and written English


Ideal skills :

  • • Education in agronomical/veterinary sciences or ecology;
  • • Previous wet lab experience (helminthology diagnostics, molecular biology)
  • • Proven experience of problem solving
  • • Ability to work independently, under a fast-pace environment and to deliver results to various stakeholders


Please include a covering letter and CV with your application, along with one reference letter sent to Guillaume.Salle@inra.frandNuria.Mach@inra.fr.


Guillaume Sallé / Núria Mach
Guillaume.Salle@inra.fr ; Nuria.Mach@inra.fr