PhD Researcher rainbow trout

Job Details

Characterization of novel post-translational modifications of histones that link, via the microbiota, the impact of the nutritional environment to phenotypes expressed in rainbow trout: paving the way

You will carry out your work within the INRAE NuMeA/UPPA laboratory (Nutrition, Metabolism, Aquaculture). Research activities are conducted in a context of limited marine resources and rapid global development of aquaculture. They aim to understand how nutrients regulate metabolic pathways in fish, using an integrative approach (from genes to the whole organism). The ultimate goal is to provide recommendations for innovative strategies in aquaculture feeds in order to optimize growth and feed efficiency while ensuring sustainability.

One of NuMeA’s objectives is to develop “new feeding strategies” to overcome the barriers that limit the replacement of fish meal and fish oil in aquaculture feeds. To address these issues, the scientific objectives are to study the dynamics of microbiota establishment and its epigenetic consequences on the intestine of rainbow trout fed a high-carbohydrate diet. The PhD project is part of this research theme.

Scientific missions and activities:

Context:
Any nutritional transition in vertebrates (diet diversification in young mammals, replacement of fish meal and fish oil in aquaculture, etc.) is accompanied by profound remodeling of the phenotype, initiated by rapid changes in the metabolic activity of the intestinal microbiota, itself dependent on diet. These changes have a cascading effect on host metabolism. A growing number of studies show that epigenetic regulations play a major role in the functional dialogue between diet, intestinal microbiota, and host metabolism (the intestinal holobiont), particularly through mechanisms dependent on metabolites produced by the microbiota.

To improve the sustainability of aquaculture while maintaining its performance, it is necessary to optimize nutrition by replacing fish meal and fish oil with more sustainable ingredients in salmonid feeds, such as digestible carbohydrates. However, these substitutions are still associated with metabolic disturbances that impair zootechnical performance, highlighting the importance of exploring new approaches such as epigenetics and the intestinal microbiota.

In trout fed a high-carbohydrate (HC) diet, the digesta-associated microbiota is enriched in Lactobacillus, which are capable of metabolizing glucose into lactate. The intestinal mucus, on the other hand, is enriched in Mycoplasma, non-pathogenic bacteria in salmonids associated with good digestive health, possessing an active lactate CoA-transferase that converts lactate into lactyl-CoA.

As part of a collaboration with Dr. Dhaenens (Ghent University), we observed—using LC-MS targeting histone post-translational modifications (PTMs) after 10 days of feeding with an HC diet—a marked increase in certain PTMs, such as lactylations or methylations, particularly on histone H3 in HC trout compared to trout fed a no-carbohydrate (NC) diet. Some of these modifications have never been described before, highlighting the originality of our results. However, the liquid chromatography (LC-MS) technique used here provides a global analysis at the whole-tissue level, whereas the intestine is highly heterogeneous in terms of cell types and metabolism. These results, based on probabilistic bioinformatics approaches, must therefore be confirmed by targeted techniques (e.g., western blot) and by a spatial description of their distribution in order to better understand their function.

The objective of this PhD project is therefore to confirm the enrichment of these PTMs identified by LC-MS, to specify their tissue distribution and their dynamics of establishment in the trout intestine—key steps for understanding their role. This first part of the thesis will allow the candidate to implement laboratory techniques across various areas of expertise, such as western blotting or in situ immunofluorescence.

The second objective of the thesis will be to establish a functional link between the presence of specific bacteria in the intestinal microbiota and the observed epigenetic modifications. In this context, the candidate will isolate and culture bacterial strains from the intestinal microbiota of trout and subsequently sequence their genomes. These strains will then be brought into contact with trout intestinal explants and cell lines. The epigenetic modifications previously identified will be monitored by western blot on these explants/cells to determine whether they are specifically induced by the isolated bacteria.

Requirements

Training and skills sought

Recommended education:
Master’s degree in biology, molecular biology, microbiology, or agronomy.

Desired knowledge:
Strong skills in molecular biology are required. Theoretical and/or practical knowledge in epigenetics, microbiota, and high-throughput techniques would be appreciated but are not mandatory.

Valued experience:
Knowledge in fish biology and nutrition would be an advantage but is not required.

Required skills:
Strong communication abilities, a good command of English, and autonomy are required. The candidate will also be involved in laboratory maintenance and sampling activities.

Specific Requirements

Specific working conditions:
Travel within France and abroad is expected, sometimes for periods of several week

Contact Information

Please send a cover letter, a CV, and the contact details of two referees in a single PDF file.

By email:lucie.marandel@inrae.fr and karine.brugirardricaud@univ-pau.fr

Application deadline: June 15, 2026
If you have not received a response from us by June 30, 2026, please consider that your application has not been successful.