Integrative analysis of gut multi-omics in European sea bass (Dicentrarchus labrax) under thermal variation

Host Environment The student will be hosted at the Ifremer experimental station in Palavas-lesFlots, integrated within the MARBEC research unit. The station gathers ~40 researchers, engineers, and students, with a strong expertise in aquaculture genomics, physiology, microbial ecology, and omics data analysis.

Project: Gut multi-omics: Host genetic, Epigenetic, and Microbiota responses to thermal variation in two genetically distinct European sea bass populations (supported by ANR FishNess and CRECHE projects).

Duration: 6 months (paid by Ifremer); Start: January/February 2026

Host laboratory: Ifremer centre Méditerranée laboratory « LAAAS », as part of MARBEC (UMR 9190, CNRS–Ifremer–IRD–Université de Montpellier), Palavas-les-Flots, France.

Supervision: Post-doc: Núria Sánchez-Baizán  – PI: François Allal 

Context This master project aims to investigate how gut microbiota, host epigenetics (DNA methylation), and transcriptomics interact to shape thermal responses in European sea bass. The species presents two genetically differentiated lineages—Atlantic (AT) and Eastern Mediterranean (EM)—with contrasting thermal regimes and phenotypic traits. Understanding how these populations respond to temperature through the holobiont (host + microbiota) is essential for predicting climate-driven impacts on wild populations and supporting sustainable aquaculture. The biological samples were collected during the ANR FishNess project, which reared AT and EM sea bass under two simulated thermal regimes (Atlantic vs. Mediterranean). Gut mucosa, gut contents, DNA/RNA, and phenotypic data (growth, metabolic traits, intestinal physiology) are already available for analysis. This master project will contribute to the processing of samples and production of multi-omic data and analysis that will be essential parts of the GELbass project.

Objectives 1. Process samples (DNA extractions) ready to library preparation for the characterization of the gut microbiota (16S and 18S metabarcoding) across population × temperature groups. 2. Process gut content samples for metabolite analysis. 3. Assist in the DNA extractions for DNA and RNA analysis for gut transcriptomic and DNA methylation data analysis. 2/2 4. Perform the statistical analysis of metabolites and transcriptome data that will later be combined.

Available Material All samples required for the project already exist. The student will work with 40 gut mucosa and gut content samples from AT and EM populations reared under two thermal regimes; Metabolite data; Gut RNA-seq; Phenotypic data. All of them, generated from the same 40 individuals. The student will also have the opportunity to participate in ongoing sampling or lab work within MARBEC depending on timing and interest. 

Level: M2 student

Skills Required • Good level of English • Background in animal biology, marine biology, genomics, aquaculture or related fields • Basic skills in statistics and R programming • Experience with bioinformatics or omics analysis is a strong advantage, but training will be provided