Understanding Host-Microbiota Assembly Through a Multi-Omics Data Integration Strategy

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INRAE presentation

The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.

Work environment, missions and activities

You will be welcomed in the MuSe group within the GenPhySE research unit or the BioComp group within the MIAT research unit (Occitanie - Toulouse INRAE research center). The MuSe team focuses on studying interactions between the microbiota and its host to promote digestive health. The BioComp group develops statistical and computational methods to provide insights into the complexity of living systems, from the molecular scale to phenotypic traits

Animals and their associated microbiota form a composite organism known as a holobiont. In particular, the gut microbiota plays a central role in nutrient transformation, the production of metabolites of interest, and resistance to pathogens. In the context of agroecological transition, selecting robust livestock animals adapted to diverse production systems represents a major challenge. An integrative holobiont-scale approach combining host and microbiome genetics appears especially promising. Understanding the mechanisms by which the host selects and shapes its microbiota, as well as the functional interactions between symbiotic partners, could provide valuable leverage for improving animal breeding and optimizing performance and resilience.

Within this framework, a dataset has been generated from two pig lines selected for differences in gut microbiota composition (DOI: 10.1186/s40168-024-01827-8) and raised under contrasting environmental conditions (conventional versus organic farming systems). The dataset includes multi-omics information characterizing both the host and its gut microbiota, including metagenomics, metabolomics, transcriptomics, and phenotypic data

You will be specifically involved in the integrative analysis of these datasets to decipher host-microbiota assembly mechanisms, including:

• Analyzing the impact of host genetics and environmental factors on the microbiota, metabolome, and host transcriptome, and providing functional interpretation of the results.
• Developing a model to infer associations between the microbiota, metabolomic profiles, and transcriptomic data (potentially extending to predictive modeling if supported by the data).
• Optionally, analyzing single-cell transcriptomics data to investigate the effects of genetics and environmental conditions on intestinal epithelial cell function …

possibility of remote work up to 2 or 3 days per week.

Training and skills

Knowledge required: Ideally, a degree in statistics with doctoral research experience related to biology. Applications from candidates holding a PhD in biology or bioinformatics with strong experience in data analysis will also be considered.

Appreciated experience: Exploratory statistics, preferably with experience in multimodal/multi-omics data integration; biostatistics; strong proficiency in R programming; experience in the analysis of transcriptomics and/or metagenomics data.

Skills sought: Good knowledge of version control systems (particularly Git) and best practices for reproducible research would be an advantage. Experience with single-cell data analysis would also be beneficial.

INRAE's life quality

By joining our teams, you benefit from (depending on the type of contract and its duration):

- up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- holiday and leisure services: holiday vouchers, accommodation at preferential rates;
- sports and cultural activities;
- collective catering.

How to apply

I send my CV and my motivation letter