Thèse Étude de l'Écologie Microbienne et des Risques Sanitaires dans des Aliments Fermentés Thaïlandais H/F Doctorat.Gouv.Fr

Établissement : Université de Bretagne Occidentale École doctorale : École doctorale Écologie, Géosciences, Agronomie et Alimentation Laboratoire de recherche : Laboratoire universitaire de biodiversité et écologie microbienne Direction de la thèse : Monika COTON Date limite de candidature : 2026-11-06T00:00:00

Contexte socio-économique et scientifique
Ecology and food safety of relevant Thaï fermented foods in link with current food transitions and innovations
Food fermentations have been used for centuries, representing a highly diversified category of food products shaped by the metabolically active microbial communities that intervene during fermentation and impact overall product quality. While many types of fermented food have been well studied, such as wine, cheeses and dry cured meats, others remain largely under-explored. These include locally produced, traditional or ethnic foods like Loog Pang or Koji in Thailand. For such products, microbial diversity and succession, particularly the fungal community which is a key element for raw material transformation, is rarely mapped as well as the functional roles of the key microbial drivers. A deeper understanding of microbial diversity and its functional interactions can directly help enhance product quality, safety and sustainability. In time, improved microbial solutions can then be designed for better fermentation control, especially in the current context in which fermentations can be impacted by multiple factors like climate change and food transitions, with shifts in raw material accessibility or quality and evolving temperature constraints. Beyond the quality aspects, safety issues can also exist such as mycotoxinogenic species which can be present in these matrices.
This project will be included in the international MYCOBIOMICS 2.0 project (13 partner institutions from 11 countries) and the PhD candidate will be required to go for at least one research mobility period to the BIOTEC research institute in Thailand.

The PhD candidate requirements:
Master's Degree or equivalent Degree in microbiology, molecular biology, and have experience in data analyses related to their specialty (culture-dependent and -independent approaches, PCR, metagenetics, statistics...)
Good lab experience with the ability to work autonomously and learn new techniques
Well-organized, rigorous and a good team player, the candidate will be required to work with a team and do regular progress reports
Be capable of adapting and simplifying a scientific discussion according to the context
Good communication and written skills (protocols, reports, synthesis...), good experience with Office Pack and statistical analyses
Fluency in English (both spoken and written), interest in working abroad as part of the PhD work will be carried out at BIOTEC in Thailand, and be able to present their research in International conferences
An interest in fermentation and food biotechnology as well as experience in biochemistry is an asset.

Hypotheses and scientific questions
In the current context of food transitions and innovations, a better understanding of the food microbiota and their functional properties, especially in plant-based products, is relevant. This is particularly true for the fermentation of locally produced ethnic products like Loog pang (produced in Thailand), for which food safety risks such as mycotoxins may also exist.
In this framework, culture-dependent and -independent approaches (-omics techniques) will be used to decipher microbial diversity and dynamics during loog pang fermentations, with a special focus on fungal diversity. Additional techniques will be implemented to determine the functional roles of the main fungal drivers for fermentation including gas chromatography-mass spectrometry (GC-MS) for volatile compounds and liquid chromatography-mass spectrometry (LC-MS) for bioactive molecules, including potential mycotoxins. In parallel, co-occurrence networks will also be used to better understand microbial interactions and functions, to guide the design of a tailor-made consortia for improved fermentation or product innovation.