Assessing Microbial Ecology and Food Safety Risks in Thaï Fermented Foods / Ecologie microbienne et risques sanitaires dans des aliments fermentés thaïlandais

Scientific context

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.

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.

Main steps of the PhD. 

This project will be divided into the following tasks :

Task 1. Collecting locally fermented Loog Pang products on markets in Thailand during a research mobility with our International partner at BIOTEC in Thailand. One fermentation will also be monitored (during a second mobility) at different stages to study the microbial communities by combining classical cultivation methods with genomic tools (metabarcoding), to not only provide an ecological view of the fungal and bacterial communities, but also to better understand the potential food safety issues. Overall, this work will provide a better understanding of microbial community diversity and dynamics in this food product and determine the main factors that influence the process, if available (i.e. storage conditions, temperature changes, pH, humidity or water activity…). This task will also involve isolating and preserving fungi from the collected samples as well as sampling the product for downstream analyses (Task 2 or 3).

Task 2. Different Loog Pang samples will be first characterized using various techniques (LC, LC-MS, GC-MS) to investigate the biochemical changes (sugars, organic acids, amino-acids, fatty acids, volatile compounds) occurring during fermentation. LC-MS will also be used to identify potent bioactive compounds (including mycotoxins). , Then, the functional roles of the main fungal drivers for fermentation will be determined. This work will also include aspects on fungal development and secondary metabolite production, especially mycotoxins, to take into account food safety risks in this fermented product.

Task 3. Based on the generated data, co-occurrence networks will be used to pinpoint the main microbial interactions and functions, and to guide the design of a tailor-made consortia for improved fermentation and potential product innovation.

Task 4. Based on project progress, pilot scale fermentations (most likely at BIOTEC in Thailand) will be carried out using solid state fermentations with the newly designed consortium to improve overall product quality and safety. If relevant, trials will also be performed to test this consortium for food innovation.

Le LUBEM est le Laboratoire Universitaire de Biodiversité et d’Ecologie Microbienne, UR 3882 /USC INRAE 1504.

Le LUBEM est un laboratoire de recherche de l’Université de Bretagne Occidentale spécialisé dans l’étude de la biodiversité et de l’écologie des micro-organismes, et ce principalement en agro-alimentaire et en environnement.

Le LUBEM est une UR reconnue par le MESRI au titre du contrat quinquennal 2021-2027, et sa stratégie et son projet à 5 ans ont été jugés Excellents par l'HCERES en 2021. Le LUBEM est également Unité Sous Contrat INRAE (USC 1504) depuis le 1/1/2022.
Il regroupe les activités de recherche en microbiologie de l’UBO (Université de Brest) rattachées à l’Ecole Doctorale EGAAL (ED 600) « Écologie, Géosciences, Agronomie, ALimentation ».
Le laboratoire est associé à l'ADRIA Développement (Quimper) au sein de l’UMT TRANSISPORE ACTIA (2024-2028) portant sur la prise en compte des micro-organismes sporulés (bactériens et fongiques), pour garantir la sécurité et la qualité des aliments dans le contexte actuel caractérisé par de multiples transitions (climatique, énergétique, alimentaire…) et est membre de l'Institut Brestois Santé- Agro- Matière (IBSAM).

Le LUBEM est une composante de l'Institut Carnot AgriFood Transition et est laboratoire d'appui de la collection de cultures de l'UBO (UBOCC).

Le LUBEM regroupe des membres de différentes composantes d’enseignement :

Bretagne INP-ESIAB (Ecole Supérieure d’Ingénieurs en Agro-alimentaire de Bretagne atlantique)
IUT de Brest
IUT de Quimper
UFR Sciences et Techniques

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.