Microbial ecology

Microbial ecology consists in characterizing the microbial biodiversity of an ecosystem or microbiota, in order to study the place and role of microorganisms in its habitat (environment, ecosystem) as well as the interactions of microorganisms with each other and with their environment. Secalim was able to take the measure of this issue in the characterization of microbial ecosystems in foods to better understand their functioning, first by using cultivation methods supplemented by molecular identifications and then acultural methods such as TTGE. The emergence of new sequencing techniques has enabled this discipline to evolve towards questions on the relationship between diversity and the functioning of the ecosystem (in terms of performance in the spoilage process).
Secalim's work now most often considers microorganisms within the food microbiota, and for this reason requires microbial ecology (see projects opposite). They belong to thematic 1 : Understand the bacterial behaviour, at the level of bacterial communities.

Currently, several SECALIM projects use sequencing technologies such as 16S rRNA amplicon sequencing to characterize bacterial communities in food. In the ESCAPE project, the microbiota of chicken carcasses was characterized in Label Rouge and standard chickens, with a view to subsequently identifying possible correlations with the food pathogen Campylobacter. In the MININSECT project, the metagenomic approach aims to characterize the microbiome of insects intended for human consumption in order to assess microbial risks. As part of Victoire Le Cozic's thesis, industrial products formulated using protein alternatives to meat will undergo metagenomic characterization with a view to proposing microbiological criteria that are better suited to these new food matrices. The Sen-BicPha project aims to improve the sanitary quality of traditional fermented products in Senegal, yeet and guedj, using biopreservation approaches. This project includes a phase of characterizing the microbial ecosystem of these fermented fishery products using 16S metabarcoding and classical microbiology analyses. The SOLMIC-FISH project aims to evaluate the effectiveness and impact of microbial solutions throughout the fish production chain, from fish farming to the finished product, by characterizing the microbiota at different stages: the intestinal (and possibly skin) microbiota of fish during farming, microbiota of fillets during packaging and after storage, using a metabarcoding approach based on MinION third-generation sequencing.

PhD theses supervised on this topic:

• Victoire Le Cozic's phD thesis focuses on the contamination of processed products made from alternative proteins to meat. In this context, the microbial ecology of these products will be characterized using MinION sequencing technology.
• In 2025, the phD. thesis of Sophie Hautefeuille dealt with microbial ecology and Campylobacter.
• in 2021, the microbiota of the agri-food plant environment and its impact on food quality and safety were studied in the case of smoked salmon. This PhD thesis was part of the ALTEROBIO project in partnership with Biofortis Mérieux Nutrisciences.
• in 2020, the characterization of pork and turkey microbiota was performed as a function of time and process factors to better predict spoilage phenomenon. This PhD thesis was included in the project ANR REDLOSSES coordinated by Secalim.
• in 2020, another PhD thesis recently defended aimed to characterize the bacterial communities and antibiotic resistance genes of fish microbiota in the framework of the RFI Food For Tomorrow, FOOD RESISTOME.

Books and book chapters:

• Zagorec, M. and M.-C. Champomier Vergès 2022. Meat microbiology and spoilage. Lawrie's meat science. F. Toldra, éd., Elsevier - Woodhead Publishing 9th edition. pp. 195-218, 978-0-323-85408-5.
• Zagorec, M. and M.-C. Champomier Vergès 2022. Microbiological issues affecting nutrition/safety of meat. Reference Module in Food Science. M. Dikeman, éd., Elsevier , Ltd. 3rd edition. pp., ISBN 9780081005965.
• La métagénomique : Développements et futures applications par Champomier Vergès, M.-C. and M. Zagorec, sortie en 2015. Collection Savoir Faires Editions Quae Collection Savoir Faire, ISBN: 978-2-7592-2293-3.
• Zagorec, M. and M.-C. Champomier Vergès 2017. Meat microbiology and spoilage. Lawrie's meat science. F. Toldra, éd., Elsevier - Woodhead Publishing 8th edition. pp. 187-230, 978-0-08-100694-8.

Contact persons at Secalim:

• Emmanuel Jaffrès, Assistant-Professor at Secalim
• Boris Misery, Assistant-professor at Secalim
• Coralie Goetz, assistant professor at Secalim

Other persons involved in this field:

• Marie-France Pilet, Professor at Secalim
• Sofia Strubbia, assistant-professor at Secalim
• Raouf Tareb, assistant-professor at Secalim

The following list of publications concerns the area of biopreservation.