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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.

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.
• es flores protectrices pour la conservation des aliments : utilisation, efficacité et interactions dans l’écosystème microbien par Zagorec, M. and S. Christeans, sortie en 2013. Collection Synthèsess Editions Quae Collection Synthèses, ISBN: 978-2-7592-1920-9.
• 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.
• Dousset, X., E. Jaffrès and M. Zagorec 2016. Spoilage: Bacterial Spoilage. The Encyclopedia of Food and Health. B. Caballero, P. M. Finglas and F. Toldra, éds.,  Oxford, UK, Academic Press 5: pp. 106-112
• Rul, F., M. Zagorec and M.-C. Champomier-Vergès 2015. Lactic acid bacteria in fermented foods. Proteomics in foods, principles and applications. F. Toldra, éd.,  New York, USA, Springer: pp.
• Renault, P., M. Zagorec and M.-C. Champomier Vergès 2015. Communautés microbiennes des aliments. La métagénomique : Développements et futures applications, Editions Quae Collection Savoir Faire. pp. 57-70, ISBN: 978-2-7592-2293-3.
• Champomier-Vergès, M.-C. and M. Zagorec 2015. Spoilage microorganisms: Risk and Control. Handbook of Fermented Meat and Poultry. F. Toldra, éd., John Wiley and Sons, Ltd. second edition. 45: pp. 385-388
• Champomier-Vergès, M. C. and M. Zagorec 2015. Lactobacillus sakei in meat fermentation. Biotechnology of Lactic Acid Bacteria: novel applications. F. Mozzi, R. R. Raya and G. M. Vignolo, éds., John Wiley & Sons, Ltd. Second Edition. Chapter 13: pp. 209-215
• Anba-Mondoloni, J., M.-C. Champomier-Vergès, M. Zagorec, S. Leroy, E. Dordet-Frisoni, S. Planchon and R. Talon 2015. The Genetics of Microbial Starters. Handbook of Fermented Meat and Poultry. F. Toldra, éd., John Wiley and Sons, Ltd. second edition. 19: pp. 161-168
• Zagorec, M., M.-C. Champomier Vergès and C. Cailliez-Grimal 2014. Identification Methods/DNA fingerprinting: whole genome sequencing. Encyclopedia of Food Microbiology. C. A. Batt and M. L. Tortorello, éds.,  Oxford, UK, Elsevier Ltd, Academic Press 2nd Edition. pp. 295-299, ISBN 9780123847300.

PhD theses supervised on this topic:

• The phD. thesis of Sophie Hautefeuille deals 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.
• in 2019, the quality and safety improvement of seafood by biopreservation required the characterization of microbial communities, in the framework of the European SAFEFISH DISH proect.
• in 2017, the PhD project dealt with the characterization and behaviour of bacterial communities of chicken meat stored under modified atmosphere
• Two PhD theses dealt with the microbial ecology of shrimps, one in 2009 and the other one in 2013, in the framework of the ANR EcoBioPro project, The characteriazation and molecular quantificationof the spoilage microbial ecosystem  was carried out on raw salmon and cooked shrimps.
• in 2008, psychrotrophic lactic acid bacteria were characterized in the purpose of their use in food biopreservation.

Contact persons at Secalim:

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

Other persons involved in this field:

• Hervé Prévost, Professor at Secalim
• Marie-France Pilet, Professor at Secalim

The following list of publications concerns the area of biopreservation.