Know more

About cookies

What is a "cookie"?

A "cookie" is a piece of information, usually small and identified by a name, which may be sent to your browser by a website you are visiting. Your web browser will store it for a period of time, and send it back to the web server each time you log on again.

Different types of cookies are placed on the sites:

  • Cookies strictly necessary for the proper functioning of the site
  • Cookies deposited by third party sites to improve the interactivity of the site, to collect statistics

Learn more about cookies and how they work

The different types of cookies used on this site

Cookies strictly necessary for the site to function

These cookies allow the main services of the site to function optimally. You can technically block them using your browser settings but your experience on the site may be degraded.

Furthermore, you have the possibility of opposing the use of audience measurement tracers strictly necessary for the functioning and current administration of the website in the cookie management window accessible via the link located in the footer of the site.

Technical cookies

Name of the cookie

Purpose

Shelf life

CAS and PHP session cookies

Login credentials, session security

Session

Tarteaucitron

Saving your cookie consent choices

12 months

Audience measurement cookies (AT Internet)

Name of the cookie

Purpose

Shelf life

atid

Trace the visitor's route in order to establish visit statistics.

13 months

atuserid

Store the anonymous ID of the visitor who starts the first time he visits the site

13 months

atidvisitor

Identify the numbers (unique identifiers of a site) seen by the visitor and store the visitor's identifiers.

13 months

About the AT Internet audience measurement tool :

AT Internet's audience measurement tool Analytics is deployed on this site in order to obtain information on visitors' navigation and to improve its use.

The French data protection authority (CNIL) has granted an exemption to AT Internet's Web Analytics cookie. This tool is thus exempt from the collection of the Internet user's consent with regard to the deposit of analytics cookies. However, you can refuse the deposit of these cookies via the cookie management panel.

Good to know:

  • The data collected are not cross-checked with other processing operations
  • The deposited cookie is only used to produce anonymous statistics
  • The cookie does not allow the user's navigation on other sites to be tracked.

Third party cookies to improve the interactivity of the site

This site relies on certain services provided by third parties which allow :

  • to offer interactive content;
  • improve usability and facilitate the sharing of content on social networks;
  • view videos and animated presentations directly on our website;
  • protect form entries from robots;
  • monitor the performance of the site.

These third parties will collect and use your browsing data for their own purposes.

How to accept or reject cookies

When you start browsing an eZpublish site, the appearance of the "cookies" banner allows you to accept or refuse all the cookies we use. This banner will be displayed as long as you have not made a choice, even if you are browsing on another page of the site.

You can change your choices at any time by clicking on the "Cookie Management" link.

You can manage these cookies in your browser. Here are the procedures to follow: Firefox; Chrome; Explorer; Safari; Opera

For more information about the cookies we use, you can contact INRAE's Data Protection Officer by email at cil-dpo@inrae.fr or by post at :

INRAE

24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

Menu Logo Principal Oniris

Home page

Microbial ecology

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.

Books and book chapters:

  • 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:

  • 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:

Other persons involved in this field:

The following list of publications concerns the area of biopreservation.

PhD thesis of Sabrina Macé (2010-2013)

Molecular characterization and quantification of raw salmon and cooked shrimp spoilage microbiota
Read more

PhD thesis of Aurore Thorigné (2009-2012)

Recherche et caractérisation de bactéries lactiques céréalières à activité probiotique anti-inflamatoire
Read more

PhD thesis of Emmanuel Jaffrès (2006-2009)

Molecular characterization of the complex microbial ecosystem of cooked shrimp and study of spoilage flora
Read more

PhD thesis of Sébastien Matamoros (2005-2008)

Characterization of psychrotrophic lactic acid bacteria for food biopreservation : physiologic and molecular study of cold adaptation mechanisms
Read more

PhD thesis of Anne Brillet-Viel (2002-2005)

Selection and characterization of Carnobacterium strains for the biopreservation of smoked salmon
Read more