Know more

Our use of cookies

Cookies are a set of data stored on a user’s device when the user browses a web site. The data is in a file containing an ID number, the name of the server which deposited it and, in some cases, an expiry date. We use cookies to record information about your visit, language of preference, and other parameters on the site in order to optimise your next visit and make the site even more useful to you.

To improve your experience, we use cookies to store certain browsing information and provide secure navigation, and to collect statistics with a view to improve the site’s features. For a complete list of the cookies we use, download “Ghostery”, a free plug-in for browsers which can detect, and, in some cases, block cookies.

Ghostery is available here for free:

You can also visit the CNIL web site for instructions on how to configure your browser to manage cookie storage on your device.

In the case of third-party advertising cookies, you can also visit the following site:, offered by digital advertising professionals within the European Digital Advertising Alliance (EDAA). From the site, you can deny or accept the cookies used by advertising professionals who are members.

It is also possible to block certain third-party cookies directly via publishers:

Cookie type

Means of blocking

Analytical and performance cookies

Google Analytics

Targeted advertising cookies


The following types of cookies may be used on our websites:

Mandatory cookies

Functional cookies

Social media and advertising cookies

These cookies are needed to ensure the proper functioning of the site and cannot be disabled. They help ensure a secure connection and the basic availability of our website.

These cookies allow us to analyse site use in order to measure and optimise performance. They allow us to store your sign-in information and display the different components of our website in a more coherent way.

These cookies are used by advertising agencies such as Google and by social media sites such as LinkedIn and Facebook. Among other things, they allow pages to be shared on social media, the posting of comments, and the publication (on our site or elsewhere) of ads that reflect your centres of interest.

Our EZPublish content management system (CMS) uses CAS and PHP session cookies and the New Relic cookie for monitoring purposes (IP, response times).

These cookies are deleted at the end of the browsing session (when you log off or close your browser window)

Our EZPublish content management system (CMS) uses the XiTi cookie to measure traffic. Our service provider is AT Internet. This company stores data (IPs, date and time of access, length of the visit and pages viewed) for six months.

Our EZPublish content management system (CMS) does not use this type of cookie.

For more information about the cookies we use, contact INRA’s Data Protection Officer by email at or by post at:

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

Dernière mise à jour : Mai 2018

Menu Logo Principal Oniris

Home page

Publications in microbial ecology

Selection of Secalim's publications relative to microbial ecology
  • Luong, N.-D. M., J.-M. Membré, L. Coroller, M. Zagorec, S. Poirier, S. Chaillou, M.-H. Desmonts, D. Werner, V. Cariou and S. Guillou 2021. Application of a path-modelling approach for deciphering causality relationships between microbiota, volatile organic compounds and off-odour profiles during meat spoilage. International Journal of Food Microbiology 348: 109208.
  • Maillet, A., P. Denojean, A. Bouju-Albert, E. Scaon, S. Leuillet, X. Dousset, E. Jaffrès, J. Combrisson and H. Prévost 2021. Characterization of bacterial communities of cold-smoked salmon during storage. Foods 10(2).
  • Maillet, A., A. Bouju-Albert, S. Roblin, P. Vaissié, S. Leuillet, X. Dousset, E. Jaffrès, J. Combrisson and H. Prévost 2021. Impact of DNA extraction and sampling methods on bacterial communities monitored by 16S rDNA metabarcoding in cold-smoked salmon and processing plant surfaces. Food Microbiology 95.
  • Helsens, N., S. Calvez, A. Bouju-Albert, A. Rossero, H. Prevost and C. Magras 2020. Comparison of stomaching versus rinsing, for recovering bacterial communities from rainbow trout (Oncorhynchus mykiss) fillets. Journal of Food Protection.
  • Helsens, N., S. Calvez, H. Prevost, A. Bouju-Albert, A. Maillet, A. Rossero, D. Hurtaud-Pessel, M. Zagorec and C. Magras 2020. Antibiotic resistance genes and bacterial communities of farmed rainbow trout fillets (Oncorhynchus mykiss). Frontiers in Microbiology 11(3070). https://doi.org10.3389/fmicb.2020.590902.
  • Luong, N.-D. M., S. Jeuge, L. Coroller, C. Feurer, M.-H. Desmonts, N. Moriceau, V. Anthoine, S. Gavignet, A. Rapin, B. Frémaux, E. Robieu, M. Zagorec, J.-M. Membré and S. Guillou 2020. Spoilage of fresh turkey and pork sausages: Influence of potassium lactate and modified atmosphere packaging. Food Research International 137: 109501.
  • Luong, N.-D. M., L. Coroller, M. Zagorec, J.-M. Membré and S. Guillou 2020. Spoilage of chilled fresh meat products during storage: A quantitative analysis of literature data. Microorganisms 8(8).
  • Poirier, S., N.-D. M. Luong, V. Anthoine, S. Guillou, J.-M. Membre, N. Moriceau, S. Reze, M. Zagorec, C. Feurer, B. Fremaux, S. Jeuge, E. Robieu, M. Champomier-Verges, G. Coeuret, E. Cauchie, G. Daube, N. Korsak, L. Coroller, N. Desriac, M.-H. Desmonts, R. Gohier, D. Werner, V. Loux, O. Rue, M.-H. Dohollou, T. Defosse and S. Chaillou 2020. Large-scale multivariate dataset on the characterization of microbiota diversity, microbial growth dynamics, metabolic spoilage volatilome and sensorial profiles of two industrially produced meat products subjected to changes in lactate concentration and packaging atmosphere. Data in brief 30: 105453-105453.
  • Wiernasz, N., F. Leroi, F. Chevalier, J. Cornet, M. Cardinal, J. Rohloff, D. Passerini, S. Skırnisdóttir and M.-F. Pilet 2020. Salmon gravlax biopreservation with lactic acid bacteria: A polyphasic approach to assessing the impact on organoleptic properties, microbial ecosystem and volatilome composition. Frontiers in Microbiology 10(3103).
  • Ziadi, M., T. Bouzaiene, S. Lakhal, K. Zaafouri, S. Massoudi, X. Dousset and M. Hamdi 2019. Screening of lactic starter from Tunisian fermented vegetables and application for the improvement of caper (Capparis spinosa) fermentation through an experimental factorial design. Annals of Microbiology 69(13): 1373-1385.
  • Bouju-Albert, A., M.-F. Pilet and S. Guillou 2018. Influence of lactate and acetate removal on the microbiota of French fresh pork sausages. Food Microbiology 76: 328-336.
  • Leroy, F., T. Aymerich, M.-C. Champomier-Vergès, L. Cocolin, L. De Vuyst, M. Flores, F. Leroi, S. Leroy, R. Talon, R. F. Vogel and M. Zagorec 2018. Fermented meats (and the symptomatic case of the Flemish food pyramid): Are we heading towards the vilification of a valuable food group? International Journal of Food Microbiology.
  • Loux, V., G. Coeuret, M. Zagorec, M.-C. Champomier Vergès and S. Chaillou 2018. Complete and draft genome sequences of nine Lactobacillus sakei strains selected from the three known phylogenetic lineages and their main clonal complexes. Microbiology Resource Announcements 6(16).
  • Poirier, S., O. Rue, R. Peguilhan, G. Coeuret, M. Zagorec, M. C. Champomier-Verges, V. Loux and S. Chaillou 2018. Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing. PLoS One 13(9): e0204629.
  • Ramaroson, M., S. Guillou, A. Rossero, S. Rezé, V. Anthoine, N. Moriceau, J.-L. Martin, F. Duranton and M. Zagorec 2018. Selection procedure of bioprotective cultures for their combined use with High Pressure Processing to control spore-forming bacteria in cooked ham. International Journal of Food Microbiology 276: 28-38.
  • Rouger, A., N. Moriceau, H. Prévost, B. Remenant and M. Zagorec 2018. Diversity of bacterial communities in French chicken cuts stored under modified atmosphere packaging. Food Microbiology 70: 7-16.
  • Hwanhlem, N., T. Ivanova, T. Haertlé, E. Jaffrès and X. Dousset 2017. Inhibition of food-spoilage and foodborne pathogenic bacteria by a nisin Z-producing Lactococcus lactis subsp. lactis KT2W2L. LWT - Food Science and Technology 82: 170-175.
  • Iskandar, C. F., F. Borges, B. Taminiau, G. Daube, M. Zagorec, B. Remenant, J. J. Leisner, M. A. Hansen, S. J. Sørensen, C. Mangavel, C. Cailliez-Grimal and A.-M. Revol-Junelles 2017. Comparative genomic analysis reveals ecological differentiation in the genus Carnobacterium. Frontiers in Microbiology 8(357).
  • Rouger, A., B. Remenant, H. Prévost and M. Zagorec 2017. A method to isolate bacterial communities and characterize ecosystems from food products: Validation and utilization in as a reproducible chicken meat model. International Journal of Food Microbiology 247: 38-47.
  • Rouger, A., O. Tresse and M. Zagorec 2017. Bacterial contaminants of poultry meat: sources, species, and dynamics. Microorganisms 5(3): 50.
  • Saraoui, T., J. Cornet, E. Guillouet, M. F. Pilet, F. Chevalier, J.-J. Joffraud and F. Leroi 2017. Improving simultaneously the quality and safety of cooked and peeled shrimp using a cocktail of bioprotective lactic acid bacteria. International Journal of Food Microbiology 241: 69-77.
  • Wiernasz, N., J. Cornet, M. Cardinal, M.-F. Pilet, D. Passerini and F. Leroi 2017. Lactic acid bacteria selection for biopreservation as a part of hurdle technology approach applied on seafood. Frontiers in Marine Science 4: 119.
  • Zagorec, M. and M.-C. Champomier-Vergès 2017. Lactobacillus sakei: A starter for sausage fermentation, a protective culture for meat products. Microorganisms 5(3): 56.
  • Assohoun-Djeni, N. M. C., N. T. Djeni, S. Messaoudi, E. Lhomme, M. Koussemon-Camara, T. Ouassa, J. M. Chobert, B. Onno and X. Dousset 2016. Biodiversity, dynamics and antimicrobial activity of lactic acid bacteria involved in the fermentation of maize flour for doklu production in Côte d'Ivoire. Food Control 62: 397-404.
  • Iskandar, C. F., C. Cailliez-Grimal, A. Rahman, E. Rondags, B. Remenant, M. Zagorec, J. J. Leisner, F. Borges and A.-M. Revol-Junelles 2016. Genes associated to lactose metabolism illustrate the high diversity of Carnobacterium maltaromaticum. Food Microbiology 58: 79-86.
  • Jérôme, M., S. Macé, X. Dousset, B. Pot and J.-J. Joffraud 2016. Genetic diversity analysis of isolates belonging to the Photobacterium phosphoreum species group collected from salmon products using AFLP fingerprinting. International Journal of Food Microbiology 217: 101-109.
  • Lhomme, E., C. Urien, J. Legrand, X. Dousset, B. Onno and D. Sicard 2016. Sourdough microbial community dynamics: An analysis during French organic bread-making processes. Food Microbiology 53: 41-50.
  • Lhomme, E., B. Onno, V. Chuat, K. Durand, S. Orain, F. Valence, X. Dousset and M.-A. Jacques 2016. Genotypic diversity of Lactobacillus sanfranciscensis strains isolated from French organic sourdoughs. International Journal of Food Microbiology 226: 13-19.
  • Michel, E., C. Monfort, M. Deffrasnes, S. Guezenec, E. Lhomme, M. Barret, D. Sicard, X. Dousset and B. Onno 2016. Characterization of relative abundance of lactic acid bacteria species in French organic sourdough by cultural, qPCR and MiSeq high-throughput sequencing methods. International Journal of Food Microbiology 239: 35-43.
  • Najjari, A., H. Amairi, S. Chaillou, D. Mora, A. Boudabous, M. Zagorec and H. Ouzari 2016. Phenotypic and genotypic characterization of peptidoglycan hydrolases of Lactobacillus sakei. Journal of Advanced Research 7(1): 155-163.
  • Pontonio, E., C. G. Rizzello, R. Di Cagno, X. Dousset, H. Clément, P. Filannino, B. Onno and M. Gobbetti 2016. How organic farming of wheat may affect the sourdough and the nutritional and technological features of leavened baked goods. International Journal of Food Microbiology 239: 44-53.
  • Chaillou, S., A. Chaulot-Talmon, H. Caekebeke, M. Cardinal, S. Christieans, C. Denis, M. Helene Desmonts, X. Dousset, C. Feurer, E. Hamon, J.-J. Joffraud, S. La Carbona, F. Leroi, S. Leroy, S. Lorre, S. Mace, M.-F. Pilet, H. Prevost, M. Rivollier, D. Roux, R. Talon, M. Zagorec and M.-C. Champomier-Verges 2015. Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage. ISME Journal(9): 1105-1118.
  • Djeni, N. T., K. M. J. P. Bouatenin, N. M. C. Assohoun, D. M. Toka, E. H. Menan, X. Dousset and K. M. Dje 2015. Biochemical and microbial characterization of cassava inocula from the three main attieke production zones in Côte d'Ivoire. Food Control 50(0): 133-140.
  • Lhomme, E., S. Orain, P. Courcoux, B. Onno and X. Dousset 2015. The predominance of Lactobacillus sanfranciscensis in French organic sourdoughs and its impact on related bread characteristics. International Journal of Food Microbiology 213: 40-48.
  • Lhomme, E., A. Lattanzi, X. Dousset, F. Minervini, M. De Angelis, G. Lacaze, B. Onno and M. Gobbetti 2015. Lactic acid bacterium and yeast microbiotas of sixteen French traditional sourdoughs. International Journal of Food Microbiology 215: 161-170.
  • Remenant, B., E. Jaffrès, X. Dousset, M.-F. Pilet and M. Zagorec 2015. Bacterial spoilers of food: Behavior, fitness and functional properties. Food Microbiology 45 (Part A): 45-53.
  • Sanders, J. W., S. J. C. M. Oomes, J. M. Membré, A. Wegkamp and M. Wels 2015. Biodiversity of spoilage lactobacilli: Phenotypic characterisation. Food Microbiology 45(A): 34-44.
  • Favaro, L., M. Basaglia, S. Casella, I. Hue, X. Dousset, B. D. Gombossy de Melo Franco and S. D. Todorov 2014. Bacteriocinogenic potential and safety evaluation of non-starter Enterococcus faecium strains isolated from home made white brine cheese. Food Microbiology 38: 228-239. 10.1016/
  • Lhomme, E., S. Mezaize, M. B. Ducasse, H. Chiron, M.-C. Champomier-Verges, S. Chaillou, M. Zagorec, X. Dousset and B. Onno 2014. A polyphasic approach to study the dynamics of microbial population of an organic wheat sourdough during its conversion to gluten-free sourdough. International Microbiology 17(1): 1-9.
  • Mace, S., M. Cardinal, E. Jaffres, J. Cornet, V. Lalanne, F. Chevalier, T. Serot, M.-F. Pilet, X. Dousset and J.-J. Joffraud 2014. Evaluation of the spoilage potential of bacteria isolated from spoiled cooked whole tropical shrimp (Penaeus vannamei) stored under modified atmosphere packaging. Food Microbiology 40: 9-17.
  • Macé, S., J.-J. Joffraud, M. Cardinal, M. Malcheva, J. Cornet, V. Lalanne, F. Chevalier, T. Sérot, M.-F. Pilet and X. Dousset 2013. Evaluation of the spoilage potential of bacteria isolated from spoiled raw salmon (Salmo salar) fillets stored under modified atmosphere packaging. International Journal of Food Microbiology 160(3): 227-238.
  • Macé, S., J. Cornet, F. Chevalier, M. Cardinal, M. F. Pilet, D. X. and J. J. Joffraud 2012. Characterisation of the spoilage microbiota in raw salmon (Salmo salar) steaks stored under vacuum or modified atmosphere packaging combining conventional methods and PCR-TTGE. Food Microbiology 30(1): 8.
  • Jaffrès, E., V. Lalanne, S. Macé, J. Cornet, M. Cardinal, T. Sérot, X. Dousset and J.-J. Joffraud 2011. Sensory characteristics of spoilage and volatile compounds associated with bacteria isolated from cooked and peeled tropical shrimps using SPME–GC–MS analysis. International Journal of Food Microbiology 147(3): 195-202.
  • Messaoudi, S., G. Kergourlay, A. Rossero, M. Ferchichi, H. Prevost, D. Drider, M. Manai and X. Dousset 2011. Identification of lactobacilli residing in chicken ceca with antagonism against Campylobacter. International Microbiology 14(2): 103-10.
  • Jaffrès, E., H. Prevost, A. Rossero, J. J. Joffraud and X. Dousset 2010. Vagococcus penaei sp. nov., isolated from spoilage microbiota of cooked shrimp (Penaeus vannamei). International Journal of Systematic and Evolutionary Microbiology 60: 2159-2164.
  • Matamoros, S., S. André, I. Hue, H. Prévost and M. F. Pilet 2010. Identification of lactic acid bacteria involved in the spoilage of pasteurized "foie gras" products. Meat Science 85: 467-471.
  • Ben Belgacem, Z., X. Dousset, H. Prévost and M. Manai 2009. Polyphasic taxonomic studies of lactic acid bacteria associated with Tunisian fermented meat based on the heterogeneity of the 16S–23S rRNA gene intergenic spacer region. Archives of Microbiology 191(9): 711-720.
  • Jaffres, E., D. Sohier, F. Leroi, M. F. Pilet, H. Prévost, J. J. Joffraud and X. Dousset 2009. Study of the bacterial ecosystem in tropical cooked and peeled shrimps using a polyphasic approach. International Journal of Food Microbiology 131(1): 20-9.
  • Matamoros, S., F. Leroi, M. Cardinal, F. Gigout, F. Kasbi Chadli, J. Cornet, H. Prévost and M. F. Pilet 2009. Psychrotrophic lactic acid bacteria used to improve the safety and quality of vacuum-packed cooked and peeled tropical shrimp and cold-smoked salmon. Journal of Food Protection 72(2): 365-374.
  • Matamoros, S., M. F. Pilet, F. Gigout, H. Prévost and F. Leroi 2009. Selection and evaluation of seafood-borne psychrotrophic lactic acid bacteria as inhibitors of pathogenic and spoilage bacteria. Food Microbiology (London) 26(6): 638-44.
  • Belgacem, Z. B., M. Ferchichi, H. Prévost, X. Dousset and M. Manai 2008. Screening for anti-listerial bacteriocin-producing lactic acid bacteria from "Gueddid" a traditionally Tunisian fermented meat. Meat Science 78(4): 513-521.
  • Ferchichi, M., R. Valcheva, N. Oheix, P. Kabadjova, H. Prévost, B. Onno and X. Dousset 2008. Rapid investigation of French sourdough microbiota by restriction fragment length polymorphism of the 16S-23S rRNA gene intergenic spacer region. World Journal of Microbiology and Biotechnology 24(11): 2425-2434.
  • Nazef, L., Y. Belguesmia, A. Tani, H. Prévost and D. Drider 2008. Identification of lactic acid bacteria from poultry feces: evidence on anti-campylobacter and anti-listeria activities. Poultry Science 87(2): 329-34.
  • Batdorj, B., V. Trinetta, M. Dalgalarrondo, H. Prévost, X. Dousset, I. Ivanova, T. Haertle and J. M. Chobert 2007. Isolation, taxonomic identification and hydrogen peroxide production by Lactobacillus delbrueckii subsp. lactis T31, isolated from Mongolian yoghurt: inhibitory activity on food-borne pathogens. Journal of Applied Microbiology 103(3): 584-93.
  • Ferchichi, M., R. Valcheva, H. Prévost, B. Onno and X. Dousset 2007. Molecular identification of the microbiota of French sourdough using temporal temperature gradient gel electrophoresis. Food Microbiology (London) 24(7-8): 678-86.
  • Leisner, J. J., B. G. Laursen, H. Prévost, D. Drider and P. Dalgaard 2007. Carnobacterium: positive and negative effects in the environment and in foods. FEMS Microbiology Reviews 31(5): 592-613.
  • Protais, J., P. Gerault, S. Queguiner, E. Boscher, B. Chidaine, G. Ermel, K. Rivoal, G. Salvat, J. Pages, D. Thuault, V. Huchet, M. Coignard, F. Bourion, M. Federighi, F. Jugiau, D. Thouvenot, T. Efstathiou and P. Lorthioir 2006. Identification et comportement des bactéries d'altération dans la matrice oeuf entier liquide. Science et Techniques Avicoles 57: 4-13.
  • Valcheva, R., M. F. Ferchichi, M. Korakli, I. Ivanova, M. G. Ganzle, R. F. Vogel, H. Prevost, B. Onno and X. Dousset 2006. Lactobacillus nantensis sp nov., isolated from French wheat sourdough. International Journal of Systematic and Evolutionary Microbiology 56: 587-591. 10.1099/ijs.0.63619-0.