Last extraction 2026-06-03 19:00:22.151979
2026
1. Karimi, E., Tap, J., Champomier-Vergès, M.-C. & Chaillou, S. Microbiome metabolic modeling as a tool for innovation in fermented foods. Current Opinion in Food Science 67, 101368 (2026).
2025
2. Kothe, C. I. & Renault, P. Metagenomic driven isolation of poorly culturable species in food. Food Microbiology 104722 (2025) doi: 10.1016/j.fm.2025.104722.
3. Humblot, C. et al. A scoping review of the health effects of fermented foods in specific human populations and their potential role in precision nutrition: Current knowledge and gaps. Frontiers in Nutrition 12, (2025).
4. Tap, J., Mohellibi, N., Tinsley, C., Loux, V. & Chaillou, S. Food Microbiome Metabolic Modules (F3M), a tool suite for functional profiling of food microbiomes. Open Research Europe 5, 324 (2025).
2024
5. Kothe, C. I. et al. Halomonas citrativorans sp. Nov., Halomonas casei sp. Nov. And Halomonas colorata sp. Nov., isolated from French cheese rinds. International Journal of Systematic and Evolutionary Microbiology 74, 006234 (2024).
6. Junker, R., Valence, F., Mistou, M.-Y., Chaillou, S. & Chiapello, H. Integration of metataxonomic data sets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables. Microbiology Spectrum 0, e00312–24 (2024).
2023
7. Ladeira, R., Tap, J. & Derrien, M. Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy. Microbiome Research Reports 2, 9 (2023).
8. Ammoun, I. et al. Lebanese fermented goat milk products: From tradition to meta-omics. Food Research International 168, 112762 (2023).
9. Rodriguez, C. I. et al. Curated and harmonized gut microbiome 16S rRNA amplicon data from dietary fiber intervention studies in humans. Scientific Data 10, 346 (2023).
10. Sessitsch, A. et al. Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet. Microbiology and Molecular Biology Reviews 0, e00212–22 (2023).
11. Poirier, S. et al. Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios. Frontiers in Microbiology 14, 1286661 (2023).
2022
12. Chaillou, S. et al. Combination of High-Pressure Treatment at 500 MPa and Biopreservation with a Lactococcus lactis Strain for Lowering the Bacterial Growth during Storage of Diced Cooked Ham with Reduced Nitrite Salt. Microorganisms 10, (2022).
13. Rul, F. et al. Underlying evidence for the health benefits of fermented foods in humans. Food & Function 13, 4804–4824 (2022).
14. Claus, P. et al. Discrimination of spoiled beef and salmon stored under different atmospheres by an optoelectronic nose. Comparison with GC-MS measurements. Future Foods 5, 100106 (2022).
15. Kothe, C. I., Mohellibi, N. & Renault, P. Revealing the microbial heritage of traditional Brazilian cheeses through metagenomics. Food Research International (Ottawa, Ont.) 157, 111265 (2022).
16. Manthou, E., Coeuret, G., Chaillou, S. & Nychas, G.-J. E. Metagenetic characterization of bacterial communities associated with ready-to-eat leafy vegetables and study of temperature effect on their composition during storage. Food Research International (Ottawa, Ont.) 158, 111563 (2022).
17. Borges, F. et al. Contribution of omics to biopreservation: Toward food microbiome engineering. Frontiers in Microbiology 13, 951182 (2022).
18. Cernava, T. et al. Metadata harmonization–Standards are the key for a better usage of omics data for integrative microbiome analysis. Environmental Microbiome 17, 33 (2022).
2021
19. Manthou, E., Coeuret, G., Chaillou, S. & Nychas, G.-J. E. Evolution of fungal community associated with ready-to-eat pineapple during storage under different temperature conditions. Food Microbiology 97, 103736 (2021).
20. Luong, N.-D. M. et al. 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 (2021).
21. Kothe, C. I., Bolotin, A., Kraïem, B.-F., Dridi, B. & Renault, P. Unraveling the world of halophilic and halotolerant bacteria in cheese by combining cultural, genomic and metagenomic approaches. International journal of food microbiology 358, 109312 (2021).
22. Grassotti, T. T. et al. Fecal bacterial communities of wild black capuchin monkeys (Sapajus nigritus) from the Atlantic Forest biome in Southern Brazil are divergent from those of other non-human primates. Current Research in Microbial Sciences 2, 100048 (2021).
2020
23. Terán, L. C. et al. Nucleotide sequence and analysis of pRC12 and pRC18, two theta-replicating plasmids harbored by Lactobacillus curvatus CRL 705. PloS one 15, e0230857 (2020).
24. Dugat-Bony, E. et al. Viral metagenomic analysis of the cheese surface: A comparative study of rapid procedures for extracting viral particles. Food Microbiology 85, 103278 (2020).
25. Sanhoun, A. R. et al. Traditional milk transformation schemes in Côte d’Ivoire and their impact on the prevalence of Streptococcus bovis complex bacteria in dairy products. PloS one 15, e0233132 (2020).
26. Poirier, S. et al. 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 (2020).
27. Aka, S. et al. Characterization of lactic acid bacteria isolated from a traditional Ivoirian beer process to develop starter cultures for safe sorghum-based beverages. International journal of food microbiology 322, 108547 (2020).
28. Kothe, C. I., Delbarre-Ladrat, C., Renault, P. & Passerini, D. Draft-genome sequence data and phylogenomic comparison of two marine-sourced bacterial strains Pseudoalteromonas sp. MIP2626 and Psychrobacter sp. BI730. Data in brief 31, 105898 (2020).
29. Papadimitriou, K., Kline, K., Renault, P. & Kok, J. Editorial: Omics and Systems Approaches to Study the Biology and Applications of Lactic Acid Bacteria. Frontiers in microbiology 11, 1786 (2020).
30. Verplaetse, E. et al. Heme Uptake in Lactobacillus sakei Evidenced by a New Energy Coupling Factor (ECF)-Like Transport System. Applied and environmental microbiology 86, (2020).
31. Zagdoun, M., Coeuret, G., N’Dione, M., Champomier-Vergès, M.-C. & Chaillou, S. Large microbiota survey reveals how the microbial ecology of cooked ham is shaped by different processing steps. Food microbiology 91, 103547 (2020).
Previous years
2019
32. Gboko, K. D. T. et al. Risk factors for the carriage of Streptococcus infantarius subspecies infantarius isolated from African fermented dairy products. PloS one 14, e0225452 (2019).
2018
33. Couvigny, B. et al. Identification of New Factors Modulating Adhesion Abilities of the Pioneer Commensal Bacterium Streptococcus salivarius. Frontiers in microbiology 9, 273 (2018).
34. Poirier, S. et al. Detection of an amplification bias associated to Leuconostocaceae family with a universal primer routinely used for monitoring microbial community structures within food products. BMC research notes 11, 802 (2018).
35. Poirier, S. et al. 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, e0204629 (2018).
36. Loux, V., Coeuret, G., Zagorec, M., Champomier Vergès, M.-C. & Chaillou, S. Complete and Draft Genome Sequences of Nine Lactobacillus sakei Strains Selected from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes. Genome announcements 6, (2018).
37. Terán, L. C. et al. Phylogenomic Analysis of Lactobacillus curvatus Reveals Two Lineages Distinguished by Genes for Fermenting Plant-Derived Carbohydrates. Genome biology and evolution 10, 1516–1525 (2018).
38. Poirier, S., Coeuret, G., Champomier-Vergès, M.-C. & Chaillou, S. Draft Genome Sequences of Nine Strains of Brochothrix thermosphacta, Carnobacterium divergens, Lactobacillus algidus, Lactobacillus fuchuensis, Lactococcus piscium, Leuconostoc gelidum subsp. Gasicomitatum, Pseudomonas lundensis, and Weissella viridescens, a Collection of Psychrotrophic Species Involved in Meat and Seafood Spoilage. Genome announcements 6, (2018).
39. Kaindi, D. W. M. et al. Colorectal cancer-associated Streptococcus infantarius subsp. Infantarius differ from a major dairy lineage providing evidence for pathogenic, pathobiont and food-grade lineages. Scientific reports 8, 9181 (2018).
2017
40. Fougy, L., Coeuret, G., Champomier-Vergès, M.-C. & Chaillou, S. Draft Genome Sequence of Serratia proteamaculans MFPA44A14-05, a Model Organism for the Study of Meat and Seafood Spoilage. Genome announcements 5, (2017).
41. Terán, L. C., Coeuret, G., Raya, R., Champomier-Vergès, M.-C. & Chaillou, S. Draft Genome Sequence of Lactobacillus curvatus FLEC03, a Meat-Borne Isolate from Beef Carpaccio Packaged in a Modified Atmosphere. Genome announcements 5, (2017).
2016
42. Fougy, L. et al. Reducing Salt in Raw Pork Sausages Increases Spoilage and Correlates with Reduced Bacterial Diversity. Applied and environmental microbiology 82, 3928–3939 (2016).
2015
43. Champomier-Verges, M.-C. et al. Transcriptomic and proteomic analysis of i Oenococcus oeni /i PSU-1 response to ethanol shock. Food Microbiology 51, 87–95 (2015).
44. Chaillou, S. et al. Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage. The ISME journal 9, 1105–1118 (2015).
2014
45. Lhomme, E. et al. A polyphasic approach to study the dynamics of microbial population of an organic wheat sourdough during its conversion to gluten-free sourdough. International microbiology : the official journal of the Spanish Society for Microbiology 17, 1–9 (2014).
46. Chaillou, S. et al. Quantification and efficiency of Lactobacillus sakei strain mixtures used as protective cultures in ground beef. Meat science 97, 332–338 (2014).
47. Nielsen, H. B. et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nature biotechnology 32, 822–828 (2014).
2013
48. Chaillou, S., Lucquin, I., Najjari, A., Zagorec, M. & Champomier-Vergès, M.-C. Population genetics of Lactobacillus sakei reveals three lineages with distinct evolutionary histories. PloS one 8, e73253 (2013).
49. Cailliez-Grimal, C. et al. Complete Chromosome Sequence of Carnobacterium maltaromaticum LMA 28. Genome announcements 1, (2013).
50. Anba-Mondoloni, J., Chaillou, S., Zagorec, M. & Champomier-Vergès, M.-C. Catabolism of N-acetylneuraminic acid, a fitness function of the food-borne lactic acid bacterium Lactobacillus sakei, involves two newly characterized proteins. Applied and environmental microbiology 79, 2012–2018 (2013).
51. Le Chatelier, E. et al. Richness of human gut microbiome correlates with metabolic markers. Nature 500, 541–546 (2013).
2012
52. Guilbaud, M., Zagorec, M., Chaillou, S. & Champomier-Vergès, M.-C. Intraspecies diversity of Lactobacillus sakei response to oxidative stress and variability of strain performance in mixed strains challenges. Food microbiology 29, 197–204 (2012).
53. Lucquin, I., Zagorec, M., Champomier-Vergès, M. & Chaillou, S. Fingerprint of lactic acid bacteria population in beef carpaccio is influenced by storage process and seasonal changes. Food microbiology 29, 187–196 (2012).
2011
54. Lakhdari, O. O. et al. Identification of NF-kappa B modulation capabilities within human intestinal commensal bacteria. Journal of Biomedicine and Biotechnology 1–9 (2011) doi: 10.1155/2011/282356.
55. Sobhani, I. et al. Microbial dysbiosis in colorectal cancer (CRC) patients. PLoS ONE 6, np (2011).
2010
56. Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, pp. 59–65 (2010).
57. Lakhdari, O. et al. Functional metagenomics: A high throughput screening method to decipher microbiota-driven NF-kappa B modulation in the human gut. PLoS ONE 5, np (2010).
2006
58. Zagorec, M., Chaillou, S., Champomier-Verges, M.-C. & Le Coq, A.-M. Du génome de Lactobacillus sakei à la bioconservation des produits carnés. La revue française de la recherche en viandes et produits carnés 25, 1–3 (2006).
2001
59. Guédon, E., Renault, P., Ehrlich, S. D. & Delorme, C. Transcriptional pattern of genes coding for the proteolytic system of lactococcus lactis and evidence for coordinated regulation of key enzymes by peptide supply. Journal of Bacteriology 183, 3614–3622 (2001).