Publications

Last extraction 2024-06-01 00:36:29.22261

1. 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).

2. 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).

3. Ammoun, I. et al. Lebanese fermented goat milk products: From tradition to meta-omics. Food Research International 168, 112762 (2023).

4. 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).

5. Tap, J. et al. Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors. Nature Communications 14, 3310 (2023).

6. 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).

7. Champomier-Vergès, M.-C. et al. Le potentiel insoupçonné des aliments fermentés. Ressources, la revue INRAE 44 (2023).

8. 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).

9. 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).

10. 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).

11. 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).

12. 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).

13. Borges, F. et al. Contribution of omics to biopreservation: Toward food microbiome engineering. Frontiers in Microbiology 13, 951182 (2022).

14. Rul, F. et al. Underlying evidence for the health benefits of fermented foods in humans. Food & Function 13, 4804–4824 (2022).

15. Lange, L. et al. Microbiome ethics, guiding principles for microbiome research, use and knowledge management. Environmental Microbiome 17, 50 (2022).

16. 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).

17. 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).

18. 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).

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. 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).

21. 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).

22. 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).

23. 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).

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. 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).

26. Couvigny, B. et al. Identification of New Factors Modulating Adhesion Abilities of the Pioneer Commensal Bacterium Streptococcus salivarius. Frontiers in microbiology 9, 273 (2018).

27. Isenring, J. et al. Streptococcus gallolyticus subsp. Gallolyticus endocarditis isolate interferes with coagulation and activates the contact system. Virulence 9, 248–261 (2018).

28. 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).

29. Kaindi, D. W. M. et al. Investigating the association between African spontaneously fermented dairy products, faecal carriage of Streptococcus infantarius subsp. Infantarius and colorectal adenocarcinoma in Kenya. Acta tropica 178, 10–18 (2018).

30. Jans, C. et al. African fermented dairy products - Overview of predominant technologically important microorganisms focusing on African Streptococcus infantarius variants and potential future applications for enhanced food safety and security. International journal of food microbiology 250, 27–36 (2017).

31. Delorme, C. et al. Study of Streptococcus thermophilus population on a world-wide and historical collection by a new MLST scheme. International journal of food microbiology 242, 70–81 (2017).

32. Couvigny, B. et al. Three glycosylated serine-rich repeat proteins play a pivotal role in adhesion and colonization of the pioneer commensal bacterium, Streptococcus salivarius. Environmental microbiology 19, 3579–3594 (2017).

33. Papadimitriou, K., Mavrogonatou, E., Bolotin, A., Tsakalidou, E. & Renault, P. Whole-Genome Sequence of the Cheese Isolate Streptococcus macedonicus 679. Genome announcements 4, (2016).

34. Delorme, C., Abraham, A.-L., Renault, P. & Guédon, E. Genomics of Streptococcus salivarius, a major human commensal. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 33, 381–392 (2015).

35. Couvigny, B. et al. Streptococcus thermophilus Biofilm Formation: A Remnant Trait of Ancestral Commensal Life? PloS one 10, e0128099 (2015).

36. Couvigny, B. et al. Commensal Streptococcus salivarius Modulates PPARγ Transcriptional Activity in Human Intestinal Epithelial Cells. PloS one 10, e0125371 (2015).

37. Papadimitriou, K. et al. Acquisition through horizontal gene transfer of plasmid pSMA198 by Streptococcus macedonicus ACA-DC 198 points towards the dairy origin of the species. PloS one 10, e0116337 (2015).

38. 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).

39. Cheeseman, K. et al. Multiple recent horizontal transfers of a large genomic region in cheese making fungi. Nature communications 5, 2876 (2014).

40. Kaci, G. et al. Anti-inflammatory properties of Streptococcus salivarius, a commensal bacterium of the oral cavity and digestive tract. Applied and environmental microbiology 80, 928–934 (2014).

41. Ceuppens, S. et al. Molecular Methods in Food Safety Microbiology: Interpretation and Implications of Nucleic Acid Detection. Comprehensive reviews in food science and food safety 13, 551–577 (2014).

42. Almeida, M. et al. Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. BMC genomics 15, 1101 (2014).

43. Papadimitriou, K. et al. Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex. BMC genomics 15, 272 (2014).

44. Le Chatelier, E. et al. Richness of human gut microbiome correlates with metabolic markers. Nature 500, 541–546 (2013).

45. Morrison, D. A., Guédon, E. & Renault, P. Competence for natural genetic transformation in the Streptococcus bovis group streptococci S. Infantarius and S. macedonicus. Journal of bacteriology 195, 2612–2620 (2013).

46. Meslier, V., Loux, V. & Renault, P. Genome sequence of Leuconostoc pseudomesenteroides strain 4882, isolated from a dairy starter culture. Journal of bacteriology 194, 6637 (2012).