RETRACTION article
Front. Microbiol.
Sec. Systems Microbiology
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1654647
Retraction: Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut
Provisionally accepted- Frontiers Media SA, Lausanne, Switzerland
Select one of your emails
You have multiple emails registered with Frontiers:
Notify me on publication
Please enter your email address:
If you already have an account, please login
You don't have a Frontiers account ? You can register here
A Retraction of the Original Research ArticleDeciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the GutBy Dubourg G, Morand A, Mekhalif F, Godefroy R, Corthier A, Yacouba A, Diakite A, Cornu F, Cresci M, Brahimi S, Caputo A, Lechevallier E, Tsimaratos M, Moal V, Lagier J-C and Raoult D (2020) Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut. Front. Microbiol. 11:513305. doi: 10.3389/fmicb.2020.513305Following publication, it was brought to our attention that the ethical approval for this study referred to the same ethics approval number 2016-011 that had been used across a series of unrelated published studies (1–45). It remains unclear whether appropriate ethics provisions, in line with Frontiers Policies and Publication Ethics policies were adhered to.The authors and a representative of Aix-Marseille Université Ethics Committee were not able to address all our concerns. As such, this article is retracted.This retraction was approved by the Chief Executive Editor of Frontiers. The authors do not agree with this retraction.References:1. Amrane S, Hocquart M, Afouda P, Kuete E, Pham TPT, Dione N, et al. Metagenomic and culturomic analysis of gut microbiota dysbiosis during Clostridium difficile infection. Sci Rep. 2019 Sep 5;9(1):12807. 2. Hamad I, Abdallah RA, Ravaux I, Mokhtari S, Tissot-Dupont H, Michelle C, et al. Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients. PLOS ONE. 2018 Jan 31;13(1):e0191913. 3. Traore SI, Khelaifia S, Armstrong N, Lagier JC, Raoult D. Isolation and culture of Methanobrevibacter smithii by co-culture with hydrogen-producing bacteria on agar plates. Clin Microbiol Infect. 2019 Dec 1;25(12):1561.e1-1561.e5. 4. Fall NS, Raoult D, Sokhna C, Lagier JC. ‘Helcococcus massiliensis’ sp. nov., a new bacterial species isolated from the vaginal sample of a woman with bacterial vaginosis living in Dielmo, Senegal. New Microbes New Infect. 2018 Sep 1;25:27–9. 5. Senghor B, Khelaifia S, Bassène H, Seck EH, Fournier PE, Sokhna C, et al. ‘Gracilibacillus phocaeensis’ sp. nov., ‘Sediminibacillus massiliensis’ sp. nov. and ‘Virgibacillus ndiopensis’ sp. nov., three halophilic species isolated from salty human stools by culturomics. New Microbes New Infect. 2017 Nov 1;20:51–4. 6. Naud S, Hasni I, Bellali S, Kieu HT, Lo CI, Anani H, et al. Genomic and phenotypic description of Streptococcus resistens sp. nov., Streptococcus buccae sp. nov. and Streptococcus mediterraneus sp. nov., three new members of the Streptococcus genus isolated from the human oral cavity [Internet]. Research Square; 2021 [cited 2025 Jun 6]. Available from: https://www.researchsquare.com/article/rs-238204/v17. Diakite A, Dubourg G, Dione N, Afouda P, Bellali S, Ngom II, et al. Extensive culturomics of 8 healthy samples enhances metagenomics efficiency. PLOS ONE. 2019 Oct 21;14(10):e0223543. 8. Takakura T, Francis R, Anani H, Naud S, Raoult D, Bou Khalil JY. Dorea phocaeensis sp. nov., a new bacterium isolated from the stool of a healthy 29-year-old male. New Microbes New Infect. 2019 Nov 1;32:100600. 9. Hassani Y, Brégeon F, Aboudharam G, Drancourt M, Grine G. Detection of Methanobrevobacter smithii and Methanobrevibacter oralis in Lower Respiratory Tract Microbiota. Microorganisms. 2020 Dec;8(12):1866. 10. Ngom II, Hasni I, Senghor B, Lo CI, Armstrong N, Sokhna C, et al. Description of Gracilibacillus phocaeensis sp. nov., a new halophilic bacterium isolated from Senegalian human stool. New Microbes New Infect. 2020 Nov 1;38:100799. 11. Senghor B, Seck EH, Khelaifia S, Bassène H, Sokhna C, Fournier PE, et al. Description of ‘Bacillus dakarensis’ sp. nov., ‘Bacillus sinesaloumensis’ sp. nov., ‘Gracilibacillus timonensis’ sp. nov., ‘Halobacillus massiliensis’ sp. nov., ‘Lentibacillus massiliensis’ sp. nov., ‘Oceanobacillus senegalensis’ sp. nov., ‘Oceanobacillus timonensis’ sp. nov., ‘Virgibacillus dakarensis’ sp. nov. and ‘Virgibacillus marseillensis’ sp. nov., nine halophilic new species isolated from human stool. New Microbes New Infect. 2017 May 1;17:45–51. 12. Afouda P, Traore SI, Dione N, Andrieu C, Tomei E, Richez M, et al. Description and genomic characterization of Massiliimalia massiliensis gen. nov., sp. nov., and Massiliimalia timonensis gen. nov., sp. nov., two new members of the family Ruminococcaceae isolated from the human gut. Antonie Van Leeuwenhoek. 2019 Jun 1;112(6):905–18. 13. Guindo CO, Terrer E, Chabrière E, Aboudharam G, Drancourt M, Grine G. Culture of salivary methanogens assisted by chemically produced hydrogen. Anaerobe. 2020 Feb 1;61:102128. 14. Dione N, Ngom II, Valles C, Cadoret F, Fournier PE, Raoult D, et al. ‘Collinsella provencensis’ sp. nov., ‘Parabacteroides bouchesdurhonensis’ sp. nov. and ‘Sutterella seckii,’ sp. nov., three new bacterial species identified from human gut microbiota. New Microbes New Infect. 2018 May 1;23:44–7. 15. Yimagou EK, Tall ML, Baudoin JP, Raoult D, Bou Khalil JY. Clostridium transplantifaecale sp. nov., a new bacterium isolated from patient with recurrent Clostridium difficile infection. New Microbes New Infect. 2019 Nov 1;32:100598. 16. Kuete E, Mbogning Fonkou MD, Mekhalif F, Anani H, Baudoin JP, Raoult D, et al. Brachybacterium timonense sp. nov., a new bacterium isolated from human sputum. New Microbes New Infect. 2019 Sep 1;31:100568. 17. Mekhalif F, Tidjani Alou M, Zgheib R, Lo CI, Fournier PE, Raoult D, et al. Brachybacterium massiliense sp. nov., a new bacterium isolated from stool from a healthy Senegalese child. New Microbes New Infect. 2019 Sep 1;31:100588. 18. Fall NS, Lo CI, Fournier PE, Sokhna C, Raoult D, Fenollar F, et al. Arcanobacterium ihumii sp. nov., Varibaculum vaginae sp. nov. and Tessaracoccus timonensis sp. nov., isolated from vaginal swabs from healthy Senegalese women. New Microbes New Infect. 2019 Sep 1;31:100585. 19. Takakura T, Francis R, Anani H, Bilen M, Raoult D, Bou Khalil JY. Anaerosphaera massiliensissp. nov., a new bacterium isolated from the stool of a 39-year-old Pygmy. New Microbes New Infect. 2020 Jan 1;33:100633. 20. Bellali S, Lagier JC, Raoult D, Bou Khalil J. Among Live and Dead Bacteria, the Optimization of Sample Collection and Processing Remains Essential in Recovering Gut Microbiota Components. Front Microbiol [Internet]. 2019 Jul 10 [cited 2025 Jun 6];10. Available from: https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.01606/full21. Afouda P, Hocquart M, Pham TPT, Kuete E, Ngom II, Dione N, et al. Alcohol pretreatment of stools effect on culturomics. Sci Rep. 2020 Mar 23;10(1):5190. 22. Bellali S, Bou Khalil J, Fontanini A, Raoult D, Lagier JC. A new protectant medium preserving bacterial viability after freeze drying. Microbiol Res. 2020 Jun 1;236:126454. 23. Mbogning Fonkou MD, Bilen M, Gouba N, Khelaifia S, Cadoret F, Nguyen TT, et al. Noncontiguous finished genome sequencing and description of Enterococcus timonensis sp. nov. isolated from human sputum. New Microbes New Infect. 2019 May 1;29:100532. 24. Andrieu C, Mailhe M, Ricaboni D, Fonkou MDM, Bilen M, Cadoret F, et al. Noncontiguous finished genome sequences and description of Bacteroides mediterraneensis sp. nov., Bacteroides ihuae sp. nov., Bacteroides togonis sp. nov., Bacteroides ndongoniae sp. nov., Bacteroides ilei sp. nov. and Bacteroides congonensis sp. nov. identified by culturomics. New Microbes New Infect. 2018 Nov 1;26:73–88. 25. Senghor B, Bassène H, Khelaifia S, Robert C, Fournier PE, Ruimy R, et al. Oceanobacillus timonensis sp. nov. and Oceanobacillus senegalensis sp. nov., two new moderately halophilic, Gram-stain positive bacteria isolated from stools sample of healthy young Senegalese. Antonie Van Leeuwenhoek. 2019 May 1;112(5):785–96. 26. Diakite A, Dubourg G, Dione N, Afouda P, Bellali S, Ngom II, et al. Optimization and standardization of the culturomics technique for human microbiome exploration. Sci Rep. 2020 Jun 15;10(1):9674. 27. Maaloum M, Lo CI, Ndongo S, Meng MM, Saile R, Alibar S, et al. Ottowia massiliensis sp. nov., a new bacterium isolated from a fresh, healthy human fecal sample. FEMS Microbiol Lett. 2022 Feb 22;369(1):fnac086. 28. Yimagou EK, Dione N, Ngom II, Tall ML, Baudoin JP, Raoult D, et al. Parabacteroides bouchesdurhonensis sp. nov., a new bacterium isolated from the stool of a healthy adult. New Microbes New Infect. 2020 Mar 1;34:100639. 29. BELKACEMI S, ALOU MT, MILLION M, LEVASSEUR A, KHELAIFIA S, RAOULT D. Prevalence of Treponema species in the Gut Microbiome is Linked to Bifidobacterium sp. and Bacteroides sp. [Internet]. Research Square; 2020 [cited 2025 Jun 6]. Available from: https://www.researchsquare.com/article/rs-117420/v130. Anani H, Guilhot E, Andrieu C, Fontanini A, Raoult D, Fournier PE. Prevotella ihumii sp. nov., a new bacterium isolated from a stool specimen of a healthy woman. New Microbes New Infect. 2019 Nov 1;32:100607. 31. Kuete Yimagou E, Mekhalif F, Lamine Tall M, Baudoin JP, Raoult D, Bou Khalil JY. Prevotella marseillensis sp. nov., a new bacterium isolated from a patient with recurrent Clostridium difficile infection. New Microbes New Infect. 2019 Nov 1;32:100606. 32. Maaloum M, Afouda P, Lo CI, Dubourg G, Nguyen TT, Levasseur A, et al. Prevotella merdae sp. nov., a new bacterial species isolated from human faeces. FEMS Microbiol Lett. 2022 Feb 22;369(1):fnac066. 33. Ndongo S, Armstrong N, Raoult D, Fournier PE. Reclassification of eight Akkermansia muciniphila strains and description of Akkermansia massiliensis sp. nov. and Candidatus Akkermansia timonensis, isolated from human feces. Sci Rep. 2022 Dec 16;12(1):21747. 34. Hamad I, Ranque S, Azhar EI, Yasir M, Jiman-Fatani AA, Tissot-Dupont H, et al. RETRACTED ARTICLE: Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota. Sci Rep. 2017 Dec 1;7(1):16788. 35. Belkacemi S, Mazel A, Tardivo D, Tavitian P, Stephan G, Bianca G, et al. RETRACTED ARTICLE: Peri-implantitis-associated methanogens: a preliminary report. Sci Rep. 2018 Jun 21;8(1):9447. 36. Grine G, Terrer E, Boualam MA, Aboudharam G, Chaudet H, Ruimy R, et al. RETRACTED ARTICLE: Tobacco-smoking-related prevalence of methanogens in the oral fluid microbiota. Sci Rep. 2018 Jun 15;8(1):9197. 37. Amrane S, Bachar D, Lagier JC, Raoult D. RETRACTED: Clostridium scindens Is Present in the Gut Microbiota during Clostridium difficile Infection: a Metagenomic and Culturomic Analysis. J Clin Microbiol. 2018 Apr 25;56(5):10.1128/jcm.01663-17. 38. Bellali S, Lagier ,Jean-Christophe, Million ,Matthieu, Anani ,Hussein, Haddad ,Gabriel, Francis ,Rania, et al. Running after ghosts: are dead bacteria the dark matter of the human gut microbiota? Gut Microbes. 2021 Jan 1;13(1):1897208. 39. Senghor B, Bassène H, Khelaifia S, Robert C, Fournier PE, Ruimy R, et al. Sediminibacillus massiliensis sp. nov., a moderately halophilic, Gram-positive bacterium isolated from a stool sample of a young Senegalese man. Antonie Van Leeuwenhoek. 2018 Jul1;111(7):1225–36. 40. Kuete E, Mbogning Fonkou MD, Mekhalif F, Anani H, Baudoin JP, Raoult D, et al. Selenomonas felix sp. nov., a new bacterium isolated from human sputum. New Microbes New Infect. 2019 Sep 1;31:100567. 41. Benabdelkader S, Andreani J, Gillet A, Terrer E, Pignoly M, Chaudet H, et al. Specific clones of Trichomonas tenax are associated with periodontitis. PLOS ONE. 2019 Mar 11;14(3):e0213338. 42. Hocquart M, Pham T, Kuete E, Tomei E, Lagier JC, Raoult D. Successful Fecal Microbiota Transplantation in a Patient Suffering From Irritable Bowel Syndrome and Recurrent Urinary Tract Infections. Open Forum Infect Dis. 2019 Oct 1;6(10):ofz398. 43. Grine G, Royer A, Terrer E, Diallo OO, Drancourt M, Aboudharam G. Tobacco Smoking Affects the Salivary Gram-Positive Bacterial Population. Front Public Health [Internet]. 2019 Jul 19 [cited 2025 Jun 6];7. Available from: https://www.frontiersin.org/journals/publichealth/articles/10.3389/fpubh.2019.00196/full44. Yimagou EK, Anani H, Yacouba A, Hasni I, Baudoin JP, Raoult D, et al. Urinicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from a human urine sample from a 7-year-old boy hospitalized for dental care. New Microbes New Infect. 2019 Nov1;32:100615. 45. Francis R, Anani H, Fontanini A, Fournier PE, Scola BLA, Raoult D, et al. Virgibacillusndiopensis sp. nov., a new halophilic bacterium isolated from the stool of a healthy 11-yearold boy. New Microbes New Infect. 2019 Jul 1;30:100541.
Keywords: Urine, microbiota, culturomics, Bladder, culture
Received: 26 Jun 2025; Accepted: 27 Jun 2025.
Copyright: © 2025 Editorial Office. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Frontiers Editorial Office, Frontiers Media SA, Lausanne, Switzerland
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.