A Retraction of the Original Research Article
Deciphering the urinary microbiota repertoire by culturomics reveals mostly anaerobic bacteria from the gut
by 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). Front. Microbiol. 11:513305. doi: 10.3389/fmicb.2020.513305
The journal retracts the October 16 2020 article cited above.
Following 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 (Afouda et al., 2020, 2019; Amrane et al., 2018, 2019; Anani et al., 2019; Andrieu et al., 2018; Belkacemi et al., 2020, 2018; Bellali et al., 2020, 2021, 2019; Benabdelkader et al., 2019; Diakite et al., 2019, 2020; Dione et al., 2018; Fall et al., 2019, 2018; Francis et al., 2019; Grine et al., 2019, 2018; Guindo et al., 2020; Hamad et al., 2018, 2017; Hassani et al., 2020; Hocquart et al., 2019; Kuete Yimagou et al., 2019; Kuete et al., 2019a,b; Maaloum et al., 2022b,a; Mbogning Fonkou et al., 2019; Mekhalif et al., 2019; Naud et al., 2021; Ndongo et al., 2022; Ngom et al., 2020; Senghor et al., 2018, 2019, 2017b,a; Takakura et al., 2020, 2019; Traore et al., 2019; Yimagou et al., 2019b, 2020, 2019a). 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
Afouda, P., Hocquart, M., Pham, T. P. T., Kuete, E., Ngom, I. I., Dione, N., et al. (2020). Alcohol pretreatment of stools effect on culturomics. Sci Rep. 10, 5190. doi: 10.1038/s41598-020-62068-x
Afouda, P., Traore, S. I., Dione, N., Andrieu, C., Tomei, E., Richez, M., et al. (2019). 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. 112, 905–918. doi: 10.1007/s10482-018-01223-x
Amrane, S., Bachar, D., Lagier, J. C., and Raoult, D. (2018). Clostridium scindens is present in the gut microbiota during Clostridium difficile infection: a metagenomic and Culturomic analysis. J. Clin. Microbiol. 56:17. doi: 10.1128/JCM.01663-17
Amrane, S., Hocquart, M., Afouda, P., Kuete, E., Pham, T. P. T., Dione, N., et al. (2019). Metagenomic and culturomic analysis of gut microbiota dysbiosis during Clostridium difficile infection. Sci Rep. 9:12807. doi: 10.1038/s41598-019-49189-8
Anani, H., Guilhot, E., Andrieu, C., Fontanini, A., Raoult, D., Fournier, P. E., et al. (2019). Prevotella ihumii sp. nov., a new bacterium isolated from a stool specimen of a healthy woman. New Microbes New Infect. 32, 100607. doi: 10.1016/j.nmni.2019.100607
Andrieu, C., Mailhe, M., Ricaboni, D., Fonkou, M. D. M., Bilen, M., Cadoret, F., et al. (2018). 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. 26, 73–88. doi: 10.1016/j.nmni.2018.06.006
Belkacemi, S., Alou M, T., Million, M., Levasseur, A., Khelaifia, S., and Raoult, D. (2020). Prevalence of Treponema species in the Gut Microbiome is Linked to Bifidobacterium sp. and Bacteroides sp. Research Square. Available online at: https://www.researchsquare.com/article/rs-117420/ (Accessed June 6, 2025).
Belkacemi, S., Mazel, A., Tardivo, D., Tavitian, P., Stephan, G., Bianca, G., et al. (2018). RETRACTED ARTICLE: Peri-implantitis-associated methanogens: a preliminary report. Sci Rep. 8:9447. doi: 10.1038/s41598-018-27862-8
Bellali, S., Bou Khalil, J., Fontanini, A., Raoult, D., and Lagier, J. C. A. (2020). A new protectant medium preserving bacterial viability after freeze drying. Microbiol Res. 236, 126454. doi: 10.1016/j.micres.2020.126454
Bellali, S., Lagier, J. C., Million, M., Anani, H., Haddad, G., Francis, R., et al. (2021). Running after ghosts: are dead bacteria the dark matter of the human gut microbiota? Gut Microbes. 13:1897208. doi: 10.1080/19490976.2021.1897208
Bellali, S., Lagier, J. C., Raoult, D., and Bou Khalil, J. (2019). Among live and dead bacteria, the optimization of sample collection and processing remains essential in recovering gut microbiota components. Front Microbiol. 10:01606. doi: 10.3389/fmicb.2019.01606
Benabdelkader, S., Andreani, J., Gillet, A., Terrer, E., Pignoly, M., Chaudet, H., et al. (2019). Specific clones of Trichomonas tenax are associated with periodontitis. PLoS ONE. 14:e0213338. doi: 10.1371/journal.pone.0213338
Diakite, A., Dubourg, G., Dione, N., Afouda, P., Bellali, S., Ngom, I. I., et al. (2019). Extensive culturomics of 8 healthy samples enhances metagenomics efficiency. PLoS ONE. 14:e0223543. doi: 10.1371/journal.pone.0223543
Diakite, A., Dubourg, G., Dione, N., Afouda, P., Bellali, S., Ngom, I. I., et al. (2020). Optimization and standardization of the culturomics technique for human microbiome exploration. Sci Rep. 10:9674. doi: 10.1038/s41598-020-66738-8
Dione, N., Ngom, I. I., Valles, C., Cadoret, F., Fournier, P. E., Raoult, D., et al. (2018). ‘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. 23, 44–47. doi: 10.1016/j.nmni.02, 003.
Fall, N. S., Lo, C. I., Fournier, P. E., Sokhna, C., Raoult, D., Fenollar, F., et al. (2019). 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. 31, 100585. doi: 10.1016/j.nmni.2019.100585
Fall, N. S., Raoult, D., Sokhna, C., and Lagier, J. C. (2018). ‘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. 25, 27–29. doi: 10.1016/j.nmni.2018.06.002
Francis, R., Anani, H., Fontanini, A., Fournier, P. E., Scola, B. L. A., Raoult, D., et al. (2019). Virgibacillus ndiopensis sp. nov., a new halophilic bacterium isolated from the stool of a healthy 11-year-old boy. New Microbes New Infect. 30:100541. doi: 10.1016/j.nmni.2019.100541
Grine, G., Royer, A., Terrer, E., Diallo, O. O., Drancourt, M., Aboudharam, G., et al. (2019). Tobacco smoking affects the salivary gram-positive bacterial population. Front. Public Health 7:00196. doi: 10.3389/fpubh.2019.00196
Grine, G., Terrer, E., Boualam, M. A., Aboudharam, G., Chaudet, H., Ruimy, R., et al. (2018). RETRACTED ARTICLE: Tobacco-smoking-related prevalence of methanogens in the oral fluid microbiota. Sci Rep. 8:9197. doi: 10.1038/s41598-018-27372-7
Guindo, C. O., Terrer, E., Chabrière, E., Aboudharam, G., Drancourt, M., Grine, G., et al. (2020). Culture of salivary methanogens assisted by chemically produced hydrogen. Anaerobe. 61:102128. doi: 10.1016/j.anaerobe.2019.102128
Hamad, I., Abdallah, R. A., Ravaux, I., Mokhtari, S., Tissot-Dupont, H., Michelle, C., et al. (2018). Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients. PLoS ONE. 13:e0191913. doi: 10.1371/journal.pone.0191913
Hamad, I., Ranque, S., Azhar, E. I., Yasir, M., Jiman-Fatani, A. A., Tissot-Dupont, H., et al. (2017). RETRACTED ARTICLE: Culturomics and amplicon-based metagenomic approaches for the study of fungal population in human gut microbiota. Sci Rep. 7:16788. doi: 10.1038/s41598-017-17132-4
Hassani, Y., Brégeon, F., Aboudharam, G., Drancourt, M., and Grine, G. (2020). Detection of Methanobrevobacter smithii and Methanobrevibacter oralis in lower respiratory tract microbiota. Microorganisms. 8:1866. doi: 10.3390/microorganisms8121866
Hocquart, M., Pham, T., Kuete, E., Tomei, E., Lagier, J. C., Raoult, D., et al. (2019). Successful fecal microbiota transplantation in a patient suffering from irritable bowel syndrome and recurrent urinary tract infections. Open Forum Infect Dis. 6:ofz398. doi: 10.1093/ofid/ofz398
Kuete Yimagou, E., Mekhalif, F., Lamine Tall, M., Baudoin, J. P., Raoult, D., Bou Khalil, J. Y., et al. (2019). Prevotella marseillensis sp. nov., a new bacterium isolated from a patient with recurrent Clostridium difficile infection. New Microbes New Infect. 32, 100606. doi: 10.1016/j.nmni.2019.100606
Kuete, E., Mbogning Fonkou, M. D., Mekhalif, F., Anani, H., Baudoin, J. P., Raoult, D., et al. (2019a). Brachybacterium timonense sp. nov., a new bacterium isolated from human sputum. New Microbes New Infect. 31:100568. doi: 10.1016/j.nmni.2019.100568
Kuete, E., Mbogning Fonkou, M. D., Mekhalif, F., Anani, H., Baudoin, J. P., Raoult, D., et al. (2019b). Selenomonas felix sp. nov., a new bacterium isolated from human sputum. New Microbes New Infect. 31, 100567. doi: 10.1016/j.nmni.2019.100567
Maaloum, M., Afouda, P., Lo, C. I., Dubourg, G., Nguyen, T. T., Levasseur, A., et al. (2022b). Prevotella merdae sp. nov., a new bacterial species isolated from human faeces. FEMS Microbiol Lett. 369:fnac066. doi: 10.1093/femsle/fnac066
Maaloum, M., Lo, C. I., Ndongo, S., Meng, M. M., Saile, R., Alibar, S., et al. (2022a). Ottowia massiliensis sp. nov., a new bacterium isolated from a fresh, healthy human fecal sample. FEMS Microbiol Lett. 369:fnac086. doi: 10.1093/femsle/fnac086
Mbogning Fonkou, M. D., Bilen, M., Gouba, N., Khelaifia, S., Cadoret, F., Nguyen, T. T., et al. (2019). Non-contiguous finished genome sequencing and description of Enterococcus timonensis sp. nov. isolated from human sputum. New Microbes New Infect. 29, 100532. doi: 10.1016/j.nmni.2019.100532
Mekhalif, F., Tidjani Alou, M., Zgheib, R., Lo, C. I., Fournier, P. E., Raoult, D., et al. (2019). Brachybacterium massiliense sp. nov., a new bacterium isolated from stool from a healthy Senegalese child. New Microbes New Infect. 31:100588. doi: 10.1016/j.nmni.2019.100588
Naud, S., Hasni, I., Bellali, S., Kieu, H. T., Lo, C. I., Anani, H., et al. (2021). 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 Research Square; Available online at: https://www.researchsquare.com/article/rs-238204/v1 (Accessed June 6, 2025)
Ndongo, S., Armstrong, N., Raoult, D., and Fournier, P. E. (2022). Reclassification of eight Akkermansia muciniphila strains and description of Akkermansia massiliensis sp. nov. and Candidatus Akkermansia timonensis, isolated from human feces. Sci Rep. 12, 21747. doi: 10.1038/s41598-022-25873-0
Ngom, I. I., Hasni, I., Senghor, B., Lo, C. I., Armstrong, N., Sokhna, C., et al. (2020). Description of Gracilibacillus phocaeensis sp. nov., a new halophilic bacterium isolated from Senegalian human stool. New Microbes New Infect. 38:100799. doi: 10.1016/j.nmni.2020.100799
Senghor, B., Bassène, H., Khelaifia, S., Robert, C., Fournier, P. E., Ruimy, R., et al. (2018). Sediminibacillus massiliensis sp. nov., a moderately halophilic, Gram-positive bacterium isolated from a stool sample of a young Senegalese man. Antonie Van Leeuwenhoek. 111, 1225–1236. doi: 10.1007/s10482-018-1032-x
Senghor, B., Bassène, H., Khelaifia, S., Robert, C., Fournier, P. E., Ruimy, R., et al. (2019). 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. 112, 785–796. doi: 10.1007/s10482-018-01212-0
Senghor, B., Khelaifia, S., Bassène, H., Seck, E. H., Fournier, P. E., Sokhna, C., et al. (2017b). ‘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. 20, 51–54. doi: 10.1016/j.nmni.2017.08.006
Senghor, B., Seck, E. H., Khelaifia, S., Bassène, H., Sokhna, C., Fournier, P. E., et al. (2017a). 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. 17, 45–51. doi: 10.1016/j.nmni.01.010
Takakura, T., Francis, R., Anani, H., Bilen, M., Raoult, D., Bou Khalil, J. Y., et al. (2020). Anaerosphaera massiliensis sp. nov., a new bacterium isolated from the stool of a 39-year-old Pygmy. New Microbes New Infect. 33:100633. doi: 10.1016/j.nmni.2019.100633
Takakura, T., Francis, R., Anani, H., Naud, S., Raoult, D., Bou Khalil, J. Y., et al. (2019). Dorea phocaeensis sp. nov., a new bacterium isolated from the stool of a healthy 29-year-old male. New Microbes New Infect. 32:100600. doi: 10.1016/j.nmni.2019.100600
Traore, S. I., Khelaifia, S., Armstrong, N., Lagier, J. C., and Raoult, D. (2019). Isolation and culture of Methanobrevibacter smithii by co-culture with hydrogen-producing bacteria on agar plates. Clin. Microbiol. Infect. 25, 1561.e1–1561.e5. doi: 10.1016/j.cmi.2019.04.008
Yimagou, E. K., Anani, H., Yacouba, A., Hasni, I., Baudoin, J. P., Raoult, D., et al. (2019b). 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. 32:100615. doi: 10.1016/j.nmni.2019.100615
Yimagou, E. K., Dione, N., Ngom, I. I., Tall, M. L., Baudoin, J. P., Raoult, D., et al. (2020). Parabacteroides bouchesdurhonensis sp. nov., a new bacterium isolated from the stool of a healthy adult. New Microbes New Infect. 34:100639. doi: 10.1016/j.nmni.2019.100639
Citation: Frontiers Editorial Office (2025) Retraction: Deciphering the urinary microbiota repertoire by culturomics reveals mostly anaerobic bacteria from the gut. Front. Microbiol. 16:1654647. doi: 10.3389/fmicb.2025.1654647
Received: 26 June 2025; Accepted: 27 June 2025;
Published: 07 July 2025.
Approved by:
Frontiers Editorial Office, Frontiers Media SA, SwitzerlandCopyright © 2025 Frontiers 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) and the copyright owner(s) 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, cmVzZWFyY2guaW50ZWdyaXR5QGZyb250aWVyc2luLm9yZw==