Your new experience awaits. Try the new design now and help us make it even better

RETRACTION article

Front. Microbiol., 07 July 2025

Sec. Systems Microbiology

Volume 16 - 2025 | https://doi.org/10.3389/fmicb.2025.1654647

Retraction: Deciphering the urinary microbiota repertoire by culturomics reveals mostly anaerobic bacteria from the gut

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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).

Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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.

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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)

Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

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

PubMed Abstract | Crossref Full Text | Google Scholar

Yimagou, E. K., Tall, M. L., Baudoin, J. P., Raoult, D., and Bou Khalil, J. Y. (2019a). Clostridium transplantifaecale sp. nov., a new bacterium isolated from patient with recurrent Clostridium difficile infection. New Microbes New Infect. 32:100598. doi: 10.1016/j.nmni.2019.100598

PubMed Abstract | Crossref Full Text | Google Scholar

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, Switzerland

Copyright © 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==

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.