The journal retracts the 19 July 2019 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 (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.
Correction note
This Retraction Notice has been corrected with minor changes to include relevant references.
Footnotes
Approved by: Aleksandra Barac, University of Belgrade, Serbia
References
- 1.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) 31:100585. doi: 10.1016/j.nmni.2019.100585 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Bellali S, Bou Khalil J, Fontanini A, Raoult D, Lagier JC. A new protectant medium preserving bacterial viability after freeze drying. Microbiol Res. (2020) 236:126454. doi: 10.1016/j.micres.2020.126454 [DOI] [PubMed] [Google Scholar]
- 3.Afouda P, Hocquart M, Pham TPT, Kuete E, Ngom II, Dione N, et al. Alcohol pretreatment of stools effect on culturomics. Sci Rep. (2020) 10:5190. doi: 10.1038/s41598-020-62068-x [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.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. (2019) 10:1606. doi: 10.3389/fmicb.2019.01606 [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
- 5.Takakura T, Francis R, Anani H, Bilen M, Raoult D, Bou Khalil JY. Anaerosphaera massiliensis sp. nov, a new bacterium isolated from the stool of a 39-year-old pygmy. New Microbes New Infect. (2020) 33:100633. doi: 10.1016/j.nmni.2019.100633 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.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) 31:100588. doi: 10.1016/j.nmni.2019.100588 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.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) 31:100568. doi: 10.1016/j.nmni.2019.100568 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.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) 32:100598. doi: 10.1016/j.nmni.2019.100598 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.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) 23:44–7. doi: 10.1016/j.nmni.2018.02.003 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Guindo CO, Terrer E, Chabrière E, Aboudharam G, Drancourt M, Grine G. Culture of salivary methanogens assisted by chemically produced hydrogen. Anaerobe. (2020) 61:102128. doi: 10.1016/j.anaerobe.2019.102128 [DOI] [PubMed] [Google Scholar]
- 11.Dubourg G, Morand A, Mekhalif F, Godefroy R, Corthier A, Yacouba A, et al. Deciphering the urinary microbiota repertoire by culturomics reveals mostly anaerobic bacteria from the gut. Front Microbiol. (2020) 11:513305. doi: 10.3389/fmicb.2020.513305 [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
- 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) 112:905–18. doi: 10.1007/s10482-018-01223-x [DOI] [PubMed] [Google Scholar]
- 13.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) 17:45–51. doi: 10.1016/j.nmni.2017.01.010 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.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) 38:100799. doi: 10.1016/j.nmni.2020.100799 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Hassani Y, Brégeon F, Aboudharam G, Drancourt M, Grine G. Detection of Methanobrevobacter smithii and Methanobrevibacter oralis in lower respiratory tract microbiota. Microorganisms. (2020) 8:1866. doi: 10.3390/microorganisms8121866 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16.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) 32:100600. doi: 10.1016/j.nmni.2019.100600 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17.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) 14:e0223543. doi: 10.1371/journal.pone.0223543 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 18.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. Res Sq. (2021). Available online at: https://www.researchsquare.com/article/rs-238204/v1 doi: 10.21203/rs.3.rs-238204/v1 (Accessed June 6, 2025). [DOI]
- 19.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) 20:51–4. doi: 10.1016/j.nmni.2017.08.006 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 20.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) 25:27–9. doi: 10.1016/j.nmni.2018.06.002 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 21.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) 25:1561.e1–5. doi: 10.1016/j.cmi.2019.04.008 [DOI] [PubMed] [Google Scholar]
- 22.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) 13:e0191913. doi: 10.1371/journal.pone.0191913 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 23.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) 9:12807. doi: 10.1038/s41598-019-49189-8 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 24.Mbogning Fonkou MD, Bilen M, Gouba N, Khelaifia S, Cadoret F, Nguyen TT, et al. Non-contiguous finished genome sequencing and description of Enterococcus timonensis sp. nov isolated from human sputum. New Microbes New Infect. (2019) 29:100532. doi: 10.1016/j.nmni.2019.100532 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 25.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) 26:73–88. doi: 10.1016/j.nmni.2018.06.006 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 26.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) 112:785–96. doi: 10.1007/s10482-018-01212-0 [DOI] [PubMed] [Google Scholar]
- 27.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) 10:9674. doi: 10.1038/s41598-020-66738-8 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 28.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) 369:fnac086. doi: 10.1093/femsle/fnac086 [DOI] [PubMed] [Google Scholar]
- 29.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) 34:100639. doi: 10.1016/j.nmni.2019.100639 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 30.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. Res Sq. (2020). Available online at: https://www.researchsquare.com/article/rs-117420/v1 doi: 10.21203/rs.3.rs-117420/v1 (Accessed June 6, 2025). [DOI]
- 31.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) 32:100607. doi: 10.1016/j.nmni.2019.100607 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 32.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) 32:100606. doi: 10.1016/j.nmni.2019.100606 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 33.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) 369:fnac066. doi: 10.1093/femsle/fnac066 [DOI] [PubMed] [Google Scholar]
- 34.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) 12:21747. doi: 10.1038/s41598-022-25873-0 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 35.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) 7:16788. doi: 10.1038/s41598-017-17132-4 [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
- 36.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) 8:9447. doi: 10.1038/s41598-018-27862-8 [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
- 37.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) 8:9197. doi: 10.1038/s41598-018-27372-7 [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
- 38.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) 56:10.1128/jcm.01663-17. doi: 10.1128/JCM.01663-17 [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
- 39.Bellali S, Lagier JC, Million M, Anani H, Haddad G, Francis R, et al. Running after ghosts: are dead bacteria the dark matter of the human gut microbiota? Gut Microbes. (2021) 13:1897208. doi: 10.1080/19490976.2021.1897208 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 40.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) 111:1225–36. doi: 10.1007/s10482-018-1032-x [DOI] [PubMed] [Google Scholar]
- 41.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) 31:100567. doi: 10.1016/j.nmni.2019.100567 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 42.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) 14:e0213338. doi: 10.1371/journal.pone.0213338 [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
- 43.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) 6:ofz398. doi: 10.1093/ofid/ofz398 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 44.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) 32:100615. doi: 10.1016/j.nmni.2019.100615 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 45.Francis R, Anani H, Fontanini A, Fournier PE, Scola BLA, Raoult D, et al. Virgibacillus ndiopensis sp. nov, a new halophilic bacterium isolated from the stool of a healthy 11-year-old boy. New Microbes New Infect. (2019) 30:100541. doi: 10.1016/j.nmni.2019.100541 [DOI] [PMC free article] [PubMed] [Google Scholar]
