Tobacco-smoking-related prevalence of methanogens in the oral fluid microbiota
Authors: Hervé Chaudet
Elodie Terrer
Gérard Aboudharam
Ghiles Grine
Michel Drancourt
Raymond Ruimy
Mahmoud Abdelwadoud Boualam
Journal: Scientific Reports (2018)
Discipline: Multidisciplinary
Keywords: oral fluid microbiome; archaea; methanogenic archaea; Methanobrevibacter oralis; Methanobrevibacter smithii
Affiliations: Aix Marseille Université, MEPHI, IRD, IHU Méditerranée Infection, Marseille, France., Pôle Odontologie, Assistance Publique - Hôpitaux de Marseille, Marseille, France., Faculté d'odontologie, Université d'Aix Marseille, Marseille, France., Laboratoire de bactériologie, Centre Hospitalier Universitaire de Nice, Hôpital de l'Archet II, Université Côte d'Azur, INSERM U1065, C3M, Team 6, Nice, France., Aix Marseille Université, MEPHI, IRD, IHU Méditerranée Infection, Marseille, France. .

Abstract:  The oral fluid microbiome comprises an important bacterial diversity, yet the presence of archaea has not been reported so far. In order to quest for the presence of methanogenic archaea (methanogens) in oral fluid, we used a polyphasic approach including PCR-sequencing detection, microscopic observation by fluorescence in-situ hybridization, isolation and culture, molecular identification and genotyping of methanogens in 200 oral fluid specimens. In the presence of negative controls, 64/200 (32%) prospectively analysed oral fluid specimens were PCR-positive for methanogens, all identified as Methanobrevibacter oralis by sequencing. Further, fluorescence in-situ hybridization detected methanogens in 19/48 (39.6%) investigated specimens; with morphology suggesting M. oralis in 10 cases and co-infecting Methanobrevibacter smithii in nine cases. M. oralis was cultured from 46/64 (71.8%) PCR-positive specimens and none of PCR-negative specimens; and one M. smithii isolate was co-cultured with M. oralis in one specimen. Multispacer Sequence Typing found one M. oralis genotype per specimen and a total of five different genotypes with 19/46 (41%) of isolates all belonging to spacer-type four. Statistical analyses showed a significant correlation between the PCR-detection of methanogens in oral fluid and tobacco smoking. These data indicate that M. oralis and M. smithii are oral fluid-borne methanogens in tobacco smokers. Both methanogens could be transmitted during intimate contacts such as mother-to-child contacts and kissing. 

Retracted: No

PubPeer comments:
 Figure 6a has two images which appear to overlap, suggesting that both were taken at the same time interval, rather than 24 hours apart as labeled. Could the authors examine the original images to check? *** Closeup ![file] *** Full figure ![file] , 
 Dear Editor, Dear reviewer, We thank you for your in depth analyses and peer post publication review . Figure 6a has two images which appear to overlap, suggesting that both were taken at the same time interval, rather than 24 hours apart as labeled. Could the authors examine the original images to check? The comment is correct we were analyzing all the recorded images, and in fact the panel was using a 48h image twice. We apologize for this and we are sending the new paneal and all the orginal images that show the photo reproduced twice and the one that should be inserted. Can we insert an errata corrige? Or how can we correct the published manuscript adding the right image panel? For this reason, we revised the panel image replacing the uncorrected picture by the original one. We confirm that the mistake occurred in preparing the panel did not affect the results obtained and discussed in the published article. In fact, at least 3 of the authors were analyzing 5-6 images per well (each treatment was in triplicate) per time of incubation and the outcomes reported are only considering the panel as representative of average behavior of the cells with the diverse treatments. We are sending to the journal , responding to Dr Sathya e-mail the new figure and teh original correct images , 
 Published 25 Jul 2020 In the article titled u201cNovel Hybrid Gels Made of High and Low Molecular Weight Hyaluronic Acid Induce Proliferation and Reduce Inflammation in an Osteoarthritis In Vitro Model Based on Human Synoviocytes and Chondrocytesu201d [1], there was an error in Figure 6. In the part of Figure 6(a), u201cHCC u2013 24hu201d is incorrect. The corrected figure is shown below, and is listed as Figure 1: ![file] , 
 Although missed by me in my initial review, the corrected figure appears to have another set of images which overlap. *** ![file] , 
 Sent to me via email: u201cDear PubPeer user, I would like to thank you again for making us aware of your concerns with the Figures. Having assessed these with the editorial board, it has been determined to retract the article. Please do not hesitate to contact me if I can be of any further assistance.u201d , 
 Retraction, February 2022: https: www.hindawi.com journals bmri 2022 9873639  BioMed Research International has retracted the article titled u201cNovel Hybrid Gels Made of High and Low Molecular Weight Hyaluronic Acid Induce Proliferation and Reduce Inflammation in an Osteoarthritis In Vitro Model Based on Human Synoviocytes and Chondrocytesu201d [1], due to concerns with the reliability of the data. In January 2020, the journal was made aware of concerns with figure duplications as noted on PubPeer [2]. The journal proceeded to investigate these concerns, however, the authors separately contacted the editorial office to request a corrigendum, which was published without consideration of the ongoing investigation [3]. The figure duplications identified are as follows: (i)tIn Figure 6(a), the 24u2009h and 48u2009h panels for HCC are overlapping (ii)tIn Figure 6(a), the 72u2009h and 96u2009h panels for H-HA are overlapping Following the conclusion of our investigation, which has also resulted in the retraction of another article [4], the article is being retracted from the journal with the agreement of the editorial board. The authors do not agree to the retraction and the notice. ,