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Malat I, Drancourt M, Grine G. Methanobrevibacter smithii cell variants in human physiology and pathology: A review. Heliyon 2024; 10:e36742. [PMID: 39347381 PMCID: PMC11437934 DOI: 10.1016/j.heliyon.2024.e36742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 08/14/2024] [Accepted: 08/21/2024] [Indexed: 10/01/2024] Open
Abstract
Methanobrevibacter smithii (M. smithii), initially isolated from human feces, has been recognised as a distinct taxon within the Archaea domain following comprehensive phenotypic, genetic, and genomic analyses confirming its uniqueness among methanogens. Its diversity, encompassing 15 genotypes, mirrors that of biotic and host-associated ecosystems in which M. smithii plays a crucial role in detoxifying hydrogen from bacterial fermentations, converting it into mechanically expelled gaseous methane. In microbiota in contact with host epithelial mucosae, M. smithii centres metabolism-driven microbial networks with Bacteroides, Prevotella, Ruminococcus, Veillonella, Enterococcus, Escherichia, Enterobacter, Klebsiella, whereas symbiotic association with the nanoarchaea Candidatus Nanopusillus phoceensis determines small and large cell variants of M. smithii. The former translocate with bacteria to induce detectable inflammatory and serological responses and are co-cultured from blood, urine, and tissular abscesses with bacteria, prototyping M. smithii as a model organism for pathogenicity by association. The sources, mechanisms and dynamics of in utero and lifespan M. smithii acquisition, its diversity, and its susceptibility to molecules of environmental, veterinary, and medical interest still have to be deeply investigated, as only four strains of M. smithii are available in microbial collections, despite the pivotal role this neglected microorganism plays in microbiota physiology and pathologies.
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Affiliation(s)
- Ihab Malat
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille-Université, MEPHI, IHU Méditerranée Infection, France
| | - Michel Drancourt
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille-Université, MEPHI, IHU Méditerranée Infection, France
| | - Ghiles Grine
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille-Université, MEPHI, IHU Méditerranée Infection, France
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2
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Zhou C, Ye X, Liu Z, Liu T, Li S, Yang J, Wei J, Yu P, Jia R, Zhao W. Dissecting the causal links between gut microbiome, immune traits and polyp using genetic evidence. Front Immunol 2024; 15:1431990. [PMID: 39346904 PMCID: PMC11427361 DOI: 10.3389/fimmu.2024.1431990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 08/19/2024] [Indexed: 10/01/2024] Open
Abstract
Background Previous research has demonstrated an association between gut microbiota and immune status with the development of several diseases. However, whether these factors contribute to polyps remains unclear. This study aims to use Mendelian randomization (MR) to investigate the causal relationship between gut microbiota and 4 types of polyps (nasal, gallbladder, colon, and gastric polyps), as well as to analyze the mediating role of immune traits. Methods This study utilized large-scale GWAS meta-analyses of gut microbiota (MiBioGen Consortium), 731 immune traits, and 4 types of polyps (one from the FinnGen Consortium and three from the NBDC Human Database). Univariate MR with the inverse variance weighted (IVW) estimation method was employed as the primary analytical approach. A two-step MR analysis was performed to identify potential mediating immune traits. Additionally, multivariable MR approach based on Bayesian model averaging (MR-BMA) was employed to further prioritize gut microbiota and immune traits associated with polyp development. Results Based on IVW method in univariate MR analysis, we identified 39 gut microbial taxa and 135 immune traits significantly causally associated with at least one type of polyp. For nasal polyps, 13 microbial taxa and 61 immune traits were causally associated. After false discovery rate (FDR) correction, CD3 on Central Memory CD8+ T cells and CD3 on CD4 regulatory T cells remained significant. MR-BMA identified 4 gut microbial taxa and 4 immune traits as high priority. For gallbladder polyps, 9 microbial taxa and 30 immune traits were causally associated. MR-BMA identified 8 microbial taxa and 6 immune traits as higher importance. For colon polyps, 6 microbial taxa and 21 immune traits were causally associated. MR-BMA identified 4 microbial taxa and 3 immune traits as higher importance. For gastric polyps, 12 microbial taxa and 33 immune traits were causally associated. Actinobacteria remained significant after FDR correction, and MR-BMA identified 7 gut microbial taxa and 6 immune traits as high priority. We identified 16 causal pathways with mediator directions consistent with the direction of gut microbiome-polyp association. Of these, 6 pathways were associated with the mechanism of nasal polyps, 1 with gallbladder polyps, 2 with colon polyps, and 7 with gastric polyps. Conclusions Our findings shed light on the causal relationships between gut microbiota, immune traits, and polyp development, underscoring the crucial roles of gut microbiota and immune status in polypogenesis. Furthermore, these findings suggest potential applications in polyp prevention, early screening, and the development of effective strategies to reduce polyp risk.
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Affiliation(s)
- Cheng Zhou
- Department of Gastroenterology, Changzhou Hospital of Traditional Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Changzhou, China
| | - Xiaofeng Ye
- Department of Gastroenterology, Changzhou Hospital of Traditional Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Changzhou, China
| | - Zhinuo Liu
- The First College of Clinical Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Tong Liu
- The First College of Clinical Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Shanzheng Li
- The First College of Clinical Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Jinqiu Yang
- The First College of Clinical Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Jingjing Wei
- Heart Center, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Peng Yu
- The First College of Clinical Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Ran Jia
- The First College of Clinical Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Wenxia Zhao
- Department of Gastroenterology, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
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Hassani Y, Aboudharam G, Drancourt M, Grine G. The discovery of Candidatus Nanopusillus phoceensis sheds light on the diversity of the microbiota nanoarchaea. iScience 2024; 27:109488. [PMID: 38595798 PMCID: PMC11001627 DOI: 10.1016/j.isci.2024.109488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/11/2023] [Accepted: 03/08/2024] [Indexed: 04/11/2024] Open
Abstract
To further assess the spectrum of nanoarchaea in human microbiota, we prospectively searched for nanoarchaea in 110 leftover stool specimens, using the complementary approaches of PCR-sequencing screening, fluorescent in situ hybridization, scanning electron microscopy and metagenomics. These investigations yielded a nanoarchaea, Candidatus Nanopusillus phoceensis sp. nov., detected in stool samples by specific PCR-based assays. Microscopic observations indicated its close contact with the archaea Methanobrevibacter smithii. Genomic sequencing revealed 607,775-bp contig with 24.5% G + C content encoding 30 tRNAs, 3 rRNA genes, and 1,403 coding DNA sequences, of which 719 were assigned to clusters of orthologous groups. Ca. Nanopusillus phoceensis is only the second nanoarchaea to be detected in humans, expanding our knowledge of the repertoire of nanoarchaea associated with the human microbiota and encouraging further research to explore the repertoire of this emerging group of nanomicrobes in clinical samples.
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Affiliation(s)
- Yasmine Hassani
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Gerard Aboudharam
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France
- Ecole de Médecine Dentaire, Aix-Marseille Université, 13005 Marseille, France
| | - Michel Drancourt
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Ghiles Grine
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France
- Ecole de Médecine Dentaire, Aix-Marseille Université, 13005 Marseille, France
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Volmer JG, McRae H, Morrison M. The evolving role of methanogenic archaea in mammalian microbiomes. Front Microbiol 2023; 14:1268451. [PMID: 37727289 PMCID: PMC10506414 DOI: 10.3389/fmicb.2023.1268451] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/18/2023] [Indexed: 09/21/2023] Open
Abstract
Methanogenic archaea (methanogens) represent a diverse group of microorganisms that inhabit various environmental and host-associated microbiomes. These organisms play an essential role in global carbon cycling given their ability to produce methane, a potent greenhouse gas, as a by-product of their energy production. Recent advances in culture-independent and -dependent studies have highlighted an increased prevalence of methanogens in the host-associated microbiome of diverse animal species. Moreover, there is increasing evidence that methanogens, and/or the methane they produce, may play a substantial role in human health and disease. This review addresses the expanding host-range and the emerging view of host-specific adaptations in methanogen biology and ecology, and the implications for host health and disease.
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Affiliation(s)
- James G. Volmer
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, Australia
| | - Harley McRae
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Mark Morrison
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, Australia
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Pilliol V, Guindo CO, Terrer E, Aboudharam G, Drancourt M, Grine G. Culturing clinical Methanobrevibacter smithii using GG medium in a minimal anaerobe atmosphere. J Microbiol Methods 2023; 207:106704. [PMID: 36907565 DOI: 10.1016/j.mimet.2023.106704] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/02/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023]
Abstract
Methanobrevibacter smithii (M. smithii), the most prevalent and abundant gut methanogen, detoxifies hydrogen into methane and is, therefore, of paramount importance for the equilibrium of the gut microbiota. The isolation by culture of M. smithii has routinely relied upon hydrogen‑carbon dioxide-enriched, oxygen-deprived atmospheres. In this study, we developed a medium referred to as "GG", which allowed for M. smithii growth and isolation by culture in an oxygen-deprived atmosphere, with no supply of either hydrogen or carbon dioxide, making it easier to detect M. smithii by culture in clinical microbiology laboratories.
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Affiliation(s)
- Virginie Pilliol
- Aix-Marseille Univ., IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, Ecole de Médecine Dentaire, Marseille, France
| | - Cheick Oumar Guindo
- Aix-Marseille Univ., IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Elodie Terrer
- Aix-Marseille Univ., IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, Ecole de Médecine Dentaire, Marseille, France
| | - Gérard Aboudharam
- Aix-Marseille Univ., IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, Ecole de Médecine Dentaire, Marseille, France
| | - Michel Drancourt
- Aix-Marseille Univ., IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Ghiles Grine
- Aix-Marseille Univ., IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France; IHU Méditerranée Infection, Marseille, France.
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Martinez SS, Stebliankin V, Hernandez J, Martin H, Tamargo J, Rodriguez JB, Teeman C, Johnson A, Seminario L, Campa A, Narasimhan G, Baum MK. Multiomic analysis reveals microbiome-related relationships between cocaine use and metabolites. AIDS 2022; 36:2089-2099. [PMID: 36382433 PMCID: PMC9673179 DOI: 10.1097/qad.0000000000003363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE Over 19 million individuals globally have a cocaine use disorder, a significant public health crisis. Cocaine has also been associated with a pro-inflammatory state and recently with imbalances in the intestinal microbiota as compared to nonuse. The objective of this pilot study was to characterize the gut microbiota and plasma metabolites in people with HIV (PWH) who use cocaine compared with those who do not. DESIGN Cross-sectional study. METHODS A pilot study in PWH was conducted on 25 cocaine users and 25 cocaine nonusers from the Miami Adult Studies on HIV cohort. Stool samples and blood plasma were collected. Bacterial composition was characterized using 16S rRNA sequencing. Metabolomics in plasma were determined using gas and liquid chromatography/mass spectrometry. RESULTS The relative abundances of the Lachnopspira genus, Oscillospira genus, Bifidobacterium adolescentis species, and Euryarchaeota phylum were significantly higher in the cocaine- using PWH compared to cocaine-nonusing PWH. Cocaine-use was associated with higher levels of several metabolites: products of dopamine catabolism (3-methoxytyrosine and 3-methoxytyramine sulfate), phenylacetate, benzoate, butyrate, and butyrylglycine. CONCLUSIONS Cocaine use was associated with higher abundances of taxa and metabolites known to be associated with pathogenic states that include gastrointestinal conditions. Understanding key intestinal bacterial functional pathways that are altered due to cocaine use in PWH will provide a better understanding of the relationships between the host intestinal microbiome and potentially provide novel treatments to improve health.
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Affiliation(s)
| | - Vitalii Stebliankin
- Florida International University, Bioinformatics Research Group (BioRG), Miami, FL, USA
| | - Jacqueline Hernandez
- Florida International University, R. Stempel College of Public Health and Social Work
| | - Haley Martin
- Florida International University, R. Stempel College of Public Health and Social Work
| | - Javier Tamargo
- Florida International University, R. Stempel College of Public Health and Social Work
| | | | - Colby Teeman
- Florida International University, R. Stempel College of Public Health and Social Work
| | - Angelique Johnson
- Florida International University, R. Stempel College of Public Health and Social Work
| | - Leslie Seminario
- Florida International University, R. Stempel College of Public Health and Social Work
| | - Adriana Campa
- Florida International University, R. Stempel College of Public Health and Social Work
| | - Giri Narasimhan
- Florida International University, Bioinformatics Research Group (BioRG), Miami, FL, USA
| | - Marianna K Baum
- Florida International University, R. Stempel College of Public Health and Social Work
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7
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Legaria M, Barberis C, Famiglietti A, De Gregorio S, Stecher D, Rodriguez C, Vay C. Urinary tract infection caused by anaerobic bacteria. Utility of anaerobic urine culture. Anaerobe 2022; 78:102636. [DOI: 10.1016/j.anaerobe.2022.102636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/22/2022] [Accepted: 08/30/2022] [Indexed: 11/01/2022]
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8
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First Detection of Methanogens in Orthopedic Prosthesis Infection: A Four-Case Founding Series. PROSTHESIS 2022. [DOI: 10.3390/prosthesis4010005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Orthopedic prosthesis infection must be medically managed after appropriate microbiological documentation. While bacteria and fungi are acknowledged to be causative opportunistic pathogens in this situation, the potential role of methanogens in orthopedic prosthesis infections is still unknown. In a retrospective study, a total of 100 joint and bone samples collected from 25 patients were screened by specific PCR assays for the detection of methanogens. PCR-positive samples were observed by autofluorescence, electron microscopy and tentatively cultured under specific culture conditions. Methanogens were detected by quantitative PCR in 4/100 samples, in the presence of negative controls. Sequencing identified Methanobrevibacter oralis in two cases, Methanobrevibacter smithii in one case and Methanobrevibacter wolinii in one case. Microscopic methods confirmed molecular findings and bacterial culture yielded two strains of Staphylococcus aureus, one strain of Staphylococcus epidermidis and one strain of Proteus mirabilis. These unprecedented data highlight the presence of methanogens in joint and bone samples of patients also diagnosed with bacterial orthopedic prosthesis infection, questioning the role of methanogens as additional opportunistic co-pathogens in this situation.
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Hassani Y, Saad J, Terrer E, Aboudharam G, Giancarlo B, Silvestri F, Raoult D, Drancourt M, Grine G. Introducing clinical nanorachaeaology: Isolation by co-culture of Nanopusillus massiliensis sp. nov. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100100. [PMID: 35005659 PMCID: PMC8718826 DOI: 10.1016/j.crmicr.2021.100100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022] Open
Abstract
The first ever detection in human microbiota of nanoarchaea. Detection and co-isolation of nanoarchaea new species in human oral microbiota. These data suggest the contribution of methanogens to the perinatal development of intestinal microbiota and physiology. Extended our knowledge of human microbiota diversity. Opening a new field of research in clinical microbiology here referred to as clinical nanoarchaeology.
Background Nanoarchaeota, obligate symbiont of some environmental archaea with reduced genomes, have been described in marine thermal vent environments, yet never detected in hosts, including humans. Methods Here, using laboratory tools geared towards the detection of nanoarchaea including PCR-sequencing, WGS, microscopy and culture. Results We discovered a novel nanoarchaea, Nanopusillus massiliensis, detected in dental plate samples by specific PCR-based assays. Combining fluorescent in situ hybridization (FISH) with scanning electron microscopy disclosed close contacts between N. massiliensis and the archaea Methanobrevibacter oralis in these samples. Culturing one sample yielded co-isolation of M. oralis and N. massiliensis with a 606,935-bp genome, with 23.6% GC encoded 16 tRNA, 3 rRNA and 942 coding DNA sequences, of which 400 were assigned to clusters of orthologous groups. Conclusion The discovery of N. massiliensis, made publicly available in collection, extended our knowledge of human microbiota diversity, opening a new field of research in clinical microbiology here referred to as clinical nanoarchaeology.
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Affiliation(s)
- Y. Hassani
- Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France
- IHU Méditerranée Infection, Marseille 13005, France
| | - J. Saad
- Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France
- IHU Méditerranée Infection, Marseille 13005, France
| | - E. Terrer
- Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France
- Faculté de médecine dentaire, Aix-Marseille Université, Marseille 13005, France
| | - G. Aboudharam
- Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France
- Faculté de médecine dentaire, Aix-Marseille Université, Marseille 13005, France
| | - B Giancarlo
- Private practice Marseille France, Marseille, France
| | - F. Silvestri
- Faculté de médecine dentaire, Aix-Marseille Université, Marseille 13005, France
| | - D. Raoult
- Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France
- IHU Méditerranée Infection, Marseille 13005, France
| | - M. Drancourt
- Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France
- IHU Méditerranée Infection, Marseille 13005, France
| | - G. Grine
- Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France
- Faculté de médecine dentaire, Aix-Marseille Université, Marseille 13005, France
- Corresponding author at: Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France.
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10
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Djemai K, Gouriet F, Sielezneff I, Mege D, Drancourt M, Grine G. Detection of methanogens in peri-appendicular abscesses: Report of four cases. Anaerobe 2021; 72:102470. [PMID: 34743984 DOI: 10.1016/j.anaerobe.2021.102470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/29/2022]
Abstract
The aetiology of appendicular abscess is predominantly microbial with aerobic and anaerobic bacteria from gut flora. In this study, by using specific laboratory tools, we co-detected Methanobrevibacter oralis and Methanobrevibacter smithii among a mixture of enterobacteria including Escherichia coli, Enterococcus faecium and Enterococcus avium in four unrelated cases of postoperative appendiceal abscesses. These unprecedented observations raise a question on the role of methanogens in peri-appendicular abscesses, supporting antibiotics as an alternative therapeutic option for appendicitis, including antibiotics active against methanogens such as metronidazole or fusidic acid.
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Affiliation(s)
- K Djemai
- Aix-Marseille Univ, IRD, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - F Gouriet
- Aix-Marseille Univ, IRD, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - I Sielezneff
- Department of Digestive Surgery, Aix Marseille Univ, APHM, Timone University Hospital, Marseille, France
| | - D Mege
- Department of Digestive Surgery, Aix Marseille Univ, APHM, Timone University Hospital, Marseille, France
| | - M Drancourt
- Aix-Marseille Univ, IRD, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - G Grine
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, UFR Odontologie, Marseille, France.
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11
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Djemai K, Gouriet F, Michel J, Radulesco T, Drancourt M, Grine G. Methanobrevibacter smithii tonsillar phlegmon: a case report. New Microbes New Infect 2021; 42:100891. [PMID: 34141438 PMCID: PMC8184653 DOI: 10.1016/j.nmni.2021.100891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/22/2022] Open
Abstract
Untreated tonsillar phlegmon is a life-threatening condition commonly caused by Streptococcus pyogenes and Fusobacterium necrophorum, among other pathogens. Here, using specific laboratory tools, we detected Methanobrevibacter smithii in addition to S. pyogenes. This unprecedented observation questions the role of methanogens in phlegmon and the optimal treatment of this mixed infection.
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Affiliation(s)
- K Djemai
- Aix-Marseille Univ, IRD, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - F Gouriet
- Aix-Marseille Univ, IRD, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - J Michel
- CHU Hôpital de la Conception, Service ORL et Chirurgie cervico-faciale, Marseille, France
| | - T Radulesco
- CHU Hôpital de la Conception, Service ORL et Chirurgie cervico-faciale, Marseille, France
| | - M Drancourt
- Aix-Marseille Univ, IRD, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - G Grine
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille Université, UFR Odontologie, Marseille, France
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12
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Guindo CO, Davoust B, Drancourt M, Grine G. Diversity of Methanogens in Animals' Gut. Microorganisms 2020; 9:microorganisms9010013. [PMID: 33374535 PMCID: PMC7822204 DOI: 10.3390/microorganisms9010013] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 12/20/2020] [Indexed: 12/13/2022] Open
Abstract
Methanogens are members of anaerobe microbiota of the digestive tract of mammals, including humans. However, the sources, modes of acquisition, and dynamics of digestive tract methanogens remain poorly investigated. In this study, we aimed to expand the spectrum of animals that could be sources of methanogens for humans by exploring methanogen carriage in animals. We used real-time PCR, PCR-sequencing, and multispacer sequence typing to investigate the presence of methanogens in 407 fecal specimens collected from nine different mammalian species investigated here. While all the negative controls remained negative, we obtained by PCR-sequencing seven different species of methanogens, of which three (Methanobrevibacter smithii, Methanobrevibacter millerae and Methanomassiliicoccus luminyensis) are known to be part of the methanogens present in the human digestive tract. M. smithii was found in 24 cases, including 12/24 (50%) in pigs, 6/24 (25%) in dogs, 4/24 (16.66%) in cats, and 1/24 (4.16%) in both sheep and horses. Genotyping these 24 M. smithii revealed five different genotypes, all known in humans. Our results are fairly representative of the methanogen community present in the digestive tract of certain animals domesticated by humans, and other future studies must be done to try to cultivate methanogens here detected by molecular biology to better understand the dynamics of methanogens in animals and also the likely acquisition of methanogens in humans through direct contact with these animals or through consumption of the meat and/or milk of certain animals, in particular cows.
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Affiliation(s)
- Cheick Oumar Guindo
- IHU Méditerranée Infection, 13005 Marseille, France; (C.O.G.); (M.D.)
- IRD, MEPHI, Aix-Marseille Université, 13005 Marseille, France;
| | - Bernard Davoust
- IRD, MEPHI, Aix-Marseille Université, 13005 Marseille, France;
| | - Michel Drancourt
- IHU Méditerranée Infection, 13005 Marseille, France; (C.O.G.); (M.D.)
- IRD, MEPHI, Aix-Marseille Université, 13005 Marseille, France;
| | - Ghiles Grine
- IRD, MEPHI, Aix-Marseille Université, 13005 Marseille, France;
- Faculty of Odontology, Aix-Marseille Université, 13005 Marseille, France
- Correspondence: ; Tel.: +33-(0)4-13-73-24-01; Fax: +33-(0)-13-73-24-02
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13
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Detection of Methanobrevobacter smithii and Methanobrevibacter oralis in Lower Respiratory Tract Microbiota. Microorganisms 2020; 8:microorganisms8121866. [PMID: 33256156 PMCID: PMC7760608 DOI: 10.3390/microorganisms8121866] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/19/2020] [Accepted: 11/24/2020] [Indexed: 12/22/2022] Open
Abstract
Methanogens, the sole microbes producing methane, are archaea commonly found in human anaerobic microbiota. Methanogens are emerging as opportunistic pathogens associated with dysbiosis and are also detected and cultured in anaerobic abscesses. Their presence in the respiratory tract is yet unknown. As a preliminary answer, prospective investigation of 908 respiratory tract samples using polyphasic approach combining PCR-sequencing, real-time PCR, fluorescent in situ hybridization (FISH), and methanogens culture was carried out. Methanobrevibacter smithii and Methanobrevibacter oralis DNA sequences, were detected in 21/527 (3.9%) sputum samples, 2/188 (1.06%) bronchoalveolar lavages, and none of 193 tracheo-bronchial aspirations. Further, fluorescence in situ hybridization detected methanogens in three sputum investigated specimens with stick morphology suggesting M. oralis and in another one bronchoalveolar lavage sample investigated, diplococal morphology suggesting M. smithii. These observations extend the known territory of methanogens to the respiratory tract and lay the foundations for further interpretation of their detection as pathogens in any future cases of isolation from bronchoalveolar lavages and the lungs.
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Guindo CO, Drancourt M, Grine G. Digestive tract methanodrome: Physiological roles of human microbiota-associated methanogens. Microb Pathog 2020; 149:104425. [PMID: 32745665 DOI: 10.1016/j.micpath.2020.104425] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/21/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023]
Abstract
Methanogens are the archaea most commonly found in humans, in particular in the digestive tract and are an integral part of the digestive microbiota. They are present in humans from the earliest moments of life and represent the only known source of methane production to date. They are notably detected in humans by microscopy, fluorescent in situ hybridization, molecular biology including PCR-sequencing, metagenomics, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and culture. Methanogens present in the human digestive tract play major roles, in particular the use of hydrogen from the fermentation products of bacteria, thus promoting digestion. They are also involved in the transformation of heavy metals and in the use of trimethylamine produced by intestinal bacteria, thus preventing major health problems, in particular cardiovascular diseases. Several pieces of evidence suggest their close physical contacts with bacteria support symbiotic metabolism. Their imbalance during dysbiosis is associated with many pathologies in humans, particularly digestive tract diseases such as Crohn's disease, ulcerative colitis, diverticulosis, inflammatory bowel disease, irritable bowel syndrome, colonic polyposis, and colorectal cancer. There is a huge deficit of knowledge and partially contradictory information concerning human methanogens, so much remains to be done to fully understand their physiological role in humans. It is necessary to develop new methods for the identification and culture of methanogens from clinical samples. This will permit to isolate new methanogens species as well as their phenotypic characterization, to explore their genome by sequencing and to study the population dynamics of methanogens by specifying in particular their exact role within the complex flora associated with the mucous microbiota of human.
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Affiliation(s)
- C O Guindo
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - M Drancourt
- IHU Méditerranée Infection, Marseille, France
| | - G Grine
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, UFR Odontologie, Marseille, France.
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15
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Drancourt M, Djemai K, Gouriet F, Grine G, Loukil A, Bedotto M, Levasseur A, Lepidi H, Bou-Khalil J, Khelaifia S, Raoult D. Methanobrevibacter smithii archaemia in febrile patients with bacteremia, including those with endocarditis. Clin Infect Dis 2020; 73:e2571-e2579. [PMID: 32668457 DOI: 10.1093/cid/ciaa998] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/10/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The spectrum of infections caused by the emerging opportunistic pathogens methanogens which escape routine detection remains to be described. To determine the prevalence of archaemia, we searched for methanogens in the blood of febrile patients using specific tools. METHODS We conducted a prospective study at Institut Hospitalier Universitaire Méditerranée Infection, Marseille, France, September 2018 - April 2020, enrolling 7,716 blood culture samples routinely collected in patients with fever. Blood samples were screened by specific PCR assays for the presence of methanogens. Positive samples were observed by autofluorescence and electron microscopy, analyzed by metagenomics and cultured using previously developed methods. Blood culture bottles experimentally inoculated were used as controls. The presence of methanogens in vascular and cardiac tissues was assessed by indirect immunofluorescence, fluorescent in situ hybridization and PCR-based investigations. RESULTS PCR detection attempted in 7,716 blood samples, was negative in all 1,312 aerobic bottles and 810 bacterial culture-negative anaerobic bottles. PCRs were positive in 27/5,594 (0.5%) bacterial culture-positive anaerobic bottles that contained cultures collected from 26 patients. Sequencing confirmed Methanobrevibacter smithii associated with staphylococci in 14 patients, fermentative Enterobacteriaceae in nine patients and streptococci in three patients. Metagenomics confirmed M. smithii in five blood samples, and M. smithii was isolated via culture in broth from two samples; the genomes of these two isolates were sequenced. Blood cultures experimentally inoculated with Enterobacteriaceae, Staphylococcus epidermidis or Staphylococcus hominis yielded hydrogen, but no methane, authentifying observational data.Three patients, all diagnosed with infectious mitral endocarditis, were diagnosed by microscopy, PCR-based detections and culture: we showed M. smithii microscopically and by a specific PCR followed by sequencing method in two of three cardiovascular tissues. CONCLUSIONS Using appropriate methods of detection, M. smithii is demonstrated as causing archaemia and endocarditis in febrile patients who are coinfected by bacteria.
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Affiliation(s)
- Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Kenza Djemai
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Frédérique Gouriet
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Ghiles Grine
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Ahmed Loukil
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Marielle Bedotto
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Anthony Levasseur
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Hubert Lepidi
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | | | | | - Didier Raoult
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
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16
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Sereme Y, Mezouar S, Grine G, Mege JL, Drancourt M, Corbeau P, Vitte J. Methanogenic Archaea: Emerging Partners in the Field of Allergic Diseases. Clin Rev Allergy Immunol 2020; 57:456-466. [PMID: 31522353 DOI: 10.1007/s12016-019-08766-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Archaea, which form one of four domains of life alongside Eukarya, Bacteria, and giant viruses, have long been neglected as components of the human microbiota and potential opportunistic infectious pathogens. In this review, we focus on methanogenic Archaea, which rely on hydrogen for their metabolism and growth. On one hand, methanogenic Archaea in the gut are functional associates of the fermentative digestion of dietary fibers, favoring the production of beneficial short-chain fatty acids and likely contributing to the weaning reaction during the neonatal window of opportunity. On the other hand, methanogenic Archaea trigger the activation of innate and adaptive responses and the generation of specific T and B cells in animals and humans. In mouse models, lung hypersensitivity reactions can be induced by inhaled methanogenic Archaea mimicking human professional exposure to organic dust. Changes in methanogenic Archaea of the microbiota are detected in an array of dysimmune conditions comprising inflammatory bowel disease, obesity, malnutrition, anorexia, colorectal cancer, and diverticulosis. At the subcellular level, methanogenic Archaea are activators of the TLR8-dependent NLRP3 inflammasome, modulate the release of antimicrobial peptides and drive the production of proinflammatory, Th-1, Th-2, and Th-17 cytokines. Our objective was to introduce the most recent and major pieces of evidence supporting the involvement of Archaea in the balance between health and dysimmune diseases, with a particular focus on atopic and allergic conditions.
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Affiliation(s)
- Youssouf Sereme
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
| | - Soraya Mezouar
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
| | - Ghiles Grine
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
| | - Jean Louis Mege
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
- APHM, Hôpital Timone, Service de Bactériologie - Epidémiologie - Hygiène hospitalière, Aix-Marseille University, Marseille, France
| | - Michel Drancourt
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
| | - Pierre Corbeau
- Institute of Human Genetics, UMR9002, CNRS-Montpellier University, Montpellier, France
- Montpellier University, Montpellier, France
- Immunology Department, University Hospital, Nîmes, France
| | - Joana Vitte
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France.
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France.
- APHM, Hôpital Timone, Service de Bactériologie - Epidémiologie - Hygiène hospitalière, Aix-Marseille University, Marseille, France.
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17
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Syntrophy via Interspecies H 2 Transfer between Christensenella and Methanobrevibacter Underlies Their Global Cooccurrence in the Human Gut. mBio 2020; 11:mBio.03235-19. [PMID: 32019803 PMCID: PMC7002349 DOI: 10.1128/mbio.03235-19] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Across human populations, 16S rRNA gene-based surveys of gut microbiomes have revealed that the bacterial family Christensenellaceae and the archaeal family Methanobacteriaceae cooccur and are enriched in individuals with a lean, compared to an obese, body mass index (BMI). Whether these association patterns reflect interactions between metabolic partners, as well as whether these associations play a role in the lean host phenotype with which they associate, remains to be ascertained. Here, we validated previously reported cooccurrence patterns of the two families and their association with a lean BMI with a meta-analysis of 1,821 metagenomes derived from 10 independent studies. Furthermore, we report positive associations at the genus and species levels between Christensenella spp. and Methanobrevibacter smithii, the most abundant methanogen of the human gut. By coculturing three Christensenella spp. with M. smithii, we show that Christensenella spp. efficiently support the metabolism of M. smithii via H2 production far better than Bacteroides thetaiotaomicron does. Christensenella minuta forms flocs colonized by M. smithii even when H2 is in excess. In culture with C. minuta, H2 consumption by M. smithii shifts the metabolic output of C. minuta's fermentation toward acetate rather than butyrate. Together, these results indicate that the widespread cooccurrence of these microorganisms is underpinned by both physical and metabolic interactions. Their combined metabolic activity may provide insights into their association with a lean host BMI.IMPORTANCE The human gut microbiome is made of trillions of microbial cells, most of which are Bacteria, with a subset of Archaea The bacterial family Christensenellaceae and the archaeal family Methanobacteriaceae are widespread in human guts. They correlate with each other and with a lean body type. Whether species of these two families interact and how they affect the body type are unanswered questions. Here, we show that species within these families correlate with each other across people. We also demonstrate that particular species of these two families grow together in dense flocs, wherein the bacteria provide hydrogen gas to the archaea, which then make methane. When the archaea are present, the ratio of bacterial products (which are nutrients for humans) is changed. These observations indicate that when these species grow together, their products have the potential to affect the physiology of their human host.
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18
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Togo AH, Grine G, Khelaifia S, des Robert C, Brevaut V, Caputo A, Baptiste E, Bonnet M, Levasseur A, Drancourt M, Million M, Raoult D. Culture of Methanogenic Archaea from Human Colostrum and Milk. Sci Rep 2019; 9:18653. [PMID: 31819085 PMCID: PMC6901439 DOI: 10.1038/s41598-019-54759-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 11/05/2019] [Indexed: 12/20/2022] Open
Abstract
Archaeal sequences have been detected in human colostrum and milk, but no studies have determined whether living archaea are present in either of these fluids. Methanogenic archaea are neglected since they are not detected by usual molecular and culture methods. By using improved DNA detection protocols and microbial culture techniques associated with antioxidants previously developed in our center, we investigated the presence of methanogenic archaea using culture and specific Methanobrevibacter smithii and Methanobrevibacter oralis real-time PCR in human colostrum and milk. M. smithii was isolated from 3 colostrum and 5 milk (day 10) samples. M. oralis was isolated from 1 milk sample. For 2 strains, the genome was sequenced, and the rhizome was similar to that of strains previously isolated from the human mouth and gut. M. smithii was detected in the colostrum or milk of 5/13 (38%) and 37/127 (29%) mothers by culture and qPCR, respectively. The different distribution of maternal body mass index according to the detection of M. smithii suggested an association with maternal metabolic phenotype. M. oralis was not detected by molecular methods. Our results suggest that breastfeeding may contribute to the vertical transmission of these microorganisms and may be essential to seed the infant's microbiota with these neglected critical commensals from the first hour of life.
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Affiliation(s)
- Amadou Hamidou Togo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - Ghiles Grine
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - Saber Khelaifia
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - Clotilde des Robert
- APHM, CHU Hôpital de la Conception, Service de médecine néonatale, F-13385, Marseille, France
| | - Véronique Brevaut
- APHM, CHU Hôpital Nord, Service de médecine néonatale, Marseille, France
| | - Aurelia Caputo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - Emeline Baptiste
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - Marion Bonnet
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - Anthony Levasseur
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - Michel Drancourt
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - Matthieu Million
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France.
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France.
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19
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Guindo CO, Terrer E, Chabrière E, Aboudharam G, Drancourt M, Grine G. Culture of salivary methanogens assisted by chemically produced hydrogen. Anaerobe 2019; 61:102128. [PMID: 31759176 DOI: 10.1016/j.anaerobe.2019.102128] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/15/2019] [Accepted: 11/16/2019] [Indexed: 10/25/2022]
Abstract
Methanogen cultures require hydrogen produced by fermentative bacteria such as Bacteroides thetaiotaomicron (biological method). We developed an alternative method for hydrogen production using iron filings and acetic acid with the aim of cultivating methanogens more efficiently and more quickly (chemical method). We developed this new method with a reference strain of Methanobrevibacter oralis, compared the method to the biological reference method with a reference strain of Methanobrevibacter smithii and finally applied the method to 50 saliva samples. Methanogen colonies counted using ImageJ software were identified using epifluorescence optical microscopy, real-time PCR and PCR sequencing. For cultures containing pure strains of M. oralis and M. smithii, colonies appeared three days postinoculation with the chemical method versus nine days with the biological method. The average number of M. smithii colonies was significantly higher with the chemical method than with the biological method. There was no difference in the delay of observation of the first colonies in the saliva samples between the two methods. However, the average number of colonies was significantly higher with the biological method than with the chemical method at six days and nine days postinoculation (Student's test, p = 0.005 and p = 0.04, respectively). The chemical method made it possible to isolate four strains of M. oralis and three strains of M. smithii from the 50 saliva samples. Establishing the chemical method will ease the routine isolation and culture of methanogens.
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Affiliation(s)
- Cheick O Guindo
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Elodie Terrer
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; Aix-Marseille-Univ, Faculty of Odontology, Marseille, France
| | - Eric Chabrière
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Gérard Aboudharam
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; Aix-Marseille-Univ, Faculty of Odontology, Marseille, France
| | - Michel Drancourt
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France.
| | - Ghiles Grine
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; Aix-Marseille-Univ, Faculty of Odontology, Marseille, France
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20
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Grine G, Drouet H, Fenollar F, Bretelle F, Raoult D, Drancourt M. Detection of Methanobrevibacter smithii in vaginal samples collected from women diagnosed with bacterial vaginosis. Eur J Clin Microbiol Infect Dis 2019; 38:1643-1649. [PMID: 31127480 DOI: 10.1007/s10096-019-03592-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/14/2019] [Indexed: 01/18/2023]
Abstract
Vaginosis is a dysbiotic condition of the vaginal cavity that has deleterious effects during pregnancy. The role of methanogens in this disease is unknown since current methods of investigation are not appropriate for the search of methanogens. We prospectively investigated the presence of methanogens in vaginal specimens collected from 33 women thereafter diagnosed with bacterial vaginosis and 92 women thereafter diagnosed without bacterial vaginosis (control group) by direct microscopic examination and fluorescent in situ hybridization, PCR-sequencing, and real-time PCR and isolation and culture. These investigations found only one methanogen, Methanobrevibacter smithii, exclusively in 97% bacterial vaginosis specimens and in two intermediate microbiota specimens. M. smithii was detected microscopically in 2/20 specimens analyzed, by PCR-based observations in 34/125 specimens with 99% sequence similarity with the reference 16S rRNA and mcrA gene sequences and was cultured in 9/40 specimens. These data suggest that the detection of M. smithii could be used as a biomarker for the laboratory diagnosis of bacterial vaginosis.
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Affiliation(s)
- Ghiles Grine
- MEPHI, IRD, IHU Méditerranée Infection, Aix Marseille University, Marseille, France.,IHU Méditerranée Infection, UMR MEPHI, 19-21, Bd Jean Moulin, 13005, Marseille, France
| | - Hortense Drouet
- VITROME, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, Marseille, France
| | - Florence Fenollar
- VITROME, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, Marseille, France
| | - Florence Bretelle
- Gynecology Department, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Didier Raoult
- MEPHI, IRD, IHU Méditerranée Infection, Aix Marseille University, Marseille, France.,IHU Méditerranée Infection, UMR MEPHI, 19-21, Bd Jean Moulin, 13005, Marseille, France
| | - Michel Drancourt
- MEPHI, IRD, IHU Méditerranée Infection, Aix Marseille University, Marseille, France. .,IHU Méditerranée Infection, UMR MEPHI, 19-21, Bd Jean Moulin, 13005, Marseille, France.
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21
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Grine G, Lotte R, Chirio D, Chevalier A, Raoult D, Drancourt M, Ruimy R. Co-culture of Methanobrevibacter smithii with enterobacteria during urinary infection. EBioMedicine 2019; 43:333-337. [PMID: 31072770 PMCID: PMC6558020 DOI: 10.1016/j.ebiom.2019.04.037] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/10/2019] [Accepted: 04/18/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Urinary tract infections are known to be caused by bacteria, but the potential implications of archaea have never been studied in this context. METHODS In two different university hospital centres we used specific laboratory methods for the detection and culture of archaeal methanogens in 383 urine specimens prospectively collected for diagnosing urinary tract infection (UTI). FINDINGS Methanobrevibacter smithii was detected by quantitative PCR and sequencing in 34 (9%) of the specimens collected from 34 patients. Escherichia coli, Klebsiella pneumoniae, Enterobacter sp., Enterococcus faecium and mixed cultures were detected along with M. smithii in eighteen, six, three, one and six urine samples, respectively. Interestingly, using our specific culture method for methanogens, we also isolated M. smithii in 31 (91%) of the 34 PCR positive urine samples. Genotyping the 31 isolates using multispacer sequence typing revealed three different genotypes which have been previously reported in intestinal microbiota. Antibiotic susceptibility testing found the 31 isolates to be in vitro susceptible to metronidazole (MIC: 1 mg/L) but resistant to fosfomycin, sulfamethoxazole-trimethoprim, amoxicillin-clavulanate and ofloxacin, commonly used to treat bacterial UTI. Finally, 19 (54%) of the 34 patients in whose urine samples M. smithii was detected were diagnosed with UTIs, including cystitis, pyelonephritis and prostatitis. INTERPRETATION Our results show that M. smithii is part of the urinary microbiota of some individuals and could play a role in community-acquired UTI in association with enteric bacteria. FUND: This study was supported by IHU Méditerranée Infection, Marseille, France.
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Affiliation(s)
- Ghiles Grine
- IHU Méditerranée Infection, Marseille, France; Aix Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; Laboratoire de bactériologie, Centre Hospitalier Universitaire de Nice, Hôpital de l'Archet II, Nice, France
| | - Romain Lotte
- Laboratoire de bactériologie, Centre Hospitalier Universitaire de Nice, Hôpital de l'Archet II, Nice, France; Université Côte d'Azur, Inserm, C3M, Nice, France; Inserm U1065, C3M, Equipe 6 « Virulence microbienne et signalisation inflammatoire », Bâtiment universitaire Archimède, Nice, France
| | - David Chirio
- Service de maladies infectieuses et tropicales, Centre Hospitalier Universitaire de Nice, Hôpital de l'Archet I, Nice, France
| | - Alicia Chevalier
- Laboratoire de bactériologie, Centre Hospitalier Universitaire de Nice, Hôpital de l'Archet II, Nice, France
| | - Didier Raoult
- Aix Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Michel Drancourt
- Aix Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Raymond Ruimy
- Laboratoire de bactériologie, Centre Hospitalier Universitaire de Nice, Hôpital de l'Archet II, Nice, France; Université Côte d'Azur, Inserm, C3M, Nice, France; Inserm U1065, C3M, Equipe 6 « Virulence microbienne et signalisation inflammatoire », Bâtiment universitaire Archimède, Nice, France.
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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.e1-1561.e5. [PMID: 30986553 DOI: 10.1016/j.cmi.2019.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/14/2019] [Accepted: 04/05/2019] [Indexed: 11/28/2022]
Abstract
OBJECTIVES Methanogenic Archaea are considered as extremely oxygen-sensitive organisms, and their culture is fastidious, requiring specific equipment. We report here conditions allowing the cultivation of Methanobrevibacter smithii in an anaerobic chamber without the addition of hydrogen. METHODS We first enriched the stool sample in an anaerobic liquid medium. To cultivate M. smithii with Bacteroides thetaiotaomicron and other hydrogen-producing bacteria on solid medium in an anaerobic chamber, we divided the agar plates into two compartments and seeded each strain on each compartment. Methane production was assessed by gas chromatography, and the growing colonies were authenticated by MALDI-TOF MS. RESULTS We successfully cultured M. smithii from a liquid culture medium inoculated with stool collected from a healthy donor in an anaerobic chamber. The isolation in pure culture permitted successful culture on agar medium by our performing a co-culture with B. thetaiotaomicron. We also successfully tested the co-cultivation of M. smithii with other known hydrogen-producing bacteria. Gas chromatographic tests showed that these strains produced hydrogen in different amounts. Agar colonies of methanogens were obtained by co-culture with these bacteria, and methane production was detected. CONCLUSIONS We propose a new approach to isolate and cultivate new strains of M. smithii by using a co-culture-based technique that can facilitate and make available the isolation of new methanogenic Archaea strains in clinical microbiology laboratories.
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Affiliation(s)
- S I Traore
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - S Khelaifia
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - N Armstrong
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - J C Lagier
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - D Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.
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23
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Sogodogo E, Fellag M, Loukil A, Nkamga VD, Michel J, Dessi P, Fournier PE, Drancourt M. Nine Cases of Methanogenic Archaea in Refractory Sinusitis, an Emerging Clinical Entity. Front Public Health 2019; 7:38. [PMID: 30886840 PMCID: PMC6409293 DOI: 10.3389/fpubh.2019.00038] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 02/13/2019] [Indexed: 01/24/2023] Open
Abstract
The authors report the cases of 9 patients eventually diagnosed with methanogenic archaea refractory or recalcitrant chronic rhinosinusitis, a condition known to involve various anaerobic bacteria but in which the role of methanogenic archaea is unknown. The authors retrospectively searched these microorganisms by PCR in surgically-collected sinusal pus specimens from patients diagnosed with refractory sinusitis, defined by the persistance of sinus inflammation and related-symptoms for more than 12 weeks despite appropriate treatment. Of the 116 tested sinus surgical specimens, 12 (10.3%) from 9 patients (six females, three males; aged 20-71 years) were PCR-positive. These specimens were further investigated by fluorescence in-situ hybridization, PCR amplicon-sequencing and culture. Methanobrevibacter smithii was documented in four patients and Methanobrevibacter oralis in another four, one of whom was also culture-positive. They were associated with a mixed flora including Gram-positive and Gram-negative bacteria. In the latter patient, "Methanobrevibacter massiliense" was the sole microorganism detected. These results highlight methanogenic archaea as being part of a mixed anaerobic flora involved in refractory sinusitis, and suggest that the treatment of this condition should include an antibiotic active against methanogens, notably a nitroimidazole derivative.
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Affiliation(s)
- Elisabeth Sogodogo
- Aix Marseille University, IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Mustapha Fellag
- Aix Marseille University, IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Ahmed Loukil
- Aix Marseille University, IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | | | - Justin Michel
- Assistance Publique-Hôpitaux de Marseille, Service ORL et Chirurgie Cervico-Faciale, Hôpital de la Conception, Marseille, France
| | - Patrick Dessi
- Assistance Publique-Hôpitaux de Marseille, Service ORL et Chirurgie Cervico-Faciale, Hôpital de la Conception, Marseille, France
| | | | - Michel Drancourt
- Aix Marseille University, IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France
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24
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Sogodogo E, Drancourt M, Grine G. Methanogens as emerging pathogens in anaerobic abscesses. Eur J Clin Microbiol Infect Dis 2019; 38:811-818. [DOI: 10.1007/s10096-019-03510-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/04/2019] [Indexed: 01/02/2023]
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25
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Belkacemi S, Mazel A, Tardivo D, Tavitian P, Stephan G, Bianca G, Terrer E, Drancourt M, Aboudharam G. Peri-implantitis-associated methanogens: a preliminary report. Sci Rep 2018; 8:9447. [PMID: 29930395 PMCID: PMC6013440 DOI: 10.1038/s41598-018-27862-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 06/07/2018] [Indexed: 01/30/2023] Open
Abstract
Methanogens have already been described in periodontitis but not in peri-implantitis. Thirty peri-implantitis samples and 28 control samples were collected in 28 consenting peri-implantitis patients. PCR-sequencing of the 16S rRNA gene was used as a broad-spectrum screening method and results were further confirmed by real-time quantitative PCR targeting the mcrA genes. Results showed a methanogen community dominated by Methanobrevibacter oralis in 31/58 (51%) samples including 16/28 (57%) control samples and 15/30 (50%) peri-implantitis samples. Methanobrevibacter massiliense was detected in 5/58 (8.6%) samples including 3/28 (1%) control samples and 2/30 (6.7%) peri-implantitis samples. The prevalence of M. oralis or M. massiliense did not significantly differ in peri-implantitis and control samples (exact Fisher test, P = 0.61 and P = 0.67, respectively). Further ponderation of the methanogen load by the real-time quantitative PCR for actin human gene again indicated non-significant difference (Wilcoxon-Mann-Whitney test, P = 0.48 and P = 0.40, respectively). These data show that the prevalence of methanogens does not differ in peri-implantitis lesions and healthy sites, when individuals are their own control. These data do not allow assigning a specific pathogenic role to methanogens in peri-implantitis; methanogens rather are part of the commensal and normal flora of the oral cavity.
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Affiliation(s)
- Souad Belkacemi
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | - Anthony Mazel
- UFR Odontologie, Aix-Marseille Université, Marseille, France
| | | | | | - Grégory Stephan
- UFR Odontologie, Aix-Marseille Université, Marseille, France
| | | | - Elodie Terrer
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France
- UFR Odontologie, Aix-Marseille Université, Marseille, France
| | - Michel Drancourt
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France.
| | - Gérard Aboudharam
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France
- UFR Odontologie, Aix-Marseille Université, Marseille, France
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26
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Lagier JC, Drancourt M, Charrel R, Bittar F, La Scola B, Ranque S, Raoult D. Many More Microbes in Humans: Enlarging the Microbiome Repertoire. Clin Infect Dis 2018; 65:S20-S29. [PMID: 28859350 DOI: 10.1093/cid/cix404] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The proportion of cultured microorganisms is dramatically lower than those predicted to be involved in colonization, acute, or chronic infections. We report our laboratory's contribution to promoting culture methods. As a result of using culturomics in our clinical microbiology laboratories (including amoeba co-culture and shell-vial culture) and through the use of matrix-assisted laser desorption/ionization-time-of-flight and the 16S rRNA gene for identification, we cultured 329 new bacterial species. This is also the first time that 327 of species have been isolated from humans, increasing the known human bacterial repertoire by 29%. We isolated 4 archaeal species for the first time from human, including 2 new species. Of the 100 isolates of giant viruses, we demonstrated the human pathogenicity of Mimivirus in pneumonia and Marseillevirus in diverse clinical situations. From sand flies, we isolated most of the known Phlebovirus strains that potentially cause human infections. Increasing the repertoire of human-associated microorganisms through culture will allow us to test pathogenicity models with viable microorganisms.
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Affiliation(s)
| | | | - Rémi Charrel
- UMR Emergence des Pathologies Virales, IRD 190, Inserm 1207, EHESP, France Fondation, IHU Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille (AP-HM) Public Hospitals of Marseille
| | | | | | - Stéphane Ranque
- Université Montpellier 1, IRBA, IP-TPT, Aix Marseille Université.,Parasitologie and Mycologie, IHU Méditerranée Infection, Hôpital de la Timone, AP-HM, Marseille, France
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27
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Nkamga VD, Lotte R, Chirio D, Lonjon M, Roger PM, Drancourt M, Ruimy R. Methanobrevibacter oralis detected along with Aggregatibacter actinomycetemcomitans in a series of community-acquired brain abscesses. Clin Microbiol Infect 2017; 24:207-208. [PMID: 28882726 DOI: 10.1016/j.cmi.2017.08.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 08/25/2017] [Accepted: 08/26/2017] [Indexed: 11/30/2022]
Affiliation(s)
- V D Nkamga
- Unité de recherche sur les maladies infectieuses tropicales et émergentes, Marseille, France; Laboratoire de bactériologie, Centre Hospitalier Universitaire de Nice, Nice, France
| | - R Lotte
- Laboratoire de bactériologie, Centre Hospitalier Universitaire de Nice, Nice, France; Université Nice Côte d'Azur, Inserm, C3M, Nice, France; INSERM U1065, C3M, Team 6, "Bacterial Toxins in Host Pathogen Interactions", Bâtiment universitaire Archimed, Nice, France
| | - D Chirio
- Service de maladies infectieuses et tropicales, Centre Hospitalier Universitaire de Nice, Nice, France
| | - M Lonjon
- Unité de Neurochirurgie, Centre Hospitalier Universitaire de Nice, Nice, France
| | - P-M Roger
- Service de maladies infectieuses et tropicales, Centre Hospitalier Universitaire de Nice, Nice, France
| | - M Drancourt
- Unité de recherche sur les maladies infectieuses tropicales et émergentes, Marseille, France
| | - R Ruimy
- Laboratoire de bactériologie, Centre Hospitalier Universitaire de Nice, Nice, France; Université Nice Côte d'Azur, Inserm, C3M, Nice, France; INSERM U1065, C3M, Team 6, "Bacterial Toxins in Host Pathogen Interactions", Bâtiment universitaire Archimed, Nice, France.
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28
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Nkamga VD, Henrissat B, Drancourt M. Archaea: Essential inhabitants of the human digestive microbiota. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.humic.2016.11.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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