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Willems E, Hamerlinck H, Messiaen AS, Schelstraete P, Van Braeckel E, Vande Weygaerde Y, Verhasselt B, Boelens J, Vandendriessche S. Expansion of MALDI-TOF MS database as a strategy for identification of Haemophilus species other than H. influenzae. Acta Clin Belg 2024:1-7. [PMID: 39101268 DOI: 10.1080/17843286.2024.2386216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
OBJECTIVES This study aimed to evaluate an expanded matrix-assisted laser desorption-ionization-time of flight mass spectrometry (MALDI-TOF MS) database for the identification of Haemophilus species other than H. influenzae (Hi). METHODS A total of 144 Haemophilus species, cultured from respiratory samples from people (living) with cystic fibrosis, were identified with MALDI-TOF MS and 16S rRNA sequencing. Of these, 99 Haemophilus strains showed >99% similarity with the best matching strain in the National Center for Biotechnology Information (NCBI) database and were assigned to a single Haemophilus subspecies using both MALDI-TOF MS and 16S rRNA sequencing. The MS profiles of a subset of strains (n = 58/99) were added to the Bruker MALDI-TOF MS database. Subsequently, 270 different strains that were analyzed previously in a routine setting were re-analyzed. RESULTS 16S rRNA sequencing reliably identified 99/144 Haemophilus strains (>99% similarity). H. haemolyticus 16S rRNA identification was suboptimal since only 3/21 H. haemolyticus strains attained a similarity of >99% with H. haemolyticus 16S rRNA sequence in the NCBI database. Expansion of the MALDI-TOF MS database improved the number of reliable identifications only moderately for H. haemolyticus, H. influenzae and H. paraphrohaemolyticus (<10%). By contrast, improved identification was more outspoken for H. parahaemolyticus, H. parainfluenzae, H. sputorum and H. pittmaniae (>85%). CONCLUSION 16S rRNA sequencing is a valuable method for the identification of Haemophilus sp. other than Hi. Expansion of the MALDI-TOF MS database, based on 16S rRNA sequencing results, increased the proportion of reliable identifications and in this study resulted in an increase of 10% of Haemophilus sp. other than Hi strain identifications.
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Affiliation(s)
- Eva Willems
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Hannelore Hamerlinck
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | | | - Petra Schelstraete
- Department of Pediatrics, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Eva Van Braeckel
- Respiratory Infection and Defense Lab (RIDL), Department of Internal Medicine and Paediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | | | - Bruno Verhasselt
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jerina Boelens
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
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2
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Sun X, Feng S, Qin B, Ye J, Xie L, Gui J, Sang M. Integrated multi-omics profiling highlights the benefits of resveratrol hydroxypropyl-β-cyclodextrin inclusion complex for A53T transgenic mice through the microbiota-gut-brain axis. Food Funct 2024; 15:1489-1512. [PMID: 38227477 DOI: 10.1039/d3fo03667g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Parkinson's disease (PD) is a neurological disorder characterized by motor and gastrointestinal dysfunctions. Resveratrol is a potent antioxidant and anti-inflammatory phytoalexin known for its health-promoting benefits. However, little is known about its potential in treating PD by modulating the microbial gut-brain axis, and its clinical application has been limited due to poor water solubility, rapid metabolism, and limited systemic bioavailability. Our study aimed to evaluate the therapeutic potential of RHSD, a resveratrol-cyclodextrin inclusion complex, in treating PD through the gut-brain axis in human SNCA-transgenic (A53T) mice PD models. Building on our previous study, we prepared RHSD and compared its efficacy with uncoated resveratrol for PD treatment. The study results demonstrated that RHSD exhibited several advantages in improving motor function, alleviating cognitive impairment, restoring intestinal barrier function, and inhibiting neuropathy. Subsequently, a series of analyses, including fecal microbiota metagenomic sequencing, non-target metabolic assays, host transcriptome sequencing, and integrative analysis were performed to reveal the potential therapeutic pathways of RHSD in A53T mice. The metagenomic sequencing results indicated a significant increase in the levels of Lactobacillus murinus, Lactobacillus reuteri, Enterorhabduscaecimuris, Lactobacillus taiwanensis, and Lactobacillus animals following RHSD administration. Furthermore, metabolomics profiling showed that the levels of gut microbiome metabolites were reversed after RHSD treatment, and differential metabolites were significantly correlated with motor function and intestinal function in PD mice. The integrated analysis of microbial metabolites and host transcriptomics suggested that abnormal amino acid metabolism, mitochondrial dysfunction, oxidative stress, and neuroinflammation in the PD model were associated with the diffusion of abnormal metabolites. This study illustrates the profound impact of RHSD administration on rectifying gut microbiota dysbiosis and improving the A53T mouse model. Notably, we observed significant alterations in the proliferation and metabolism of multiple probiotic strains of Lactobacillus. Furthermore, our research supports the hypothesis that microbiota-related metabolites may regulate the transcription of host genes, including dopamine receptors and calcium stabilization. Consequently, our findings underscore the potential of RHSD as a promising therapeutic candidate for the treatment of PD through the modulation of several signaling pathways within the microbiota-gut-brain axis.
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Affiliation(s)
- Xiaodong Sun
- Research Center for Translational Medicine, Hubei Provincial Clinical Research Center for Parkinson's Disease at Xiangyang No.1 People's Hospital, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, China.
| | - Shenglan Feng
- Research Center for Translational Medicine, Hubei Provincial Clinical Research Center for Parkinson's Disease at Xiangyang No.1 People's Hospital, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, China.
| | - Bingqing Qin
- Research Center for Translational Medicine, Hubei Provincial Clinical Research Center for Parkinson's Disease at Xiangyang No.1 People's Hospital, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, China.
| | - Junjie Ye
- Research Center for Translational Medicine, Hubei Provincial Clinical Research Center for Parkinson's Disease at Xiangyang No.1 People's Hospital, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, China.
- Clinical Laboratory, Wuhan Asia Heart Hospital, Wuhan 430022, China
| | - Lixia Xie
- Research Center for Translational Medicine, Hubei Provincial Clinical Research Center for Parkinson's Disease at Xiangyang No.1 People's Hospital, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, China.
| | - Jianjun Gui
- Research Center for Translational Medicine, Hubei Provincial Clinical Research Center for Parkinson's Disease at Xiangyang No.1 People's Hospital, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, China.
| | - Ming Sang
- Research Center for Translational Medicine, Hubei Provincial Clinical Research Center for Parkinson's Disease at Xiangyang No.1 People's Hospital, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, China.
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Chen X, Zhang H, Feng J, Zhang L, Zheng M, Luo H, Zhuo H, Xu N, Zhang X, Chen C, Qu P, Li Y. Comparative Genomic Analysis Reveals Genetic Diversity and Pathogenic Potential of Haemophilus seminalis and Emended Description of Haemophilus seminalis. Microbiol Spectr 2023; 11:e0477222. [PMID: 37382545 PMCID: PMC10434262 DOI: 10.1128/spectrum.04772-22] [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] [Received: 11/22/2022] [Accepted: 06/10/2023] [Indexed: 06/30/2023] Open
Abstract
Haemophilus seminalis is a newly proposed species that is phylogenetically related to Haemophilus haemolyticus. The distribution of H. seminalis in the human population, its genomic diversity, and its pathogenic potential are still unclear. This study reports the finding of our comparative genomic analyses of four newly isolated Haemophilus strains (SZY H8, SZY H35, SZY H36, and SZY H68) from human sputum specimens (Guangzhou, China) along with the publicly available genomes of other phylogenetically related Haemophilus species. Based on pairwise comparisons of the 16S rRNA gene sequences, the four isolates showed <98.65% sequence identity to the type strains of all known Haemophilus species but were identified as belonging to H. seminalis, based on comparable phenotypic and genotypic features. Additionally, the four isolates showed high genome-genome relatedness indices (>95% ANI values) with 17 strains that were previously identified as either "Haemophilus intermedius" or hemin (X-factor)-independent H. haemolyticus and therefore required a more detailed classification study. Phylogenetically, these isolates, along with the two previously described H. seminalis isolates (a total of 23 isolates), shared a highly homologous lineage that is distinct from the clades of the main H. haemolyticus and Haemophilus influenzae strains. These isolates present an open pangenome with multiple virulence genes. Notably, all 23 isolates have a functional heme biosynthesis pathway that is similar to that of Haemophilus parainfluenzae. The phenotype of hemin (X-factor) independence and the analysis of the ispD, pepG, and moeA genes can be used to distinguish these isolates from H. haemolyticus and H. influenzae. Based on the above findings, we propose a reclassification for all "H. intermedius" and two H. haemolyticus isolates belonging to H. seminalis with an emended description of H. seminalis. This study provides a more accurate identification of Haemophilus isolates for use in the clinical laboratory and a better understanding of the clinical significance and genetic diversity in human environments. IMPORTANCE As a versatile opportunistic pathogen, the accurate identification of Haemophilus species is a challenge in clinical practice. In this study, we characterized the phenotypic and genotypic features of four H. seminalis strains that were isolated from human sputum specimens and propose the "H. intermedius" and hemin (X-factor)-independent H. haemolyticus isolates as belonging to H. seminalis. The prediction of virulence-related genes indicates that H. seminalis isolates carry several virulence genes that are likely to play an important role in its pathogenicity. In addition, we depict that the genes ispD, pepG, and moeA can be used as biomarkers for distinguishing H. seminalis from H. haemolyticus and H. influenzae. Our findings provide some insights into the identification, epidemiology, genetic diversity, pathogenic potential, and antimicrobial resistance of the newly proposed H. seminalis.
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Affiliation(s)
- Xiaowei Chen
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hanyun Zhang
- Department of Laboratory Medicine, The Affiliated Hexian Memorial Hospital of Southern Medical University, Guangzhou, China
| | - Junhui Feng
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lei Zhang
- Guangzhou Kingmed Center for Clinical Laboratory, Guangzhou, China
| | - Minling Zheng
- Department of Clinical Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
| | - Haimin Luo
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Huiyan Zhuo
- Department of Laboratory Medicine, The Affiliated Hexian Memorial Hospital of Southern Medical University, Guangzhou, China
| | - Ning Xu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xuan Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Cha Chen
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Pinghua Qu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Youqiang Li
- Department of Laboratory Medicine, The Affiliated Hexian Memorial Hospital of Southern Medical University, Guangzhou, China
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4
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Lo CI, Traore SI, Diop A, Bilen M, Azhar EI, Bibi F, Jiman-Fatani A, Yasir M, Lagier JC, Raoult D, Fenollar F, Fournier PE. Arabiibacter massiliensis gen. nov. sp. nov., New Anaerobic Bacterium Isolated from the Human Gut. Curr Microbiol 2022; 79:47. [PMID: 34982255 DOI: 10.1007/s00284-021-02739-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/06/2021] [Indexed: 02/07/2023]
Abstract
Using microbial culturomics, we were able to isolate strain Marseille-P3078 from a stool sample of a healthy 50-year-old Saudi Arabian woman. To this end, we used taxonogenomics that combines phenotypic, biochemical and genomic analyses, to describe this bacterium. Cells from strain Marseille-P3078 are anaerobic and Gram-negative rods that are motile and unable to sporulate. Its genome size is 3,377,914-bp-long with a 66.33 mol% G + C content. Based on its phenotypic and genomic features, including a 94.6% 16S rRNA similarity with Paraeggerthella hongkongensis strain JCM 14552, its closest phylogenetic neighbor withstanding in nomenclature, we propose that strain Marseille-P3078T (= CSUR P3078 = DSM 104007) is the representative strain of a new genus for which we propose the name Arabiibacter massiliensis gen. nov., sp. nov.
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Affiliation(s)
- Cheikh Ibrahima Lo
- UMR VITROME, Aix Marseille Univ, IRD, AP-HM, SSA, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Sory Ibrahima Traore
- IHU-Méditerranée Infection, Marseille, France
- UMR MEPHI, Aix Marseille Univ, IRD, AP-HM, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Awa Diop
- UMR VITROME, Aix Marseille Univ, IRD, AP-HM, SSA, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Melhem Bilen
- IHU-Méditerranée Infection, Marseille, France
- UMR MEPHI, Aix Marseille Univ, IRD, AP-HM, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fehmida Bibi
- Department of Medical Laboratory Technology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asif Jiman-Fatani
- Department of Medical Laboratory Technology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jean-Christophe Lagier
- IHU-Méditerranée Infection, Marseille, France
- UMR MEPHI, Aix Marseille Univ, IRD, AP-HM, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Florence Fenollar
- UMR VITROME, Aix Marseille Univ, IRD, AP-HM, SSA, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Pierre-Edouard Fournier
- UMR VITROME, Aix Marseille Univ, IRD, AP-HM, SSA, Marseille, France.
- IHU-Méditerranée Infection, Marseille, France.
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5
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Antezack A, Boxberger M, Rolland C, Ben Khedher M, Monnet-Corti V, La Scola B. Isolation and characterization of Campylobacter massiliensis sp. nov., a novel Campylobacter species detected in a gingivitis subject. Int J Syst Evol Microbiol 2021; 71. [PMID: 34751644 DOI: 10.1099/ijsem.0.005039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative bacterium, designated strain Marseille-Q3452T, was isolated from subgingival dental plaque of a subject suffering from dental plaque biofilm-induced gingivitis on an intact periodontium in Marseille, France. The strain was characterized by 16S rRNA and atpA gene sequence analysis and by conventional phenotypic and chemotaxonomic testing. The average nucleotide identity (ANI) and core genome phylogeny were determined using whole-genome sequences. Although strain Marseille-Q3452T showed 99.72 % 16S rRNA gene sequence similarity with Campylobacter showae strain ATCC 51146T, atpA and ANI analyses revealed divergence between the two strains. The two species could also be distinguished phenotypically on the basis of the absence of flagella and nitrate reduction. On the basis of the results from phenotypic, chemotaxonomic, genomic and phylogenetic analyses and data, we concluded that strain Marseille-Q3452T represents a novel species of the genus Campylobacter, for which the name Campylobacter massiliensis sp. nov. is proposed (=CSUR Q3452=CECT 30263).
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Affiliation(s)
- Angéline Antezack
- Aix-Marseille Université, Faculté des Sciences Médicales et Paramédicales, Ecole de Médecine Dentaire, 27 boulevard Jean Moulin, 13385 Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), Hôpital Timone, Service de Parodontologie, 264, rue Saint Pierre, 13385 Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Manon Boxberger
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Clara Rolland
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Mariem Ben Khedher
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Virginie Monnet-Corti
- Aix-Marseille Université, Faculté des Sciences Médicales et Paramédicales, Ecole de Médecine Dentaire, 27 boulevard Jean Moulin, 13385 Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), Hôpital Timone, Service de Parodontologie, 264, rue Saint Pierre, 13385 Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Bernard La Scola
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
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6
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Ben Khedher M, Diouf FS, Lo CI, Alibar S, Durand G, Raoult D, Fournier PE, Fenollar F. Collinsella ihumii sp. nov., a new anaerobic bacterium isolated from human stool. Arch Microbiol 2021; 203:6315-6322. [DOI: 10.1007/s00203-021-02562-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
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7
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Antezack A, Boxberger M, Ben Khedher M, La Scola B, Monnet-Corti V. Isolation and description of Selenomonas timonae sp. nov., a novel Selenomonas species detected in a gingivitis patient. Int J Syst Evol Microbiol 2021; 71. [PMID: 34612809 DOI: 10.1099/ijsem.0.005040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative bacterium, designated strain Marseille-Q3039T, was isolated from subgingival dental plaque of a woman with gingivitis in Marseille, France. Strain Marseille-Q3039T was found to be an anaerobic, motile and spore-forming crescent-shaped bacterium that grew at 25-41.5 °C (optimum, 37 °C), pH 5.5-8.5 (optimum, pH 7.5) and salinity of 5.0 g l-1 NaCl. The results of 16S rRNA gene sequence analysis revealed that strain Marseille-Q3039T was closely related to Selenomonas infelix ATCC 43532T (98.42 % similarity), Selenomonas dianae ATCC 43527T (97.25 %) and Centipedia periodontii DSM 2778T (97.19 %). The orthologous average nucleotide identity and digital DNA-DNA hybridization relatedness between strain Q3039T and its closest phylogenetic neighbours were respectively 84.57 and 28.2 % for S. infelix ATCC 43532T and 83.93 and 27.2 % for C. periodontii DSM 2778T. The major fatty acids were identified as C13 : 0 (27.7 %), C15 : 0 (24.4 %) and specific C13 : 0 3-OH (12.3 %). Genome sequencing revealed a genome size of 2 351 779 bp and a G+C content of 57.2 mol%. On the basis of the results from phenotypic, chemotaxonomic, genomic and phylogenetic analyses and data, we concluded that strain Marseille-Q3039T represents a novel species of the genus Selenomonas, for which the name Selenomonas timonae sp. nov. is proposed (=CSUR Q3039=CECT 30128).
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Affiliation(s)
- Angéline Antezack
- Aix-Marseille Université, Faculté des Sciences Médicales et Paramédicales, Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), Hôpital Timone, Service de Parodontologie, 264, Rue Saint Pierre, 13385 Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Manon Boxberger
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Mariem Ben Khedher
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Bernard La Scola
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Virginie Monnet-Corti
- Aix-Marseille Université, Faculté des Sciences Médicales et Paramédicales, Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), Hôpital Timone, Service de Parodontologie, 264, Rue Saint Pierre, 13385 Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
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8
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Lo CI, Dione N, Mbaye A, Gómez PFM, Ngom II, Valles C, Alibar S, Lagier JC, Fenollar F, Fournier PE, Raoult D, Diene SM. Limosilactobacillus caccae sp. nov., a new bacterial species isolated from the human gut microbiota. FEMS Microbiol Lett 2021; 368:6373442. [PMID: 34549292 DOI: 10.1093/femsle/fnab128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/17/2021] [Indexed: 11/14/2022] Open
Abstract
Strain Marseille-P3519T isolated from the fecal flora of a 25-year-old healthy French woman was a Gram-positive anaerobic bacterium, non-motile and non-spore forming. The 16S rRNA gene sequence of Marseille-P3519 showed 97.73% of sequence similarity with Limosilactobacillus reuteri DSM 20016, the closest species, phylogenetically. Furthermore, the average nucleotide identity of strain Marseille-3519 with its closest related species was 75.8% that was very below the recommended threshold (>95-96%). Its genome had 2 237 367 bp with 45.42 mol% of G + C content. Major fatty acids were C16:0 (50.8%), C18:1n9 (18.0%), C18:2n6 (9.8%) and C19:1n9 (8.9%). It was catalase negative and fermented glycerol, glucose, fructose, D-maltose, lactose and mannose. These findings support that strain Marseille-P3519 ( = CSURP3519 = CECT 30110) is a new member of the genus Limosilactobacillus for which the name Limosilactobacillus caccae sp. nov., is proposed.
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Affiliation(s)
- Cheikh Ibrahima Lo
- Aix Marseille Uni versity, IRD, AP-HM, SSA, VITROME, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Niokhor Dione
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Aminata Mbaye
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Patricia Fernández-Mellado Gómez
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Issa Isaac Ngom
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Camille Valles
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Stéphane Alibar
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Jean-Christophe Lagier
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Florence Fenollar
- Aix Marseille Uni versity, IRD, AP-HM, SSA, VITROME, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Pierre-Edouard Fournier
- Aix Marseille Uni versity, IRD, AP-HM, SSA, VITROME, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Seydina M Diene
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
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9
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Di Sante G, Gremese E, Tolusso B, Cattani P, Di Mario C, Marchetti S, Alivernini S, Tredicine M, Petricca L, Palucci I, Camponeschi C, Aragon V, Gambotto A, Ria F, Ferraccioli G. Haemophilus parasuis ( Glaesserella parasuis) as a Potential Driver of Molecular Mimicry and Inflammation in Rheumatoid Arthritis. Front Med (Lausanne) 2021; 8:671018. [PMID: 34485325 PMCID: PMC8415917 DOI: 10.3389/fmed.2021.671018] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/19/2021] [Indexed: 01/07/2023] Open
Abstract
Background:Haemophilus parasuis (Hps; now Glaesserella parasuis) is an infectious agent that causes severe arthritis in swines and shares sequence similarity with residues 261–273 of collagen type 2 (Coll261−273), a possible autoantigen in rheumatoid arthritis (RA). Objectives/methods: We tested the presence of Hps sequencing 16S ribosomal RNA in crevicular fluid, synovial fluids, and tissues in patients with arthritis (RA and other peripheral arthritides) and in healthy controls. Moreover, we examined the cross-recognition of Hps by Coll261−273-specific T cells in HLA-DRB1*04pos RA patients, by T-cell receptor (TCR) beta chain spectratyping and T-cell phenotyping. Results:Hps DNA was present in 57.4% of the tooth crevicular fluids of RA patients and in 31.6% of controls. Anti-Hps IgM and IgG titers were detectable and correlated with disease duration and the age of the patients. Peripheral blood mononuclear cells (PBMCs) were stimulated with Hps virulence-associated trimeric autotransporter peptide (VtaA10755−766), homologous to human Coll261−273 or co-cultured with live Hps. In both conditions, the expanded TCR repertoire overlapped with Coll261−273 and led to the production of IL-17. Discussion: We show that the DNA of an infectious agent (Hps), not previously described as pathogen in humans, is present in most patients with RA and that an Hps peptide is able to activate T cells specific for Coll261−273, likely inducing or maintaining a molecular mimicry mechanism. Conclusion: The cross-reactivity between VtaA10755−766 of a non-human infectious agent and human Coll261−273 suggests an involvement in the pathogenesis of RA. This mechanism appears emphasized in predisposed individuals, such as patients with shared epitope.
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Affiliation(s)
- Gabriele Di Sante
- Section of General Pathology, Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Elisa Gremese
- Division of Rheumatology, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Rome, Italy.,Division of Rheumatology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Barbara Tolusso
- Division of Rheumatology, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Rome, Italy
| | - Paola Cattani
- Dipartimento di Scienze di laboratorio e infettivologiche, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy.,Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Sezione di Microbiologia, Università Cattolica del S. Cuore, Rome, Italy
| | - Clara Di Mario
- Division of Rheumatology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Simona Marchetti
- Dipartimento di Scienze di laboratorio e infettivologiche, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Stefano Alivernini
- Division of Rheumatology, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Rome, Italy
| | - Maria Tredicine
- Section of General Pathology, Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Luca Petricca
- Division of Rheumatology, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Rome, Italy
| | - Ivana Palucci
- Dipartimento di Scienze di laboratorio e infettivologiche, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy.,Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Sezione di Microbiologia, Università Cattolica del S. Cuore, Rome, Italy
| | - Chiara Camponeschi
- Section of General Pathology, Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Virginia Aragon
- Institut de Recerca i Tecnologies Agroalimentaries, Centre de Recerca en Sanitat Animal (CReSA IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Andrea Gambotto
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Francesco Ria
- Section of General Pathology, Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di laboratorio e infettivologiche, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
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10
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Mbaye B, Tidjani Alou M, Fadlane A, Fregiere L, Alibar S, Million M, Fenollar F, Lo CI. Neobacillus massiliamazoniensis sp. nov., a new bacterial species isolated from stool sample of an inhabitant of the Amazon region. New Microbes New Infect 2021; 42:100900. [PMID: 34168882 PMCID: PMC8209264 DOI: 10.1016/j.nmni.2021.100900] [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: 02/01/2021] [Revised: 04/16/2021] [Accepted: 05/09/2021] [Indexed: 11/26/2022] Open
Abstract
Using a culturomics approach, a strain was isolated, identified and characterised following the taxonogenomics concept. Neobacillus massiliamazoniensis sp. nov., strain LF1T (=CSURP1359) was isolated from human stool. The 16S rRNA gene sequence analysis of strain LF1T (accession number: LK021124) exhibits 98.32% similarity levels with Neobacillus bataviensis strain IDA1115 (accession number: NR_036766.1), the phylogenetically closest related species with standing in nomenclature. The draft genome size of strain LF1T (accession number: CVRB00000000) is 4.6 Mbp with a G+C content of 34.1 mol%. Analysis of phylogenic tree, genomic analysis and phenotypic criteria described here sufficiently prove that this bacterium is different from previously known bacterial species with standing in nomenclature and represents a new Neobacillus species belonging to Firmicutes phylum.
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Affiliation(s)
- B Mbaye
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - M Tidjani Alou
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - A Fadlane
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - L Fregiere
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - S Alibar
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - M Million
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - F Fenollar
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - C I Lo
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
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11
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Traore SI, Lo CI, Bilen M, Raoult D, Fenollar F, Fournier PE. Lagierella massiliensis gen. nov., sp. nov., Isolated from a Stool Sample. Curr Microbiol 2021; 78:2481-2487. [PMID: 34043027 DOI: 10.1007/s00284-021-02539-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
Strain Marseille-P2012T was described to represent a new bacterial genus belonging to the phylum Firmicutes using the taxonogenomics concept. It was isolated from stool samples of a healthy 2-year-old Senegalese boy in a study of the human gut microbiota. This strain is a Gram-positive, anaerobic, non-motile and coccus-shaped bacterium. The 16S rRNA gene sequence of strain Marseille-P2012 exhibited 90.5% similarity with Finegoldia magna strain ATCC 29,328, the phylogenetically closest species with standing in nomenclature. The genome of strain Marseille-P2012T is 1,832,315 bp-long with 32.46 mol% of G + C content. With regard to its phenotypic, biochemical and genomic characteristics, this bacterium was classified as a new bacterial genus and species, Lagierella massiliensis gen. nov., sp. nov., with strain Marseille-P2012T (= CSUR P2012 = DSM100854) as type strain.
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Affiliation(s)
- Sory Ibrahima Traore
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, cedex 05, Marseille, France
| | - Cheikh Ibrahima Lo
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, cedex 05, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, cedex 05, Marseille, France
| | - Melhem Bilen
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, cedex 05, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, cedex 05, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Florence Fenollar
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, cedex 05, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, cedex 05, Marseille, France
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, cedex 05, Marseille, France. .,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, cedex 05, Marseille, France.
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12
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Ben Khedher M, Lo C, Diop K, Morand A, Armstrong N, Raoult D, Fenollar F. Taxonogenomics description of Arcanobacterium urinimassiliense sp. nov., a new bacterial species isolated from urine sample. New Microbes New Infect 2021; 41:100854. [PMID: 33854785 PMCID: PMC8027287 DOI: 10.1016/j.nmni.2021.100854] [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: 12/23/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/22/2022] Open
Abstract
Strain Marseille-P3248т is a new species from the order Actinomycetales that was isolated from the urine sample of a girl aged 20 months with rotavirus gastroenteritis. It is a facultative anaerobic Gram-positive rod-shaped bacterium. Strain Marseille-P3248т exhibits 94.73% sequence similarity with Arcanobacterium pluranimalium strain M430/94/2, a phylogenetically related species with standing in nomenclature. Its genome size is 1 667 964 bp with 49.1% G + C content. Strain Marseille-P3248т (= CSURP3248) is the type strain of the new species Arcanobacterium urinimassiliense sp. nov.
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Affiliation(s)
- M. Ben Khedher
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - K. Diop
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - A. Morand
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - N. Armstrong
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - F. Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
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13
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Naud S, Bellali S, Anani H, Lo C, Yacouba A, Tidjani Alou M, Armstrong N, Bonvalet M, Zitvogel L, Raoult D, Lagier JC. Luxibacter massiliensis gen. nov., sp. nov., a new bacterium isolated from the human gut microbiota. New Microbes New Infect 2021; 40:100850. [PMID: 33732473 PMCID: PMC7941043 DOI: 10.1016/j.nmni.2021.100850] [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: 12/11/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/22/2022] Open
Abstract
An anaerobic facultative Gram-stain positive bacterium was isolated from human gut microbiota. Strain Marseille-P5551T was considered to be a new genus within the phylum Firmicutes, as it exhibits a 91.87% similarity level with Faecalicatena orotica (NR_117129.1), the phylogenetically closest related species. The draft genome size of strain Marseille-P5551T is 4 142 938 bp with 44.4% of G + C content. We hereby suggest the creation of Luxibacter massiliensis gen. nov., sp. nov., as a new bacterial genus.
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Affiliation(s)
- S. Naud
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - S. Bellali
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - H. Anani
- IHU-Méditerranée Infection, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - C.I. Lo
- IHU-Méditerranée Infection, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - A. Yacouba
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - M. Tidjani Alou
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
| | - N. Armstrong
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - M. Bonvalet
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
| | - L. Zitvogel
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
| | - D. Raoult
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - J.-C. Lagier
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
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14
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Isolation and Characterization of Kingella bonacorsii sp. nov., A Novel Kingella Species Detected in a Stable Periodontitis Subject. Pathogens 2021; 10:pathogens10020240. [PMID: 33669894 PMCID: PMC7923279 DOI: 10.3390/pathogens10020240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 11/24/2022] Open
Abstract
Members of the genus Kingella are mostly commensals of the oral cavity, but some of them are involved in invasive infections, especially in young children. This study provides new knowledge on the diversity of this genus by describing a novel species of Kingella isolated from a dental plaque sample from a 51-year-old man with a history of periodontitis. Morphological and chemotaxonomic characteristic were investigated using different growth conditions, pH and temperature. Cellular fatty acid methyl ester (FAME) analysis was performed by gas chromatography/mass spectrometry (GC/MS). Phylogenetic analysis based on 16S rRNA, orthologous average nucleotide identity (OrthoANI) and digital DNA–DNA hybridization (dDDH) relatedness were also performed. Strain Marseille-Q4569T was found to be a facultative aerobic, nonmotile and non-spore-forming rod-shaped bacterium that grows at 28–41.5 °C (optimum 37 °C), pH 5.5–8.5 (optimum pH 7.5) and 5–15 g/L of NaCl. The major fatty acids were Hexadecanoic acid (32.7%), 11-Octadecenoic acid (26.1 %) and 9-Hexadecenoic acid (21.3 %). Despite high 16S rRNA gene sequence similarity (98.72%) between strain Marseille-Q4569T and Kingella oralis strain UB-38T, the degree of OrthoANI was at the limit of the cutoff (95.83%), and the degree of dDDH was lower (63.6%) than thresholds used to delineate prokaryotic species. Therefore, it is proposed that strain Marseille-Q4569T represents a novel species of the genus Kingella, for which the name Kingella bonacorsii sp. nov. is proposed (=CSUR Q4569).
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15
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Morand A, Tall ML, Kuete Yimagou E, Ngom II, Lo CI, Cornu F, Tsimaratos M, Lagier JC, Levasseur A, Raoult D, Fournier PE. Anaerococcus urinimassiliensis sp. nov., a new bacterium isolated from human urine. Sci Rep 2021; 11:2684. [PMID: 33514860 PMCID: PMC7846727 DOI: 10.1038/s41598-021-82420-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 10/20/2020] [Indexed: 12/22/2022] Open
Abstract
To date there are thirteen species validly assigned to the genus Anaerococcus. Most of the species in this genus are anaerobic and of human origin. Anaerococcus urinimassiliensis sp. nov., strain Marseille-P2143T is member of family Peptoniphilaceae, which was isolated from the urine of a 17-year-old boy affected by autoimmune hepatitis and membranoproliferative glomerulonephritis using the culturomic approach. In the current study, a taxono-genomics method was employed to describe this new species. The strain Marseille-P2143T was gram positive cocci with translucent colonies on blood agar. Its genome was 2,189,509 bp long with a 33.5 mol% G + C content and exhibited 98.48% 16S rRNA similarity with Anaerococcus provencensis strain 9,402,080. When Anaerococcus urinomassiliensis strain Marseill-P2143T is compared with closely related species, the values ranged from 71.23% with A. hydrogenalis strain DSM 7454T (NZ_ABXA01000052.1) to 90.64% with A. provencensis strain 9402080T (NZ_HG003688.1). This strain has implemented the repertoire of known bacteria of the human urinary tract.
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Affiliation(s)
- Aurélie Morand
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. .,Pédiatrie Spécialisée Et Médecine Infantile, Hôpital de La Timone, AP-HM, Marseille, France.
| | - Mamadou Lamine Tall
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Edmond Kuete Yimagou
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Issa Isaac Ngom
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Cheikh Ibrahima Lo
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Florent Cornu
- Pédiatrie Multidisciplinaire, Hôpital de La Timone, AP-HM, Marseille, France
| | - Michel Tsimaratos
- Pédiatrie Multidisciplinaire, Hôpital de La Timone, AP-HM, Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Anthony Levasseur
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Institut Universitaire de France (IUF), Paris, France
| | - Didier Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Pierre-Edouard Fournier
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
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16
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Naud S, Khelaifia S, Mbogning Fonkou MD, Dione N, Lagier JC, Raoult D. Proof of Concept of Culturomics Use of Time of Care. Front Cell Infect Microbiol 2020; 10:524769. [PMID: 33330116 PMCID: PMC7719802 DOI: 10.3389/fcimb.2020.524769] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 10/22/2020] [Indexed: 12/22/2022] Open
Abstract
Culturomics, a high throughput culture method with rapid identification of the colonies by Matrix Assisted Laser Desorption Ionization/Time Of Flight Mass Spectrometry (MALDI-TOF MS), has demonstrated its contribution to the exploration of the gut microbiota over the past 10 years. However, the cost, work time and workload, considerably limit its use on a large scale or emergency context. Here, by testing two different stool samples, including a stool sample from a patient requiring rapid immunotherapy treatment, we tested a new fast culturomic protocol using two pre-incubation media, blood culture bottle and YCFA modified medium. Both media were supplemented with 2 ml of rumen fluid filtered at 0.2 μm and 2 ml of defibrinated and sterile sheep blood. Unlike the standard culturomics, subculturing of blood culture bottle were performed at reduced incubation time (3 h, 6 h, 9 h, 24 h) and at a longer incubation time (3 days, 7 days, and 10 days) at 37°C. By testing 5,200 colonies per MALDI-TOF MS and obtaining a comparable number of cultured bacterial species (131 to 143) in a stool sample, this new protocol reduced the number of colonies tested by 57%, working time by 78.6% and cost by 72.2%. In addition, we highlighted that the proportion of strict anaerobic species has increased by 24%, known to be the preferential targets for biotherapy, including Faecalibacterium prausnitzii, Akkermansia muciniphila, Christensenella minuta, and Phascolarctobacterium faecium. Finally, this work showed that some bacterial species grew earlier but disappeared with prolonged incubation times.
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Affiliation(s)
- Sabrina Naud
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Saber Khelaifia
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Maxime Descartes Mbogning Fonkou
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Niokhor Dione
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, France, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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17
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Camara A, Konate S, Lo C, Kuete E, Sarr M, Amsrtong N, Niare S, Thera M, Fenollar F, Raoult D, Million M. Virgibacillus ihumii sp. nov., a new bacterium isolated from the stool of healthy African children. New Microbes New Infect 2020; 38:100790. [PMID: 33294190 PMCID: PMC7695897 DOI: 10.1016/j.nmni.2020.100790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 11/30/2022] Open
Abstract
During a case–control study on severe acute malnutrition, strain Marseille-Q1233 was isolated. It is a Gram-positive, rod-shaped and halophilic bacillus isolated from a stool sample of Malian child under the age of 5. The fatty acid profile of the strain consisted of C15:0-anteiso and C14:0-iso as major components. Digital DNA-DNA hybridization and average nucleotide identity calculation showed 23.10% and 80.81% similarity respectively between strain Marseille-Q1233 and Virgibacillus siamensis strain Marseille-P2607, the phylogenetically closely related species with standing in nomenclature. On the basis of these results, we report the description of Virgibacillus ihumii sp. nov. strain Marseille-Q1233 as a new bacterial species.
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Affiliation(s)
- A. Camara
- Aix-Marseille Université, IRD, APHM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - S. Konate
- Aix-Marseille Université, IRD, APHM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - C.I. Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, APHM, SSA, VITROME, Marseille, France
| | - E. Kuete
- Aix-Marseille Université, IRD, APHM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - M. Sarr
- Aix-Marseille Université, IRD, APHM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - N. Amsrtong
- Aix-Marseille Université, IRD, APHM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - S. Niare
- Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - M.A. Thera
- Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - F. Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, APHM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, APHM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - M. Million
- Aix-Marseille Université, IRD, APHM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- Corresponding author: M. Million, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
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18
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Tall M, Lo C, Yimagou EK, Ndongo S, Pham T, Raoult D, Fournier PE, Fenollar F, Levasseur A. Description of Clostridium cagae sp. nov., Clostridium rectalis sp. nov. and Hathewaya massiliensis sp. nov., new anaerobic bacteria isolated from human stool samples. New Microbes New Infect 2020; 37:100719. [PMID: 32944255 PMCID: PMC7481820 DOI: 10.1016/j.nmni.2020.100719] [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: 05/26/2020] [Accepted: 06/19/2020] [Indexed: 12/22/2022] Open
Abstract
Using culturomics methods, three strains were isolated, identified and characterized following the taxonogenomics concept. Clostridium cagae strain Marseille-P4344T (=CSURP4344), Clostridium rectalis strain Marseille-P4200T (=CSURP4200) and Hathewaya massiliensis strain Marseille-P3545T (=CSURP3545) were isolated from human stool samples. The phylogenetic reconstruction, phenotypic criteria and genomic analyses were carried out and demonstrated that these three bacteria are different from previously known bacterial species with standing in nomenclature and were classified as new members of the Clostridiaceae family.
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Affiliation(s)
- M.L. Tall
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - E. Kuete Yimagou
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- IHU-Méditerranée Infection, Marseille, France
| | - S. Ndongo
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- IHU-Méditerranée Infection, Marseille, France
| | - T.P.T. Pham
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- IHU-Méditerranée Infection, Marseille, France
| | - P.-E. Fournier
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- IHU-Méditerranée Infection, Marseille, France
| | - F. Fenollar
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - A. Levasseur
- Aix-Marseille Université, UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, 13005, France
- IHU-Méditerranée Infection, Marseille, France
- Institut Universitaire de France (IUF), Paris, France
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19
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Sarr M, Lo C, Tall M, Fadlane A, Senghor B, Sokhna C, Raoult D, Million M, Fenollar F. Taxonogenomics description of Bacillus dakarensis sp. nov., Bacillus sinesaloumensis sp. nov. and Bacillus massiliogabonensis sp. nov., three new species isolated from human stools. New Microbes New Infect 2020; 37:100718. [PMID: 32983544 PMCID: PMC7491149 DOI: 10.1016/j.nmni.2020.100718] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/12/2020] [Accepted: 06/17/2020] [Indexed: 12/22/2022] Open
Abstract
Using microbial culturomics, three Bacillus strains were isolated, identified and characterized following the taxonogenomics strategy. Bacillus dakarensis strain Marseille-P3515T (=CSURP3515), Bacillus sinesaloumensis strain Marseille-P3516T (=CSURP3516), and Bacillus massiliogabonensis strain Marseille-P2639T (=CSURP2639) were isolated from human stool samples. The phylogenetic analysis, phenotypic characteristics and genotypic data presented here prove that these three bacteria are different from previously known bacterial species with standing in nomenclature and represent new Bacillus species.
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Affiliation(s)
- M. Sarr
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - C.I. Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - M.L. Tall
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - A. Fadlane
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - B. Senghor
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - C. Sokhna
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - D. Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - M. Million
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - F. Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
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20
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Bordigoni A, Lo C, Yimagou E, Diop K, Nicaise B, Raoult D, Desnues C, Fenollar F. Megasphaera vaginalis sp. nov. and Anaerococcus vaginimassiliensis sp. nov., new bacteria isolated from vagina of French woman with bacterial vaginosis. New Microbes New Infect 2020; 37:100706. [PMID: 32774867 PMCID: PMC7404545 DOI: 10.1016/j.nmni.2020.100706] [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: 04/29/2020] [Revised: 05/26/2020] [Accepted: 05/29/2020] [Indexed: 11/25/2022] Open
Abstract
Using the culturomics method, two strains were isolated, identified and characterized following the taxonogenomics concept. Megasphaera vaginalis sp. nov. strain Marseille-P4512 (= CSURP4512) and Anaerococcus vaginimassiliensis sp. nov. strain Marseille-P4857 (= CSURP4857) were isolated from the vagina of a French woman. The phylogenic tree, phenotypic criteria and genomic analysis described here clearly show that these two bacteria are different from previously known bacterial species with standing in nomenclature and new members of Firmicutes phylum.
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Affiliation(s)
- A. Bordigoni
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - E.K. Yimagou
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - K. Diop
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - B. Nicaise
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C. Desnues
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - F. Fenollar
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
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21
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Traore S, Ngom I, Lo C, Di Pinto F, Sokhna C, Fournier PE, Raoult D, Fenollar F. Detailed description of Senegalia massiliensis strain SIT17 T , a bacterium isolated from the human gut. New Microbes New Infect 2020; 37:100700. [PMID: 32793352 PMCID: PMC7414013 DOI: 10.1016/j.nmni.2020.100700] [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: 12/19/2019] [Revised: 04/30/2020] [Accepted: 05/15/2020] [Indexed: 11/21/2022] Open
Abstract
Strain SIT17T was isolated from the stool of a healthy 13-month-old Senegalese boy. It is a Gram-positive, anaerobic, rod-shaped, non-spore-forming and mobile bacterium. It exhibited 92.74% 16S rRNA gene sequence similarity with the Brassicibacter thermophilus strain Cel2f, the phylogenetically most closely related species. Its genome is about 2.87 Mb long with 27.39 mol% G + C content. We provide more details of Senegalia massiliensis strain SIT17T (= CSURP2130 = DSM 103071), the creation of which was previously announced.
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Affiliation(s)
- S.I. Traore
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - I.I. Ngom
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - F. Di Pinto
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C. Sokhna
- IHU-Méditerranée Infection, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - P.-E. Fournier
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - F. Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
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22
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Konate S, Lo CI, Kuete E, Sarr M, Amsrtong N, Levasseur A, Caputo A, Thera MA, Raoult D, Million M. Halobacillus ihumii sp. nov., a new bacterium isolated from stool of healthy children living in Mali. New Microbes New Infect 2020; 37:100708. [PMID: 32793353 PMCID: PMC7408719 DOI: 10.1016/j.nmni.2020.100708] [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: 02/20/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/02/2022] Open
Abstract
Strain Marseille-Q1234T is a new species from the genus Halobacillus that was isolated in 2019 from a stool sample in a healthy Malian child <5 years old. Cells are Gram-positive and strictly halophilic bacilli. Strain Marseille-Q1234T exhibits 98.46% 16S rRNA gene sequence similarity to Halobacillus naozhouensis strain JSM 071068T (NR_116505.1), the phylogenetically closely related species with standing in nomenclature. Based on the phenotypic and phylogenetic evidence, OrthoANI values and results of the biochemical tests, the new species is named Halobacillus ihumii sp. nov., for which strain Marseille-Q1234T (= CSURQ1234) is proposed as the type strain.
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Affiliation(s)
- S Konate
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - C I Lo
- IHU-Méditerranée Infection, Marseille, France.,Université des Sciences, des Techniques et des Technologies de Bamako, Mali
| | - E Kuete
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - M Sarr
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - N Amsrtong
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - A Levasseur
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - A Caputo
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - M A Thera
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - M Million
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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23
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Belkacemi S, Lo C, Khelaifia S, Raoult D, Fournier PE, Fenollar F. Description of Prevotella rectalis sp. nov., a new bacterium isolated from human rectum. New Microbes New Infect 2020; 36:100703. [PMID: 32566232 PMCID: PMC7298541 DOI: 10.1016/j.nmni.2020.100703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/19/2020] [Accepted: 05/22/2020] [Indexed: 12/22/2022] Open
Abstract
Using a taxonogenomics method, we describe here a Gram-negative bacterium named Prevotella rectalis sp. nov., strain Marseille-P4334T (= CSUR P4334) isolated from the rectum. Strain Marseille-P4334T has a genome that measure 3.03 Mbp with 43.3 mol% G + C content.
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Affiliation(s)
- S. Belkacemi
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - S. Khelaifia
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - P.-E. Fournier
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - F. Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
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24
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Clostridium massiliamazoniense sp. nov., New Bacterial Species Isolated from Stool Sample of a Volunteer Brazilian. Curr Microbiol 2020; 77:2008-2015. [PMID: 32613254 PMCID: PMC7415036 DOI: 10.1007/s00284-020-02099-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/18/2020] [Indexed: 12/20/2022]
Abstract
The study of the gut microbiota by the "culturomics concept" permitted us to isolate, from human stool sample, an unknown anaerobic bacterium within the genus Clostridium for which we propose the name Clostridium massiliamazoniense sp. nov. It was isolated from the fecal flora of a healthy 49-year-old Brazilian male. Here, we describe the characteristics of this organism and its complete genome sequencing and annotation. Clostridium massiliamazoniense sp. nov., ND2T (= CSURP1360 = DSMZ 27309) is a Gram-positive, obligate anaerobic member of Firmicutes with a 3,732,600 bp-long genome and a G+C content of 27.6%.
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25
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Zheng ML, Li LH, Liu B, Lin YB, Zhang XT, Chen C, Qu PH, Zeng J. Haemophilus seminalis sp. nov., isolated from human semen. Int J Syst Evol Microbiol 2020; 70:2588-2595. [PMID: 32163029 DOI: 10.1099/ijsem.0.004074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Haemophilus-like isolates with similar biochemical characteristics, designated strains SZY H1T and SZY H2, were isolated from human semen specimens. Cells were Gram-negative, non-motile, non-acid-fast, pleomorphic rods or coccobacilli. The major fatty acids (>10 %) were C16 : 0, C14 : 0, iso-C16 : 0 and/or C14 : 0 3-OH and C16 : 1 ω6c and/or C16 : 1 ω7c. The polar lipids were determined to be phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminophospholipid, two unidentified polar lipids and four unidentified aminolipids. The major polyamine was found to be cadaverine. The near-full-length (1462 nt) 16S rRNA gene sequences analysis showed the two isolates were nearly identical (>99.8 %), and closely matched Haemophilus haemolyticus ATCC 33390T with 98.9-99.1 % sequence similarities. Phylogenetic analysis based on 16S rRNA gene sequences and concatenation of 30 protein markers also revealed that the isolates clustered together with H. haemolyticus ATCC 33390T, and formed a distinct lineage well separated from the other members of the genus Haemophilus. Further, the average nucleotide identity values between the two isolates and their related species were below the established cut-off values for species delineation (95 %). Based on these findings, the two isolates are considered to represent a new species of the genus Haemophilus, for which name Haemophilus seminalis sp. nov. is proposed. The type strain is SZY H1T (=NBRC 113782T=CGMCC 1.17137T).
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Affiliation(s)
- Min-Ling Zheng
- The Second Clinic Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, PR China
| | - Liang-Hui Li
- The Second Clinic Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, PR China
| | - Bin Liu
- The Second Hospital, University of South China, Hengyang 421001, PR China
| | - Yu-Bo Lin
- Department of Clinical Laboratory, Wuchuan Maternity and Child Health Care Hospital, Wuchuan 524500, PR China
| | - Xiao-Tuan Zhang
- The Second Hospital, University of South China, Hengyang 421001, PR China
| | - Cha Chen
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou 510006, PR China.,The Second Clinic Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, PR China
| | - Ping-Hua Qu
- The Second Clinic Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, PR China.,Department of Clinical Laboratory, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou 510006, PR China
| | - Jian Zeng
- The Second Hospital, University of South China, Hengyang 421001, PR China
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26
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Benabdelkader S, Naud S, Lo CI, Fadlane A, Traore SI, Aboudharam G, La Scola B. Parabacteroides pacaensis sp. nov. and Parabacteroides provencensis sp. nov., two new species identified from human gut microbiota. New Microbes New Infect 2020; 34:100642. [PMID: 32071723 PMCID: PMC7013006 DOI: 10.1016/j.nmni.2019.100642] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 12/27/2019] [Indexed: 12/12/2022] Open
Abstract
Strains Marseille-P4001 and Marseille-P3668 are new species from the order Bacteroidales isolated from healthy French volunteers. They are anaerobic Gram-negative rod-shaped bacteria. They exhibited 92.68% and 96.68% 16S rRNA sequence identities with Parabacteroides gordonii strain MS-1 and Parabacteroides chinchillae JCM 17104, respectively, the phylogenetically closest species. Their respective draft genomes measured 5.23 Mb and 3.73 Mb with 39.2 mol% and 40.8 mol% of G + C content. Using a taxonogenomics method, we propose here a brief description of Parabacteroides pacaensis sp. nov., strain Marseille-P4001T and Parabacteroides provencensis sp. nov., strain Marseille-P3668T as new bacterial species.
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Affiliation(s)
- S Benabdelkader
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - S Naud
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - C I Lo
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - A Fadlane
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - S I Traore
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - G Aboudharam
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,UFR Odontologie, Aix-Marseille Université, Marseille, France
| | - B La Scola
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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27
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Benabdelkader S, Boxberger M, Lo CI, Aboudharam G, La Scola B, Fenollar F. Corynebacterium dentalis sp. nov., a new bacterium isolated from dental plaque of a woman with periodontitis. New Microbes New Infect 2020; 33:100625. [PMID: 31908782 PMCID: PMC6939014 DOI: 10.1016/j.nmni.2019.100625] [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: 09/17/2019] [Accepted: 10/30/2019] [Indexed: 11/16/2022] Open
Abstract
Strain Marseille-P4122T is a new species from the order Corynebacteriales that was isolated from the dental plaque of a woman with periodontitis. It is a facultative anaerobic Gram-positive rod-shaped bacterium. Strain Marseille-P4122T exhibited a 98.19% sequence identity with Corynebacterium suicordis strain P81/02, the phylogenetically closely related species with standing in nomenclature. The draft genome size of strain Marseille-P4122T is 2.49 Mb with 60.1% G + C content. We propose that strain Marseille-P4122T (=CSURP4122) is the type strain of the new species Corynebacterium dentalis sp. nov.
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Affiliation(s)
- S Benabdelkader
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - M Boxberger
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - C I Lo
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - G Aboudharam
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,UFR Odontologie, Aix-Marseille Université, Marseille, France
| | - B La Scola
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - F Fenollar
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
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28
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Lo C, Fall N, Fadlane A, Armstrong N, Fournier PE, Sokhna C, Raoult D, Fenollar F, Lagier JC. Vaginisenegalia massiliensis gen. nov., sp. nov., a new bacterium isolated from the vagina flora and its taxono-genomic description. New Microbes New Infect 2019; 32:100601. [PMID: 31641516 PMCID: PMC6796746 DOI: 10.1016/j.nmni.2019.100601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 08/30/2019] [Indexed: 12/22/2022] Open
Abstract
Strain Marseille-P5643T was isolated from a vaginal sample of a healthy Senegalese woman. It is an anaerobic Gram-negative, rod-shaped bacterium. Strain Marseille-P5643T exhibits 93.7% similarity levels with the Facklamia hominis strain ATCC 700628T, the phylogenetically closest related species with standing in nomenclature. The draft genome size of strain Marseille-P5643T is 1.79 Mb with 39.0 mol% of G+C content. We propose here the creation of Vaginisenegalia massiliensis gen. nov., sp. nov., as a new bacterial genus from the phylum Firmicutes.
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Affiliation(s)
- C.I. Lo
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - N.S. Fall
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - A. Fadlane
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - N. Armstrong
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - P.-E. Fournier
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C. Sokhna
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - F. Fenollar
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - J.-C. Lagier
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
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29
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Bellali S, Lo C, Naud S, Fonkou M, Armstrong N, Raoult D, Fournier PE, Fenollar F. Parabacteroides massiliensis sp. nov., a new bacterium isolated from a fresh human stool specimen. New Microbes New Infect 2019; 32:100602. [PMID: 31641517 PMCID: PMC6796604 DOI: 10.1016/j.nmni.2019.100602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 08/30/2019] [Indexed: 12/22/2022] Open
Abstract
Parabacteroides massiliensis sp. nov., strain Marseille-P2231T (= CSURP2231 = DSM 101860) is a new species within the family Tannerellaceae. It was isolated from a stool specimen of a 25-year-old healthy woman. Its genome was 5 013 798 bp long with a 45.7 mol% G+C content. The closest species based on 16S rRNA sequence was Parabacteroides merdae strain JCM 9497T with 98.19% sequence similarity. Considering phenotypic features and comparative genome studies, we proposed the strain Marseille-P2231T as the type strain of Parabacteroides massiliensis sp. nov., a new species within the genus Parabacteroides.
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Affiliation(s)
- S. Bellali
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - S. Naud
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - M.D.M. Fonkou
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - N. Armstrong
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - P.-E. Fournier
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - F. Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
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30
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Ndiaye C, Fall N, Kuete E, Lo C, Raoult D, Sokhna C, Lagier JC. Corynebacterium senegalense sp. nov. and Arthrobacter senegalensis sp. nov., two new Actinobacteria isolated from skin swab from the palm of hand. New Microbes New Infect 2019; 31:100583. [PMID: 31372232 PMCID: PMC6658988 DOI: 10.1016/j.nmni.2019.100583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/24/2019] [Indexed: 12/22/2022] Open
Abstract
Corynebacterium senegalense strain Marseille-P4329T (= CSURP4329) and Arthrobacter senegalensis strain Marseille-P4329T (= CSURP4198) are new species first isolated from human skin. A culturomics approach and taxonogenomics methods were used for these new bacterial species.
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Affiliation(s)
- C. Ndiaye
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - N.S. Fall
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - E. Kuete
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - C. Sokhna
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - J.-C. Lagier
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- Corresponding author: J.-C. Lagier, Institut Hospitalo-Universitaire Méditerranée-Infection, 19–21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
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31
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Mekhalif F, Tidjani Alou M, Zgheib R, Lo C, Fournier PE, Raoult D, Lagier JC. Brachybacterium massiliense sp. nov., a new bacterium isolated from stool from a healthy Senegalese child. New Microbes New Infect 2019; 31:100588. [PMID: 31463068 PMCID: PMC6710231 DOI: 10.1016/j.nmni.2019.100588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
Based on our phenotypic and genotypic analyses, Brachybacterium massiliense strain Marseille-P2240T (= CSURP2240; = DSM 101766) is a new species isolated from stool of a healthy subject. The strain was stained Gram-positive. It was aerobic, catalase-positive and oxidase-negative. Its optimal growth occurs at 37°C in aerobic condition. The 16S ribosomal RNA sequence analysis revealed that strain Marseille-P2240T shown 98.18% similarity with Brachybacterium saurashtrense strain JG 06, the more closely related species with standing in nomenclature.
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Affiliation(s)
- F. Mekhalif
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - M. Tidjani Alou
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - R. Zgheib
- IHU-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - C.I. Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - P.-E. Fournier
- IHU-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - J.-C. Lagier
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
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32
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Lo C, Niang E, Guilhot E, Raoult D, Fournier PE, Fenollar F. Varibaculum timonense sp. nov., a new bacterial species isolated from human stool sample. New Microbes New Infect 2019; 31:100575. [PMID: 31333849 PMCID: PMC6624321 DOI: 10.1016/j.nmni.2019.100575] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/30/2019] [Accepted: 06/05/2019] [Indexed: 12/22/2022] Open
Abstract
Varibaculum timonense sp. nov. strain Marseille-P3369T (= CSURP3369) is a new species from the order Actinomycetales that has been isolated from a fresh stool sample of a healthy French woman.
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Affiliation(s)
- C.I. Lo
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - E.H.A. Niang
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
| | - E. Guilhot
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
| | - D. Raoult
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
| | - P.-E. Fournier
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - F. Fenollar
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
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33
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Fall N, Lo C, Fournier PE, Sokhna C, Raoult D, Fenollar F, Lagier JC. 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. [PMID: 31367386 PMCID: PMC6656688 DOI: 10.1016/j.nmni.2019.100585] [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: 05/02/2019] [Revised: 06/19/2019] [Accepted: 06/26/2019] [Indexed: 12/22/2022] Open
Abstract
Culturomics studies the microbial variety of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. This study identifies three putative new bacterial species: Arcanobacterium ihumii sp. nov. strain Marseille-P5647T, Varibaculum vaginae sp. nov. strain Marseille-P5644T and Tessaracoccus timonensis sp. nov. strain Marseille-P5995T, which we describe according to the concept of taxonogenomics.
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Affiliation(s)
- N.S. Fall
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - P.-E. Fournier
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C. Sokhna
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - F. Fenollar
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - J.-C. Lagier
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
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34
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Ndiaye C, Lo CI, Bassene H, Raoult D, Lagier JC, Sokhna C. Lysinibacillus timonensis sp. nov., Microbacterium timonense sp. nov., and Erwinia mediterraneensis sp. nov., three new species isolated from the human skin. New Microbes New Infect 2019; 31:100579. [PMID: 31338200 PMCID: PMC6626113 DOI: 10.1016/j.nmni.2019.100579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 06/12/2019] [Indexed: 11/05/2022] Open
Abstract
Lysinibacillus timonensis strain Marseille-P5727T (=CSURP5727), Microbacterium timonense strain Marseille-P5731T (=CSURP5731) and Erwinia mediterraneensis strain Marseille-P5165T (=CSURP5165) are three new species isolated from the human skin.
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Affiliation(s)
- C Ndiaye
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - C I Lo
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - H Bassene
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - J-C Lagier
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - C Sokhna
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
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35
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Munson E, Carroll KC. An Update on the Novel Genera and Species and Revised Taxonomic Status of Bacterial Organisms Described in 2016 and 2017. J Clin Microbiol 2019; 57:e01181-18. [PMID: 30257907 PMCID: PMC6355528 DOI: 10.1128/jcm.01181-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recognition and acknowledgment of novel bacterial taxonomy and nomenclature revisions can impact clinical practice, disease epidemiology, and routine clinical microbiology laboratory operations. The Journal of Clinical Microbiology (JCM) herein presents its biannual report summarizing such changes published in the years 2016 and 2017, as published and added by the International Journal of Systematic and Evolutionary Microbiology Noteworthy discussion centers around descriptions of novel Corynebacteriaceae and an anaerobic mycolic acid-producing bacterium in the suborder Corynebacterineae; revisions within the Propionibacterium, Clostridium, Borrelia, and Enterobacter genera; and a major reorganization of the family Enterobacteriaceae. JCM intends to sustain this series of reports as advancements in molecular genetics, whole-genome sequencing, and studies of the human microbiome continue to produce novel taxa and clearer understandings of bacterial relatedness.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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36
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Chabriere E, Bassène H, Drancourt M, Sokhna C. MALDI-TOF MS and point of care are disruptive diagnostic tools in Africa. New Microbes New Infect 2018; 26:S83-S88. [PMID: 30402248 PMCID: PMC6205576 DOI: 10.1016/j.nmni.2018.08.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/30/2018] [Accepted: 08/30/2018] [Indexed: 12/13/2022] Open
Abstract
We review reviewing our experience of point-of-care and mass spectrometry in Senegal as two disruptive technologies promoting the rapid diagnosis of infection, permitting better medical management of patients.
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Affiliation(s)
- E. Chabriere
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - H. Bassène
- Aix Marseille Université, IRD, APHM, VITROME, IHU-Méditerranée Infection, Marseille, France
- VITROME, Campus International IRD-UCAD de Hann, Dakar, Senegal
| | - M. Drancourt
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - C. Sokhna
- Aix Marseille Université, IRD, APHM, VITROME, IHU-Méditerranée Infection, Marseille, France
- VITROME, Campus International IRD-UCAD de Hann, Dakar, Senegal
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37
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Oren A, Garrity GM. List of novel names and novel combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2017; 67:2075-2078. [DOI: 10.1099/ijsem.0.002122] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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38
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Janda JM. Taxonomic update on proposed nomenclature and classification changes for bacteria of medical importance, 2016. Diagn Microbiol Infect Dis 2017; 88:100-105. [PMID: 28238386 DOI: 10.1016/j.diagmicrobio.2017.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/06/2017] [Indexed: 12/22/2022]
Abstract
A key aspect of medical, public health, and diagnostic microbiology laboratories is the accurate identification and rapid reporting and communication to medical staff regarding patients with infectious agents of clinical importance. Microbial taxonomy in the age of molecular diagnostics and phylogenetics creates changes in taxonomy at a logarithmic rate further complicating this process. This update focuses on the description of new species and classification changes proposed in 2016.
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Affiliation(s)
- J Michael Janda
- Public Health Laboratory, Public Health Services Department, Kern County, Bakersfield, CA, 93306-3302.
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