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Decadt H, Vermote L, Díaz-Muñoz C, Weckx S, De Vuyst L. Decarboxylase activity of the non-starter lactic acid bacterium Loigolactobacillus rennini gives crack defects in Gouda cheese through the production of γ-aminobutyric acid. Appl Environ Microbiol 2024; 90:e0165523. [PMID: 38231565 PMCID: PMC10880667 DOI: 10.1128/aem.01655-23] [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: 09/18/2023] [Accepted: 11/29/2023] [Indexed: 01/18/2024] Open
Abstract
Ten Gouda cheese wheels with an age of 31 weeks from six different batch productions were affected by a crack defect and displayed an unpleasant off-flavor. To unravel the causes of these defects, the concentrations of free amino acids, other organic acids, volatile organic compounds, and biogenic amines were quantified in zones around the cracks and in zones without cracks, and compared with those of similar Gouda cheeses without crack defect. The Gouda cheeses with cracks had a significantly different metabolome. The production of the non-proteinogenic amino acid γ-aminobutyric acid (GABA) could be unraveled as the key mechanism leading to crack formation, although the production of the biogenic amines cadaverine and putrescine contributed as well. High-throughput amplicon sequencing of the full-length 16S rRNA gene based on whole-community DNA revealed the presence of Loigolactobacillus rennini and Tetragenococcus halophilus as most abundant non-starter lactic acid bacteria in the zones with cracks. Shotgun metagenomic sequencing allowed to obtain a metagenome-assembled genome of both Loil. rennini and T. halophilus. However, only Loil. rennini contained genes necessary for the production of GABA, cadaverine, and putrescine. Metagenetics further revealed the brine and the rennet used during cheese manufacturing as the most plausible inoculation sources of both Loil. rennini and T. halophilus.IMPORTANCECrack defects in Gouda cheeses are still poorly understood, although they can lead to major economic losses in cheese companies. In this study, the bacterial cause of a crack defect in Gouda cheeses was identified, and the pathways involved in the crack formation were unraveled. Moreover, possible contamination sources were identified. The brine bath might be a major source of bacteria with the potential to deteriorate cheese quality, which suggests that cheese producers should regularly investigate the quality and microbial composition of their brines. This study illustrated how a multiphasic approach can understand and mitigate problems in a cheese company.
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Affiliation(s)
- Hannes Decadt
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Louise Vermote
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Cristian Díaz-Muñoz
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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Subramanian P, Kim Y, Naito H, Asano T, Hamada M, Weon HY, Kwon SW, Heo J. Gracilibacillus salinarum sp. nov. and Gracilibacillus caseinilyticus sp. nov., halotolerant bacteria isolated from a saltern environment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37787383 DOI: 10.1099/ijsem.0.005965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
Abstract
Two aerobic, Gram-stain-positive, spore-forming motile bacterial strains, designated SSPM10-3T and SSWR10-1T, were isolated from salterns in Jeollanam province of South Korea. Both strains were halotolerant and grew well in 5 % NaCl but not in 20 and 25% NaCl, respectively. Optimal growth was observed with 5 % NaCl, at 30 °C and at pH 7.0-8.0. On the basis of the results of phylogenetic analysis using 16S rRNA gene sequence, both the strains were placed within the genus Gracilibacillus with Gracilibacillus massiliensis (98.65 % similarity) as their nearest neighbour. Menaquinone-7 (MK-7) (97 %) was the major isoprenoid quinone in both strains and major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. Orthologous average nucleotide identity with usearch (OrthoANIu) and digital DNA-DNA hybridisation (dDDH) percentage comparison indicated that SSPM10-3T and SSWR10-1T exhibited highest similarity with G. massiliensis Awa-1T at 74.27 % and 21.0 and 74.23 % and 20.0 %, respectively. The DNA G+C contents of the strains were 39.1 % (SSPM10-3T) and 38.5 % (SSWR10-1T). Members of the genus Gracilibacillus, both strains were distinct from each other with respect to their ability to produce urease, β-glucosidase, assimilation of inulin and methyl-α-d-glucopyranoside and degradation of casein. Compared with each other, ANI and d4 dDDH calculations were only 88.2 % and 36.3 %, well below the cut-off values for species delineation for each index. On the basis of their phenotypic, physiological, biochemical and phylogenetic characteristics,SSPM10-3T and SSWR10-1T represent distinct novel species for which names Gracilibacillus salinarum SSPM10-3T and Gracilibacillus caseinilyticus SSWR10-1T are proposed. The type strains are SSPM10-3T (=KACC 21933T =NBRC 115502T) and SSWR10-1T (=KACC 21934T =NBRC 115503T).
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Affiliation(s)
- Parthiban Subramanian
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Yiseul Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Hanako Naito
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomomi Asano
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
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3
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Guindo CO, Morsli M, Bellali S, Drancourt M, Grine G. A Tetragenococcus halophilus human gut isolate. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100112. [PMID: 35243447 PMCID: PMC8866149 DOI: 10.1016/j.crmicr.2022.100112] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 10/28/2022] Open
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Deutch CE, Farden AM, DiCesare ES. Characterization of β-galactosidase and α-galactosidase activities from the halophilic bacterium Gracilibacillus dipsosauri. ANN MICROBIOL 2021. [DOI: 10.1186/s13213-021-01657-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Gracilibacillus dipsosauri strain DD1 is a salt-tolerant Gram-positive bacterium that can hydrolyze the synthetic substrates o-nitrophenyl-β-d-galactopyranoside (β-ONP-galactose) and p-nitrophenyl-α-d-galactopyranoside (α-PNP-galactose). The goals of this project were to characterize the enzymes responsible for these activities and to identify the genes encoding them.
Methods
G. dipsosauri strain DD1 was grown in tryptic soy broth containing various carbohydrates at 37 °C with aeration. Enzyme activities in cell extracts and whole cells were measured colorimetrically by hydrolysis of synthetic substrates containing nitrophenyl moieties. Two enzymes with β-galactosidase activity and one with α-galactosidase activity were partially purified by ammonium sulfate fractionation, ion-exchange chromatography, and gel-filtration chromatography from G. dipsosauri. Coomassie Blue-stained bands corresponding to each activity were excised from nondenaturing polyacrylamide gels and subjected to peptide sequencing after trypsin digestion and HPLC/MS analysis.
Result
Formation of β-galactosidase and α-galactosidase activities was repressed by d-glucose and not induced by lactose or d-melibiose. β-Galactosidase I had hydrolytic and transgalactosylation activity with lactose as the substrate but β-galactosidase II showed no activity towards lactose. The α-galactosidase had hydrolytic and transgalactosylation activity with d-melibiose but not with d-raffinose. β-Galactosidase I had a lower Km with β-ONP-galactose as the substrate (0.693 mmol l−1) than β-galactosidase II (1.662 mmol l−1), was active at more alkaline pH, and was inhibited by the product d-galactose. β-Galactosidase II was active at more acidic pH, was partially inhibited by ammonium salts, and showed higher activity with α-PNP-arabinose as a substrate. The α-galactosidase had a low Km with α-PNP-galactose as the substrate (0.338 mmol l−1), a pH optimum of about 7, and was inhibited by chloride-containing salts. β-Galactosidase I activity was found to be due to the protein A0A317L6F0 (encoded by gene DLJ74_04930), β-galactosidase II activity to the protein A0A317KZG3 (encoded by gene DLJ74_12640), and the α-galactosidase activity to the protein A0A317KU47 (encoded by gene DLJ74_17745).
Conclusions
G. dipsosauri forms three intracellular enzymes with different physiological properties which are responsible for the hydrolysis of β-ONP-galactose and α-PNP-galactose. BLAST analysis indicated that similar β-galactosidases may be formed by G. ureilyticus, G. orientalis, and G. kekensis and similar α-galactosidases by these bacteria and G. halophilus.
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Kangale LJ, Raoult D, Ghigo E, Fournier PE. Chryseobacterium schmidteae sp. nov. a novel bacterial species isolated from planarian Schmidtea mediterranea. Sci Rep 2021; 11:11002. [PMID: 34040129 PMCID: PMC8155073 DOI: 10.1038/s41598-021-90562-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/13/2021] [Indexed: 02/07/2023] Open
Abstract
Marseille-P9602T is a Chryseobacterium-like strain that we isolated from planarian Schmidtea mediterranea and characterized by taxono-genomic approach. We found that Marseille-P9602T strain exhibits a 16S rRNA gene sequence similarity of 98.76% with Chryseobacterium scophthalmum LMG 13028T strain, the closest phylogenetic neighbor. Marseille-P9602T strain was observed to be a yellowish-pigmented, Gram-negative, rod-shaped bacterium, growing in aerobic conditions and belonging to the Flavobacteriaceae family. The major fatty acids detected are 13-methyl-tetradecanoic acid (57%), 15-methylhexadecenoic acid (18%) and 12-methyl-tetradecanoic acid (8%). Marseille-P9602 strain size was found from genome assembly to be of 4,271,905 bp, with a 35.5% G + C content. The highest values obtained for Ortho-ANI and dDDH were 91.67% and 44.60%, respectively. Thus, hereby we unravel that Marseille-P9602 strain is sufficiently different from other closed related species and can be classified as a novel bacterial species, for which we propose the name of Chryseobacterium schmidteae sp. nov. Type strain is Marseille-P9602T (= CSUR P9602T = CECT 30295T).
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Affiliation(s)
- Luis Johnson Kangale
- IRD, AP-HM, SSA, VITROME, Aix-Marseille Univ, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, IHU-Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée Infection, IHU-Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
- IRD, AP-HM, MEPHI, Aix-Marseille Univ, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Eric Ghigo
- Institut Hospitalo-Universitaire Méditerranée Infection, IHU-Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.
- TechnoJouvence, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.
| | - Pierre-Edouard Fournier
- IRD, AP-HM, SSA, VITROME, Aix-Marseille Univ, Marseille, France.
- Institut Hospitalo-Universitaire Méditerranée Infection, IHU-Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.
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6
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Direct Diagnosis of Echovirus 12 Meningitis Using Metagenomic Next Generation Sequencing. Pathogens 2021; 10:pathogens10050610. [PMID: 34067526 PMCID: PMC8156364 DOI: 10.3390/pathogens10050610] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/02/2021] [Accepted: 05/12/2021] [Indexed: 11/17/2022] Open
Abstract
The current point-of-care diagnosis of enterovirus meningitis does not identify the viral genotype, which is prognostic. In this case report, more than 81% of an Echovirus 12 genome were detected and identified by metagenomic next-generation sequencing, directly from the cerebrospinal fluid collected in a 6-month-old child with meningeal syndrome and meningitis: introducing Echovirus 12 as an etiological agent of acute meningitis in the pediatric population.
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Morsli M, Vincent JJ, Milliere L, Colson P, Drancourt M. Direct next-generation sequencing diagnosis of echovirus 9 meningitis, France. Eur J Clin Microbiol Infect Dis 2021; 40:2037-2039. [PMID: 33694039 DOI: 10.1007/s10096-021-04205-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/17/2021] [Indexed: 12/15/2022]
Abstract
The prognosis of central nervous system infections caused by enteroviruses partially depends on the viral genotype, which is not provided by current point-of-care diagnostic methods. In this study, next-generation sequencing identified an echovirus 9 directly from the cerebrospinal fluid of a patient presenting with meningitis.
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Affiliation(s)
- Madjid Morsli
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, IHU Méditerranée Infection, Marseille, France
| | - Jean-Jacques Vincent
- IHU Méditerranée Infection, Marseille, France
- Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU Méditerranée Infection, Marseille, France
| | - Laurine Milliere
- IHU Méditerranée Infection, Marseille, France
- Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU Méditerranée Infection, Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, IHU Méditerranée Infection, Marseille, France
| | - Michel Drancourt
- IHU Méditerranée Infection, Marseille, France.
- Aix-Marseille Université, IRD, IHU Méditerranée Infection, Marseille, France.
- Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU Méditerranée Infection, Marseille, France.
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8
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He SW, Wang X, Guo HB, Han JG, Thin KK, Gao JS, Ma LA, Zhang XX. Gracilibacillus oryzae sp. nov., isolated from rice seeds. Int J Syst Evol Microbiol 2020; 70:5467-5472. [PMID: 32894210 DOI: 10.1099/ijsem.0.004427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, facultatively anaerobic, endospore-forming bacterium, designated strain TD8T, was isolated from surface-sterilized rice seeds (Oryza sativa L.). Phylogenetic analysis of the 16S rRNA gene indicated that strain TD8T should be placed within the genus Gracilibacillus (95.2-99.0 % sequence similarity); it exhibited highest similarities to Gracilibacillus ureilyticus CGMCC 1.7727T (99.0 %), 'Gracilibacillus xinjiangensis' CGMCC 1.12449T (98.9 %) and Gracilibacillus dipsosauri CGMCC 1.3642T (97.5 %). Chemotaxonomic analysis showed that menaquinone-7 (MK-7) was the major isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid were the major cellular polar lipids, and the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0, which supported the allocation of the strain to the genus Gracilibacillus. The digital DNA-DNA hybridization value between strain TD8T and Gracilibacillus ureilyticus CGMCC 1.7727T was lower than 70 % (22.60 %), and the average nucleotide identity score was 79.54±5.09 %, suggesting that strain TD8T represented a novel species in the genus Gracilibacillus. The genomic DNA G+C content was 37.5 %. Based on physiological and biochemical characteristics and genotypic data, strain TD8T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus oryzae sp. nov. is proposed. The type strain is TD8T (=ACCC 61556T=CICC 24889T=JCM 33537T).
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Affiliation(s)
- Shan-Wen He
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,College of Life Science, The Yangtze University, Jingzhou 434025, PR China
| | - Xing Wang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - He-Bao Guo
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Ji-Gang Han
- Shanghai Academy of Landscape Architecture Science and Planning, Shanghai 200232, PR China
| | - Kyu Kyu Thin
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Ju-Sheng Gao
- Qiyang Agro-ecosystem of National Field Experimental Station, Institute of Agricultural Resources and Regional, Chinese Academy of Agricultural Sciences, Qiyang 426182, PR China.,Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Li-An Ma
- College of Life Science, The Yangtze University, Jingzhou 434025, PR China
| | - Xiao-Xia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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9
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Enterococcus burkinafasonensis sp. nov . isolated from human gut microbiota. New Microbes New Infect 2020; 36:100702. [PMID: 32528688 PMCID: PMC7283139 DOI: 10.1016/j.nmni.2020.100702] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/14/2020] [Accepted: 05/19/2020] [Indexed: 12/22/2022] Open
Abstract
Strain Marseille-Q0835T is an aerobic, non-motile and non-spore-forming Gram-positive coccus isolated from the stools of a Burkinabe woman. In this report, we present its phenotypic description including MALDI-TOF mass spectrometry analysis and genome sequencing. Strain Marseille-Q0835T; 2.9768-Mb genome exhibited a 41.9 mol% G+C content and 2699 predicted genes. Considering phenotypic features and comparative genome studies, we propose the strain Marseille-Q0835T as the type strain of Enterococcus burkinafasonensis sp. nov., a new species within the family Enterococcaceae.
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10
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Deutch CE, Yang S. Genomic sequencing of Gracilibacillus dipsosauri reveals key properties of a salt-tolerant α-amylase. Antonie Van Leeuwenhoek 2020; 113:1049-1059. [PMID: 32318981 DOI: 10.1007/s10482-020-01417-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/09/2020] [Indexed: 11/26/2022]
Abstract
Gracilibacillus dipsosauri is a moderately-halophilic Gram-positive bacterium which forms an extracellular α-amylase that is induced by starch, repressed by D-glucose, and active in 2.0 M KCl. Previous studies showed that while enzyme activity could be measured with the synthetic substrate 2-chloro-4-nitrophenyl-α-D-maltotrioside (CNPG3), other assays were inconsistent and the protein showed aberrant mobility during nondenaturing gel electrophoresis. To clarify the properties of this enzyme, the genome of G. dipsosauri was sequenced and was found to be 4.19 Mb in size with an overall G+C content of 36.9%. A gene encoding an α-amylase composed of 691 amino acids was identified. The protein was a member of the glycosyl hydrolase 13 family, which had a molecular mass of 77,396 daltons and a pI of 4.39 due to an unusually large number of aspartate and glutamate residues (95/691 or 13.7%). BLAST analysis of the amino acid sequence revealed significant matches to other proteins with cyclodextrin glycosyltransferase activity. Partial purification of the protein from G. dipsosauri showed that fractions catalyzing the hydrolysis of CNPG3 and p-nitrophenyl-D-maltoheptoside also catalyzed the formation of β-cyclodextrin but not α-cyclodextrin or γ-cyclodextrin. Formation of β-cyclodextrin was not stimulated by high salt concentrations but did occur with rice, potato, wheat, and corn starches and amylopectin. These studies explain the unusual features of the α-amylase from G. dipsosauri and indicate it should be classified as EC 2.4.1.19. The availability of the complete genomic sequence of G. dipsosauri will provide the basis for studies on other enzymes from this halophile which may be useful for biotechnology.
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Affiliation(s)
- Charles E Deutch
- Microbion Research, 8931 W. Deanna Dr., Peoria, AZ, 85382, USA.
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ, 85306, USA.
| | - Shanshan Yang
- Bioinformatics Core Facility, Knowledge Enterprise, Arizona State University, Tempe, AZ, 85281, USA
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11
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Kangale LJ, Raoult D, Ghigo E, Fournier PE. Pedobacter schmidteae sp. nov., a new bacterium isolated from the microbiota of the planarian Schmidtea mediterranea. Sci Rep 2020; 10:6113. [PMID: 32273530 PMCID: PMC7145819 DOI: 10.1038/s41598-020-62985-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 03/17/2020] [Indexed: 12/22/2022] Open
Abstract
Pedobacter schmidteae sp. nov. strain EGT (Collection de Souches de l'Unité des Rickettsie CSUR P6417 = Colección Española de Cultivos Tipo CECT 9771) is a new Pedobacter species isolated from the planarian Schmidtea mediterranea. Schmidtea mediterranea are flatworms living in freshwater and exhibiting an unusual ability to regenerate amputated parts. To date, the gut microbiota of Schmidtea mediterranea remains poorly studied. Here, via the culturomics strategy that consists in using diversified culture conditions, we isolated a new bacterium, strain EG, that we characterized using the taxono-genomics approach that combines phenotypic assays and genome sequencing and analysis. Strain EG exhibits a 16S rRNA sequence similarity of 98.29% with Pedobacter nyackensis strain NWG-II14T, its closest neighbour with standing in nomenclature. It is an aerobic bacterium belonging to the family Sphingobacteriaceae. Colonies are small, round, smooth and transparent. Bacterial cells are Gram-negative, rod-shaped, motile and non-spore-forming bacilli with positive catalase and oxidase activities. The genome sequence is 6,198,518 bp-long with a G + C content of 41.13%, and the Ortho-ANI and dDDH values when compared to P. nyackensis are 77.34% and 21.50%, respectively. Strain EGT exhibits unique characteristics that classify it as the type strain of new bacterial species for which we propose the name Pedobacter schmidteae sp. nov.
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Affiliation(s)
- Luis Johnson Kangale
- Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- IHU-Méditerranée-Infection, Marseille, France
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- TechnoJouvence, 19-21 Boulevard Jean Moulin 13385, Marseille, cedex, 05, France
| | - Eric Ghigo
- Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.
- IHU-Méditerranée-Infection, Marseille, France.
- TechnoJouvence, 19-21 Boulevard Jean Moulin 13385, Marseille, cedex, 05, France.
| | - Pierre-Edouard Fournier
- Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.
- IHU-Méditerranée-Infection, Marseille, France.
- TechnoJouvence, 19-21 Boulevard Jean Moulin 13385, Marseille, cedex, 05, France.
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12
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Afouda P, Dubourg G, Tomeï E, Raoult D, Fournier PE. Dialister massiliensis sp. nov., a new bacterium isolated from the human gut. New Microbes New Infect 2020; 34:100657. [PMID: 32194963 PMCID: PMC7075989 DOI: 10.1016/j.nmni.2020.100657] [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: 11/28/2019] [Revised: 01/02/2020] [Accepted: 02/10/2020] [Indexed: 12/22/2022] Open
Abstract
Dialister massiliensis strain Marseille-P5638T (= CSUR P5638) is a new species from the genus Dialister and family Veillonellaceae which was isolated from the gut microbiota of a healthy individual.
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Affiliation(s)
- P Afouda
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - G Dubourg
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - E Tomeï
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - D Raoult
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France.,Special Infections Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P-E Fournier
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU Méditerranée Infection, Marseille, France
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13
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Yimagou E, Dione N, Ngom I, Tall M, Baudoin J, Raoult D, Khalil JB. Parabacteroides bouchesdurhonensis sp. nov., a new bacterium isolated from the stool of a healthy adult. New Microbes New Infect 2020; 34:100639. [PMID: 31993208 PMCID: PMC6974780 DOI: 10.1016/j.nmni.2019.100639] [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: 08/19/2019] [Accepted: 12/10/2019] [Indexed: 12/22/2022] Open
Abstract
Parabacteroides bouchesdurhonensis strain Marseille-P3763T (= CSURP3763) is a new species isolated from the stool of a heathy adult.
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Affiliation(s)
- E.K. Yimagou
- Aix Marseille Univ, IRD (Development Research Institute), AP-HM (Public Assistance of Marseille Hospitals), MEPHI (Microbes Evolution Phylogenie Et Infections), IHU (University Hospital Institute)-Méditerranée Infection, Marseille, France
| | - N. Dione
- Aix Marseille Univ, IRD (Development Research Institute), AP-HM (Public Assistance of Marseille Hospitals), MEPHI (Microbes Evolution Phylogenie Et Infections), IHU (University Hospital Institute)-Méditerranée Infection, Marseille, France
| | - I.I. Ngom
- Aix Marseille Univ, IRD (Development Research Institute), AP-HM (Public Assistance of Marseille Hospitals), MEPHI (Microbes Evolution Phylogenie Et Infections), IHU (University Hospital Institute)-Méditerranée Infection, Marseille, France
| | - M.L. Tall
- Aix Marseille Univ, IRD (Development Research Institute), AP-HM (Public Assistance of Marseille Hospitals), MEPHI (Microbes Evolution Phylogenie Et Infections), IHU (University Hospital Institute)-Méditerranée Infection, Marseille, France
| | - J.P. Baudoin
- Aix Marseille Univ, IRD (Development Research Institute), AP-HM (Public Assistance of Marseille Hospitals), MEPHI (Microbes Evolution Phylogenie Et Infections), IHU (University Hospital Institute)-Méditerranée Infection, Marseille, France
| | - D. Raoult
- Aix Marseille Univ, IRD (Development Research Institute), AP-HM (Public Assistance of Marseille Hospitals), MEPHI (Microbes Evolution Phylogenie Et Infections), IHU (University Hospital Institute)-Méditerranée Infection, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - J.Y. Bou Khalil
- Aix Marseille Univ, IRD (Development Research Institute), AP-HM (Public Assistance of Marseille Hospitals), MEPHI (Microbes Evolution Phylogenie Et Infections), IHU (University Hospital Institute)-Méditerranée Infection, Marseille, France
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14
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Afouda P, Dubourg G, Nguyen T, Raoult D, Fournier PE. Pseudoruminococcus massiliensis gen. nov., sp. nov., a new bacterium isolated from the human gut microbiota. New Microbes New Infect 2020; 34:100645. [PMID: 32071725 PMCID: PMC7011079 DOI: 10.1016/j.nmni.2019.100645] [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: 11/28/2019] [Accepted: 12/27/2019] [Indexed: 12/20/2022] Open
Abstract
Pseudoruminococcus massiliensis strain Marseille-P3876T (= CSUR P3876) is a new genus from the family Ruminococcaceae that was isolated from the gut microbiota of a healthy Senegalese man.
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Affiliation(s)
- P. Afouda
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - G. Dubourg
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - T.T. Nguyen
- IHU Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Special Infections Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P.-E. Fournier
- IHU Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
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15
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Takakura T, Francis R, Anani H, Bilen M, Raoult D, Bou Khalil J. Anaerosphaera massiliensis sp. nov., a new bacterium isolated from the stool of a 39-year-old Pygmy. New Microbes New Infect 2020; 33:100633. [PMID: 32021694 PMCID: PMC6994800 DOI: 10.1016/j.nmni.2019.100633] [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: 07/27/2019] [Revised: 11/25/2019] [Accepted: 12/04/2019] [Indexed: 12/22/2022] Open
Abstract
Anaerosphaera massiliensis strain Marseille-P4592T (= CSURP4592T; = CCUG72452T) is a new species isolated from the stool of a 39-year-old male Pygmy from the Democratic Republic of Congo.
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Affiliation(s)
- T. Takakura
- Hitachi High-Technologies Corporation, Analytical & Medical Solution Business Group, Ibaraki-ken, Japan
| | - R. Francis
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Developpement, UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - H. Anani
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
- Aix Marseille Université, Institut de Recherche pour le Développement, Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditeranéennes (VITROME), Marseille, France
| | - M. Bilen
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - D. Raoult
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Developpement, UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - J.Y. Bou Khalil
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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16
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Yimagou E, Tall M, Baudoin J, Raoult D, Bou Khalil J. Clostridium transplantifaecale sp. nov., a new bacterium isolated from patient with recurrent Clostridium difficile infection. New Microbes New Infect 2019; 32:100598. [PMID: 31719994 PMCID: PMC6838804 DOI: 10.1016/j.nmni.2019.100598] [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: 07/16/2019] [Accepted: 08/30/2019] [Indexed: 12/22/2022] Open
Abstract
Clostridium transplantifaecale strain Marseille-P8228T (= CSURP8228) is a new species isolated from a patient with recurrent Clostridium difficile infection.
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Affiliation(s)
- E.K. Yimagou
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - M.L. Tall
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - J.P. Baudoin
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - J.Y. Bou Khalil
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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17
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Takakura T, Anani H, Fadlane A, Fontanini A, Raoult D, Bou Khalil J. Enterobacter timonensis sp. nov., a new bacterium isolated from a fresh human stool specimen. New Microbes New Infect 2019; 32:100586. [PMID: 31719992 PMCID: PMC6839016 DOI: 10.1016/j.nmni.2019.100586] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/17/2019] [Accepted: 06/26/2019] [Indexed: 12/22/2022] Open
Abstract
Enterobacter timonensis strain mt20T (= CSUR P2201T, = DSM101775T) is a new species isolated from a fresh human stool specimen.
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Affiliation(s)
- T. Takakura
- Hitachi High-Technologies Corporation, Analytical & Medical Solution Business Group, Ibaraki-ken, Japan
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - H. Anani
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - A. Fadlane
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - A. Fontanini
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - D. Raoult
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Developpement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - J.Y. Bou Khalil
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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18
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Bellali S, Naud S, Ndongo S, Lo C, Anani H, Raoult D, Lagier JC. Corynebacterium pacaense sp. nov., Alistipes megaguti sp. nov., Alistipes provencensis sp. nov., 3 new bacteria isolated from fresh human stool specimens. New Microbes New Infect 2019; 32:100593. [PMID: 31641510 PMCID: PMC6796624 DOI: 10.1016/j.nmni.2019.100593] [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: 06/11/2019] [Revised: 08/06/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022] Open
Abstract
Here we describe the basic characteristics of Corynebacterium pacaense strain Marseille-P2417T (= CSUR P2417), Alistipes megaguti strain Marseille-P5997T (= CSUR P5997) and Alistipes provencensis strain Marseille-P2431T (= CSUR P2431 = DSM 102308). The phenotypic criteria, the 16S ribosomal RNA sequencing and MALDI-TOF MS spectra analysis were used to identify and characterize these new bacteria species, which were isolated from fresh human stool specimens.
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Affiliation(s)
- S. Bellali
- Aix-Marseille Université, IRD, MEPHI, Marseille, France
- IHU–Méditerranée Infection, Marseille, France
| | - S. Naud
- Aix-Marseille Université, IRD, MEPHI, Marseille, France
- IHU–Méditerranée Infection, Marseille, France
| | - S. Ndongo
- Aix-Marseille Université, IRD, 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
| | - H. Anani
- IHU–Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, MEPHI, Marseille, France
- IHU–Méditerranée Infection, Marseille, France
| | - J.-C. Lagier
- Aix-Marseille Université, IRD, MEPHI, Marseille, France
- IHU–Méditerranée Infection, Marseille, France
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19
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Takakura T, Francis R, Anani H, Bilen M, Raoult D, Bou Khalil J. Enterococcus mediterraneensis sp. nov., a new bacterium isolated from the stool of a 39-year-old Pygmy. New Microbes New Infect 2019; 32:100599. [PMID: 31641514 PMCID: PMC6796601 DOI: 10.1016/j.nmni.2019.100599] [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: 07/24/2019] [Accepted: 08/30/2019] [Indexed: 12/22/2022] Open
Abstract
Enterococcus mediterraneensis strain Marseille-P4358T (= CSURP4358T) is a new species isolated from the stool of a 39-year-old male Pygmy from the Democratic Republic of Congo.
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Affiliation(s)
- T. Takakura
- Hitachi High-Technologies Corporation, Analytical & Medical Solution Business Group, Ibaraki-ken, Japan
| | - R. Francis
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Developpement, UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - H. Anani
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
- Aix Marseille Université, Institut de Recherche pour le Développement, Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditeranéennes (VITROME), Marseille, France
| | - M. Bilen
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - D. Raoult
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Developpement, UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - J.Y. Bou Khalil
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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20
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Yimagou E, Anani H, Yacouba A, Hasni I, Baudoin JP, Raoult D, Bou Khalil J. Urinicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from a human urine sample from a 7-year-old boy hospitalized for dental care. New Microbes New Infect 2019; 32:100615. [PMID: 31871684 PMCID: PMC6909223 DOI: 10.1016/j.nmni.2019.100615] [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: 07/16/2019] [Revised: 10/10/2019] [Accepted: 10/17/2019] [Indexed: 12/22/2022] Open
Abstract
Urinicoccus massiliensis strain Marseille-P1992T (= CSURP1992 = DSM100581) is a species of a new genus isolated from human urine.
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Affiliation(s)
- E.K. Yimagou
- Aix Marseille University, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - H. Anani
- Aix Marseille Univ, IRD, AP-HM, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - A. Yacouba
- Aix Marseille University, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - I. Hasni
- Aix Marseille University, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - J.-P. Baudoin
- Aix Marseille University, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - J.Y. Bou Khalil
- Aix Marseille University, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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21
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Kuete Yimagou E, Mekhalif F, Lamine Tall M, Baudoin JP, Raoult D, Bou Khalil JY. Prevotella marseillensis sp. nov., a new bacterium isolated from a patient with recurrent Clostridium difficile infection. New Microbes New Infect 2019; 32:100606. [PMID: 31749965 PMCID: PMC6849444 DOI: 10.1016/j.nmni.2019.100606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/02/2019] [Accepted: 09/29/2019] [Indexed: 12/22/2022] Open
Abstract
Prevotella marseillensis strain Marseille-P8229T (= CSURP8229) is a new species isolated from a patient with recurrent Clostridium difficile infection. It is an anaerobic, non-motile, non-spore-forming Gram-negative coccobacillus isolated from the stool of patient with recurrent Clostridium difficile infection in Marseille. We present herein its phenotypic description together with MALDI-TOF mass spectrometry analysis and genome sequencing and comparison. The genome of P. marseillensis is 4.1607 Mbp long with 45.80 mol% of G+C content, and it contains 3078 protein-coding genes.
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Affiliation(s)
- E Kuete Yimagou
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - F Mekhalif
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - M Lamine Tall
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - J P Baudoin
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - D Raoult
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - J Y Bou Khalil
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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22
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Anani H, Guilhot E, Andrieu C, Fontanini A, Raoult D, Fournier PE. Prevotella ihumii sp. nov., a new bacterium isolated from a stool specimen of a healthy woman. New Microbes New Infect 2019; 32:100607. [PMID: 31719996 PMCID: PMC6838980 DOI: 10.1016/j.nmni.2019.100607] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/10/2019] [Accepted: 09/29/2019] [Indexed: 12/22/2022] Open
Abstract
Prevotella ihumii strain Marseille-P3385T (= CSURP3385T; = DSM106428T) is a new species isolated from a fresh stool specimen of a healthy woman.
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Affiliation(s)
- H Anani
- UMR VITROME, SSA, Aix-Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - E Guilhot
- IHU Méditerranée Infection, Marseille, France.,UMR MEPHI, Aix Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, Marseille, France
| | - C Andrieu
- IHU Méditerranée Infection, Marseille, France.,UMR MEPHI, Aix Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, Marseille, France
| | - A Fontanini
- IHU Méditerranée Infection, Marseille, France.,UMR MEPHI, Aix Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, Marseille, France
| | - D Raoult
- IHU Méditerranée Infection, Marseille, France.,UMR MEPHI, Aix Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, Marseille, France.,Special Infections Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P E Fournier
- UMR VITROME, SSA, Aix-Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, Marseille, France.,IHU Méditerranée Infection, Marseille, France
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23
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Niang EHA, Lo CI, Brahimi S, Armstrong N, Raoult D, Fournier PE, Fenollar F. Varibaculum massiliense sp. nov., a new bacterium isolated from human urine with culturomics. New Microbes New Infect 2019; 32:100591. [PMID: 31641508 PMCID: PMC6796757 DOI: 10.1016/j.nmni.2019.100591] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/30/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022] Open
Abstract
Varibaculum massiliense sp. nov. strain Marseille-P2802T (= CSUR P2802 = DSM 103074) is a new species within the genus Varibaculum in the phylum Actinobacteria that was isolated from the urine of a 59-year-old man treated with chronic haemodialysis for diabetic nephropathy.
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Affiliation(s)
- E H A Niang
- 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
| | - S Brahimi
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - N Armstrong
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - D Raoult
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - P-E Fournier
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - F Fenollar
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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24
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Mion S, Rémy B, Plener L, Brégeon F, Chabrière E, Daudé D. Quorum Quenching Lactonase Strengthens Bacteriophage and Antibiotic Arsenal Against Pseudomonas aeruginosa Clinical Isolates. Front Microbiol 2019; 10:2049. [PMID: 31551983 PMCID: PMC6734170 DOI: 10.3389/fmicb.2019.02049] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/20/2019] [Indexed: 01/21/2023] Open
Abstract
Many bacteria use quorum sensing (QS), a bacterial communication system based on the diffusion and perception of small signaling molecules, to synchronize their behavior in a cell-density dependent manner. QS regulates the expression of many genes associated with virulence factor production and biofilm formation. This latter is known to be involved in antibiotic and phage resistance mechanisms. Therefore, disrupting QS, a strategy known as quorum quenching (QQ), appears to be an interesting way to reduce bacterial virulence and increase antibiotic and phage treatment efficiency. In this study, the ability of the QQ enzyme SsoPox-W263I, a lactonase able to degrade acyl-homoserine lactones, was investigated for quenching both virulence and biofilm formation in clinical isolates of Pseudomonas aeruginosa from diabetic foot ulcers, as well as in the PA14 model strain. These strains were further evolved to resist to bacteriophage cocktails. Overall, 10 antibiotics or bacteriophage resistant strains were evaluated and SsoPox-W263I was shown to decrease pyocyanin, protease and elastase production in all strains. Furthermore, a reduction of more than 70% of biofilm formation was achieved in six out of ten strains. This anti-virulence potential was confirmed in vivo using an amoeba infection model, showing enhanced susceptibility toward amoeba of nine out of ten P. aeruginosa isolates upon QQ. This amoeba model was further used to demonstrate the ability of SsoPox-W263I to enhance the susceptibility of sensitive and phage resistant bacteria to bacteriophage and antibiotic.
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Affiliation(s)
- Sonia Mion
- Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Benjamin Rémy
- Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Gene&GreenTK, Marseille, France
| | | | - Fabienne Brégeon
- Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Service des Explorations Fonctionnelles Respiratoires Centre Hospitalo Universitaire Nord, Pôle Cardio-Vasculaire et Thoracique, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Eric Chabrière
- Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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25
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Kuete E, Mbogning Fonkou M, Mekhalif F, Anani H, Baudoin JP, Raoult D, Bou Khalil J. Selenomonas felix sp. nov., a new bacterium isolated from human sputum. New Microbes New Infect 2019; 31:100567. [PMID: 31333847 PMCID: PMC6614701 DOI: 10.1016/j.nmni.2019.100567] [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: 04/23/2019] [Accepted: 05/15/2019] [Indexed: 12/22/2022] Open
Abstract
Selenomonas felix strain Marseille-P3560T (=CSURP3560) is a new species isolated from human sputum.
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Affiliation(s)
- E. Kuete
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - M.D. Mbogning Fonkou
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - F. Mekhalif
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - H. Anani
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - J.-P. Baudoin
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - J.Y. Bou Khalil
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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26
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Lo C, Niang E, Ndongo S, Raoult D, Fournier PE, Fenollar F. Corynebacterium bouchesdurhonense sp. nov., and Corynebacterium provencense sp. nov., two new species isolated from obese patients. New Microbes New Infect 2019; 31:100581. [PMID: 31360527 PMCID: PMC6639746 DOI: 10.1016/j.nmni.2019.100581] [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: 03/22/2019] [Revised: 06/12/2019] [Accepted: 06/24/2019] [Indexed: 12/22/2022] Open
Abstract
Corynebacterium bouchesdurhonense sp. nov. strain Marseille-P2067T (= CSURP2067; = DSM100846) and Corynebacterium provencense sp. nov. strain Marseille-P2161T (= CSURP2161; = DSM101074) are two new species from the order Corynebacteriales that were isolated from obese French individuals.
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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, MEPHI, Marseille, France
| | - S. Ndongo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - D. Raoult
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, MEPHI, 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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27
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Kuete E, Mbogning Fonkou M, Mekhalif F, Anani H, Baudoin JP, Raoult D, Bou Khalil J. Brachybacterium timonense sp. nov., a new bacterium isolated from human sputum. New Microbes New Infect 2019; 31:100568. [PMID: 31333848 PMCID: PMC6614501 DOI: 10.1016/j.nmni.2019.100568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 05/15/2019] [Indexed: 12/22/2022] Open
Abstract
Brachybacterium timonense strain Marseille-P4339T (=CSURP4339, =CECT9821) is a new species isolated from human sputum.
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Affiliation(s)
- E. Kuete
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - M.D. Mbogning Fonkou
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - F. Mekhalif
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - H. Anani
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - J.-P. Baudoin
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - J.Y. Bou Khalil
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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28
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Niang E, Lo C, Morand A, Ndongo S, Raoult D, Fournier PE, Fenollar F. Corynebacterium urinapleomorphum sp. nov., a new bacterial species isolated from human urine sample. New Microbes New Infect 2019; 31:100576. [PMID: 31333850 PMCID: PMC6624320 DOI: 10.1016/j.nmni.2019.100576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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
Corynebacterium urinapleomorphum sp. nov. stain Marseille-P2799T (= CSURP2799; = DSM103272) is a new species from the order Corynebacteriales that was isolated from urine of a 2-month-old child with gastroenteritis.
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Affiliation(s)
- E.H.A. Niang
- 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. Morand
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - S. Ndongo
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - P.-E. Fournier
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - F. Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
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29
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Bonnet M, Ricaboni D, Mailhe M, Vitton V, Benezech A, Delerce J, Raoult D, Cassir N, Lascola B, Khelaifia S. Genome sequence and description of Coprococcus phoceensis gen. nov., sp. nov., a new bacterial genus isolated from the human left colon. New Microbes New Infect 2019; 30:100548. [PMID: 31193060 PMCID: PMC6515130 DOI: 10.1016/j.nmni.2019.100548] [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: 01/25/2019] [Revised: 03/20/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022] Open
Abstract
We report here the main characteristics of Coprococcus phoceensis strain Marseille-P3062T (CSUR P3062). The 16S rDNA sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry spectrum analysis were used to identify and characterize this new anaerobic bacterial species, which was isolated from the left colon cleansing of a 25-year-old French man with Crohn's disease.
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Affiliation(s)
- M. Bonnet
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - D. Ricaboni
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseillle, France
- Département des sciences cliniques et biomédicales, Luigi Sacco, Division des Maladies Infectieuses III, Université de Milan, Milan, Italy
| | - M. Mailhe
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - V. Vitton
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - A. Benezech
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - J. Delerce
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseillle, France
| | - N. Cassir
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - B. Lascola
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - S. Khelaifia
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseillle, France
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30
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Francis R, Anani H, Fontanini A, Fournier P, Scola B, Raoult D, Bou Khalil J. Virgibacillus ndiopensis sp. nov., a new halophilic bacterium isolated from the stool of a healthy 11-year-old boy. New Microbes New Infect 2019; 30:100541. [PMID: 31193282 PMCID: PMC6522852 DOI: 10.1016/j.nmni.2019.100541] [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: 02/04/2019] [Revised: 03/25/2019] [Accepted: 03/28/2019] [Indexed: 11/28/2022] Open
Abstract
Virgibacillus ndiopensis strain Marseille-P3835T (= CSURP3835T; = CCUG70388T) is a new specie isolated from the stool of a healthy 11-year-old boy from N'Diop, Senegal.
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Affiliation(s)
- R. Francis
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - H. Anani
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditeranéennes (VITROME), Marseille, France
| | - A. Fontanini
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - P.E. Fournier
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditeranéennes (VITROME), Marseille, France
| | - B.L.A. Scola
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - D. Raoult
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Special Infectious Agents Unit, King Fahed Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - J.Y. Bou Khalil
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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31
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Boxberger M, Anani H, La Scola B. Genome sequence and description of Alterileibacterium massiliense gen. nov., sp. nov., a new bacterium isolated from human ileum of a patient with Crohn's disease. New Microbes New Infect 2019; 30:100533. [PMID: 31198562 PMCID: PMC6556832 DOI: 10.1016/j.nmni.2019.100533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/14/2019] [Indexed: 12/22/2022] Open
Abstract
Alterileibacterium massiliense gen. nov. sp. nov. strain Marseille-P3115T (= CSURP-3115; DSM 103486), formerly proposed as Ileibacterium massiliense, is a new genus of bacteria isolated from the ileum of a human patient with Crohn's disease.
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Affiliation(s)
- M Boxberger
- Aix Marseille University, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - H Anani
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - B La Scola
- Aix Marseille University, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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32
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Diop A, Diop K, Tomei E, Armstrong N, Bretelle F, Raoult D, Fenollar F, Fournier PE. Collinsella vaginalis sp. nov. strain Marseille-P2666 T, a new member of the Collinsella genus isolated from the genital tract of a patient suffering from bacterial vaginosis. Int J Syst Evol Microbiol 2019; 69:949-956. [PMID: 30806613 DOI: 10.1099/ijsem.0.003221] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A strictly anaerobic, Gram-stain-positive, non motile and non-spore-forming rod-shaped bacterium, strain Marseille-P2666T, was isolated using the culturomics approach from a vaginal sample of a French patient suffering from bacterial vaginosis. Cells were saccharolytic and were negative for catalase, oxidase, urease, nitrate reduction, indole production, hydrolysis of aesculin and gelatin. Strain Marseille-P2666T exhibited 97.04 % 16S rRNA sequence similarity to Collinsella tanakaei type strain YIT 12063T, the phylogenetically closest species with standing in nomenclature. The major fatty acids were C18:1ω9 (38 %), C16 : 0 (24 %) and C18 : 0 (19 %). The G+C content of the genome sequence of strain Marseille-P2666T is 64.6 mol%. On the basis of its phenotypic, phylogenetic and genomic features, strain Marseille-P2666T (=CSUR 2666T=DSM103342T) was classified as type strain of a novel species within the genus Collinsella for which the name Collinsella vaginalis sp. nov. is proposed.
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Affiliation(s)
- Awa Diop
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
| | - Khoudia Diop
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
| | - Enora Tomei
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
| | - Nicholas Armstrong
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
| | - Florence Bretelle
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France.,Department of Gynecology and Obstetrics, Gynépole, Marseille, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Didier Raoult
- UMR MEPHI, Aix-Marseille University, IRD, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Uuniversitaire 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 Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
| | - Pierre-Edouard Fournier
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
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33
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Description of Janibacter massiliensis sp. nov., cultured from the vaginal discharge of a patient with bacterial vaginosis. Antonie van Leeuwenhoek 2019; 112:1147-1159. [PMID: 30798490 DOI: 10.1007/s10482-019-01247-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/15/2019] [Indexed: 01/22/2023]
Abstract
Strain Marseille-P4121T was isolated from a vaginal sample of a 45-year-old French woman with bacterial vaginosis. It is a Gram-positive, asporogenous, non-motile and aerobic bacterium. Strain Marseille-P4121T exhibits 98.2% 16S rRNA sequence similarity with Janibacter alkaliphilus strain SCSIO 10480T, a phylogenetically closely related species with standing in nomenclature. Its major fatty acids were identified as C18:1ω9 (34.4%), C16:0 (30.1%), and C18:0 (19%). The draft genome size of strain Marseille-P4121T is 2,452,608 bp long with a 72.5% G+C content and contains 2351 protein-coding genes and 49 RNA genes including 3 rRNA genes. We propose that strain Marseille-P4121T (= CECT 9671T = CSUR P4121T) is the type strain of the new species Janibacter massiliensis sp. nov.
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34
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Seck EH, Diop A, Armstrong N, Delerce J, Fournier PE, Raoult D, Khelaifia S. Microbial culturomics to isolate halophilic bacteria from table salt: genome sequence and description of the moderately halophilic bacterium Bacillus salis sp. nov. New Microbes New Infect 2018; 23:28-38. [PMID: 29707210 PMCID: PMC5917939 DOI: 10.1016/j.nmni.2017.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/13/2017] [Accepted: 12/20/2017] [Indexed: 11/15/2022] Open
Abstract
Bacillus salis strain ES3T (= CSUR P1478 = DSM 100598) is the type strain of B. salis sp. nov. It is an aerobic, Gram-positive, moderately halophilic, motile and spore-forming bacterium. It was isolated from commercial table salt as part of a broad culturomics study aiming to maximize the culture conditions for the in-depth exploration of halophilic bacteria in salty food. Here we describe the phenotypic characteristics of this isolate, its complete genome sequence and annotation, together with a comparison with closely related bacteria. Phylogenetic analysis based on 16S rRNA gene sequences indicated 97.5% similarity with Bacillus aquimaris, the closest species. The 8 329 771 bp long genome (one chromosome, no plasmids) exhibits a G+C content of 39.19%. It is composed of 18 scaffolds with 29 contigs. Of the 8303 predicted genes, 8109 were protein-coding genes and 194 were RNAs. A total of 5778 genes (71.25%) were assigned a putative function.
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Affiliation(s)
- E H Seck
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - A Diop
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - N Armstrong
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - J Delerce
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - P-E Fournier
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - D Raoult
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - S Khelaifia
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
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35
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Khelaifia S, Caputo A, Andrieu C, Cadoret F, Armstrong N, Michelle C, Lagier JC, Djossou F, Fournier PE, Raoult D. Genome sequence and description of Haloferax massiliense sp. nov., a new halophilic archaeon isolated from the human gut. Extremophiles 2018; 22:485-498. [PMID: 29435649 PMCID: PMC5862939 DOI: 10.1007/s00792-018-1011-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/05/2018] [Indexed: 12/22/2022]
Abstract
By applying the culturomics concept and using culture conditions containing a high salt concentration, we herein isolated the first known halophilic archaeon colonizing the human gut. Here we described its phenotypic and biochemical characterization as well as its genome annotation. Strain Arc-HrT (= CSUR P0974 = CECT 9307) was mesophile and grew optimally at 37 °C and pH 7. Strain Arc-HrT was also extremely halophilic with an optimal growth observed at 15% NaCl. It showed gram-negative cocci, was strictly aerobic, non-motile and non-spore-forming, and exhibited catalase and oxidase activities. The 4,015,175 bp long genome exhibits a G + C% content of 65.36% and contains 3911 protein-coding and 64 predicted RNA genes. PCR-amplified 16S rRNA gene of strain Arc-HrT yielded a 99.2% sequence similarity with Haloferax prahovense, the phylogenetically closest validly published species in the Haloferax genus. The DDH was of 50.70 ± 5.2% with H. prahovense, 53.70 ± 2.69% with H. volcanii, 50.90 ± 2.64% with H. alexandrinus, 52.90 ± 2.67% with H. gibbonsii and 54.30 ± 2.70% with H. lucentense. The data herein represented confirm strain Arc-HrT as a unique species and consequently we propose its classification as representative of a novel species belonging to the genus Haloferax, as Haloferax massiliense sp. nov.
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Affiliation(s)
- Saber Khelaifia
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France.
| | - Aurelia Caputo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Claudia Andrieu
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Frederique Cadoret
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Nicholas Armstrong
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Caroline Michelle
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Felix Djossou
- Infectious and Tropical Diseases Department, Centre Hospitalier Andrée-Rosemon, Cayenne, French Guiana
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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Diop A, Seck EH, Dubourg G, Armstrong N, Blanc-Tailleur C, Raoult D, Fournier PE. Genome sequence and description of Gracilibacillus timonensis sp. nov. strain Marseille-P2481 T , a moderate halophilic bacterium isolated from the human gut microflora. Microbiologyopen 2018; 8:e00638. [PMID: 29675845 PMCID: PMC6485780 DOI: 10.1002/mbo3.638] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/31/2018] [Accepted: 03/09/2018] [Indexed: 12/19/2022] Open
Abstract
Microbial culturomics represents an ongoing revolution in the characterization of the human gut microbiota. By using three culture media containing high salt concentrations (10, 15, and 20% [w/v] NaCl), we attempted an exhaustive exploration of the halophilic microbial diversity of the human gut and isolated strain Marseille‐P2481 (= CSUR P2481 = DSM 103076), a new moderately halophilic bacterium. This bacterium is a Gram‐positive, strictly aerobic, spore‐forming rod that is motile by use of a flagellum and exhibits catalase, but not oxidase activity. Strain Marseille‐P2481 was cultivated in media containing up to 20% (w/v) NaCl, with optimal growth being obtained at 37°C, pH 7.0–8.0, and 7.5% [w/v] NaCl). The major fatty acids were 12‐methyl‐tetradecanoic acid and hexadecanoic acid. Its draft genome is 4,548,390 bp long, composed of 11 scaffolds, with a G+C content of 39.8%. It contains 4,335 predicted genes (4,266 protein coding including 89 pseudogenes and 69 RNA genes). Strain Marseille‐P2481 showed 96.57% 16S rRNA sequence similarity with Gracilibacillus alcaliphilus strain SG103T, the phylogenetically closest species with standing in nomenclature. On the basis of its specific features, strain Marseille‐P2481T was classified as type strain of a new species within the genus Gracilibacillus for which the name Gracilibacillus timonensis sp. nov. is formally proposed.
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Affiliation(s)
- Awa Diop
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
| | - El Hadji Seck
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
| | - Gregory Dubourg
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
| | - Nicholas Armstrong
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
| | - Caroline Blanc-Tailleur
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
| | - Didier Raoult
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2017; 67:1095-1098. [PMID: 28581921 DOI: 10.1099/ijsem.0.001986] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] 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 and Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Abdallah RA, Beye M, Diop A, Bakour S, Raoult D, Fournier PE. The impact of culturomics on taxonomy in clinical microbiology. Antonie van Leeuwenhoek 2017; 110:1327-1337. [PMID: 28389704 DOI: 10.1007/s10482-017-0871-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/04/2017] [Indexed: 02/06/2023]
Abstract
Over the past decade, new culture methods coupled to genome and metagenome sequencing have enabled the number of isolated bacterial species with standing in nomenclature to rise to more than 15,000 whereas it was only 1791 in 1980. 'Culturomics', a new approach based on the diversification of culture conditions, has enabled the isolation of more than 1000 distinct human-associated bacterial species since 2012, including 247 new species. This strategy was demonstrated to be complementary to metagenome sequencing for the exhaustive study of the human microbiota and its roles in health and diseases. However, by identifying a large number of new bacterial species in a short time, culturomics has highlighted a need for taxonomic approaches adapted to clinical microbiology that would include the use of modern and reproducible tools, including high throughput genomic and proteomic analyses. Herein, we review the development of culturomics and genomics in the clinical microbiology field and their impact on bacterial taxonomy.
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Affiliation(s)
- Rita Abou Abdallah
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63CNRS 7278IRD 198Inserm 1095IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, 13385, Marseille Cedex5, France
| | - Mamadou Beye
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63CNRS 7278IRD 198Inserm 1095IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, 13385, Marseille Cedex5, France
| | - Awa Diop
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63CNRS 7278IRD 198Inserm 1095IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, 13385, Marseille Cedex5, France
| | - Sofiane Bakour
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63CNRS 7278IRD 198Inserm 1095IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, 13385, Marseille Cedex5, France
| | - Didier Raoult
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63CNRS 7278IRD 198Inserm 1095IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, 13385, Marseille Cedex5, France
| | - Pierre-Edouard Fournier
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63CNRS 7278IRD 198Inserm 1095IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, 13385, Marseille Cedex5, France.
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