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Modestobacter caceresii sp. nov., novel actinobacteria with an insight into their adaptive mechanisms for survival in extreme hyper-arid Atacama Desert soils. Syst Appl Microbiol 2016; 39:243-251. [DOI: 10.1016/j.syapm.2016.03.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 03/16/2016] [Accepted: 03/18/2016] [Indexed: 11/20/2022]
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Keita MB, Padhmanabhan R, Robert C, Delaporte E, Raoult D, Fournier PE, Bittar F. Non-contiguous-Finished Genome Sequence and Description of Paenibacillus camerounensis sp. nov. MICROBIAL ECOLOGY 2016; 71:990-998. [PMID: 26714966 DOI: 10.1007/s00248-015-0722-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 12/15/2015] [Indexed: 06/05/2023]
Abstract
Strain G4(T) was isolated from the stool sample of a wild gorilla (Gorilla gorilla gorilla) from Cameroon. It is a facultative anaerobic, Gram-negative, rod-shaped bacterium. This strain exhibits a 16S rRNA nucleotide sequence similarity of 97.48% with Paenibacillus typhae, the phylogenetically closest species with standing nomenclature. Moreover, the strain G4(T) presents some phenotypic differences when compared to other Paenibacillus species and shows a low MALDI-TOF Mass Spectrometry score that does not allow any identification. Thus, it is likely that this strain represents a new species. Here, we describe the characteristics of this organism, complete genome sequence, and annotation. The 6,933,847 bp size genome (1 chromosome but no plasmid) contains 5972 protein-coding genes and 54 RNAs genes, including 44 tRNA genes. In addition, digital DNA-DNA hybridization values for the genome of the strain G4(T) against the closest Paenibacillus genomes range between 19.7 and 22.1, once again confirming its new status as a new species. On the basis of these polyphasic data, consisting of phenotypic and genomic analyses, we propose the creation of Paenibacillus camerounensis sp. nov. that contains the strain G4(T).
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Affiliation(s)
| | | | - Catherine Robert
- Faculté de médecine, URMITE, Aix-Marseille Université, Marseille, France
| | | | - Didier Raoult
- Faculté de médecine, URMITE, Aix-Marseille Université, Marseille, France
- King Fahad Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | | | - Fadi Bittar
- Faculté de médecine, URMITE, Aix-Marseille Université, Marseille, France.
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Hadjadj L, Rathored J, Keita MB, Michelle C, Levasseur A, Raoult D, Fournier PE, Rolain JM, Bittar F. Non contiguous-finished genome sequence and description of Microbacterium gorillae sp. nov. Stand Genomic Sci 2016; 11:32. [PMID: 27087892 PMCID: PMC4832456 DOI: 10.1186/s40793-016-0152-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 04/08/2016] [Indexed: 11/10/2022] Open
Abstract
Strain G3(T) (CSUR P207 = DSM 26203) was isolated from the fecal sample of a wild gorilla (Gorilla gorilla subsp gorilla) from Cameroon. It is a Gram-positive, facultative anaerobic short rod. This strain exhibits a 16S rRNA sequence similarity of 98.2 % with Microbacterium thalassium, the closest validly published Microbacterium species and member of the family Microbacteriaceae. Moreover, it shows a low MALDI-TOF-MS score (1.1 to 1.3) that does not allow any identification. Thus, it is likely that this strain represents a new species. Here we describe the phenotypic features of this organism, the complete genome sequence and annotation. The 3,692,770 bp long genome (one chromosome but no plasmid) contains 3,505 protein-coding and 61 RNA genes, including 4 rRNA genes. In addition, digital DNA-DNA hybridization values for the genome of the strain G3(T) against the closest Microbacterium genomes range between 19.7 to 20.5, once again confirming its new status as a new species. On the basis of these polyphasic data, consisting of phenotypic and genomic analyses, we propose the creation of Microbacterium gorillae sp. nov. that contains the strain G3(T).
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Affiliation(s)
- Linda Hadjadj
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM63, CNRS7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - Jaishriram Rathored
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM63, CNRS7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - Mamadou Bhoye Keita
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM63, CNRS7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - Caroline Michelle
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM63, CNRS7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - Anthony Levasseur
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM63, CNRS7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM63, CNRS7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France ; King Fahad Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM63, CNRS7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - Jean-Marc Rolain
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM63, CNRS7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - Fadi Bittar
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM63, CNRS7278, IRD 198, Inserm 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
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High-quality genome sequence and description of Paenibacillus dakarensis sp. nov. New Microbes New Infect 2016; 10:132-41. [PMID: 26958345 PMCID: PMC4773451 DOI: 10.1016/j.nmni.2016.01.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/18/2015] [Accepted: 01/14/2016] [Indexed: 12/03/2022] Open
Abstract
Strain FF9T was isolated in Dakar (Senegal) from a blood-culture taken from a 16-month-old child. MALDI-TOF analysis did not allow for identification. After sequencing, strain FF9T exhibited 98.18% similarity with the 16SrRNA sequence of Paenibacillus uliginis. A polyphasic study of phenotypic and genomic analyses showed that strain FF9T is Gram variable, catalase-positive, and presents a genome of 4,569,428 bp (one chromosome but no plasmid) with 4,427genes (4,352 protein-coding and 75 RNA genes (including 3 rRNA operons). The G+C content is 45.7%. On the basis of these genomic and phenotypic data analyses, we propose the creation of Paenibacillus dakarensis strain FF9T.
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55
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Noncontiguous finished genome sequence and description of Diaminobutyricimonas massiliensis strain FF2T sp. nov. New Microbes New Infect 2015. [DOI: 10.1016/j.nmni.2015.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Lo C, Padhmanabhan R, Mediannikov O, Caputo A, Michelle C, Faye N, Sokhna C, Raoult D, Fournier PE, Fenollar F. High-quality genome sequence and description of Bacillus ndiopicus strain FF3(T) sp. nov. New Microbes New Infect 2015; 8:154-63. [PMID: 27257496 PMCID: PMC4877407 DOI: 10.1016/j.nmni.2015.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/07/2015] [Accepted: 10/09/2015] [Indexed: 11/19/2022] Open
Abstract
Strain FF3(T) was isolated from the skin-flora of a 39-year-old healthy Senegalese man. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry did not allow any identification. This strain exhibited a 16S rRNA sequence similarity of 96.8% with Bacillus massiliensis, the phylogenetically closest species with standing nomenclature. Using a polyphasic study made of phenotypic and genomic analyses, strain FF3(T) was Gram-positive, aeroanaerobic and rod shaped and exhibited a genome of 4 068 720 bp with a G+C content of 37.03% that coded 3982 protein-coding and 67 RNA genes (including four rRNA operons). On the basis of these data, we propose the creation of Bacillus ndiopicus sp. nov.
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Affiliation(s)
- C.I. Lo
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
- Campus International UCAD-IRD, Dakar, Senegal
| | - R. Padhmanabhan
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
| | - O. Mediannikov
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
- Campus International UCAD-IRD, Dakar, Senegal
| | - A. Caputo
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
| | - C. Michelle
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
| | - N. Faye
- Université Cheikh Anta Diop de Dakar, Laboratoire de Parasitologie générale, Fann, Senegal
| | - C. Sokhna
- Campus International UCAD-IRD, Dakar, Senegal
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
- Campus International UCAD-IRD, Dakar, Senegal
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P.-E. Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
| | - F. Fenollar
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
- Campus International UCAD-IRD, Dakar, Senegal
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Sankar S, Lo C, Fall B, Sambe-Ba B, Mediannikov O, Diallo I, Labas N, Faye N, Wade B, Raoult D, Fournier PE, Fenollar F. Noncontiguous finished genome sequence and description of Weeksella massiliensis sp. nov. New Microbes New Infect 2015; 8:89-98. [PMID: 26649182 PMCID: PMC4644262 DOI: 10.1016/j.nmni.2015.09.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/21/2015] [Accepted: 09/23/2015] [Indexed: 11/19/2022] Open
Abstract
Strain FF8(T) (= CSUR P860 = DSM 28259) was isolated in Dakar, Senegal, from the urine of a 65-year-old man with acute cystitis. This strain shows a similarity of sequence of 16S rRNA of 98.38% with Weeksella virosa, and its GenBank accession numbers are HG931340 and CCMH00000000. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis had a poor score, ranging from 1.32 to 1.56, that did not allow identification of the bacterium. Using a polyphasic study made of phenotypic and genomic analyses, strain FF8(T) was a Gram-negative, aerobic rod and a member of the family Flavobacteriaceae. The sequenced genome is 2 562 781 bp with one chromosome but no plasmid. It exhibits a G + C content of 35.9% and contains 2390 protein-coding and 56 RNA genes, including a complete rRNA operon. On the basis of these data, we propose the creation of Weeksella massiliensis sp. nov.
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Affiliation(s)
- S.A. Sankar
- )Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
| | - C.I. Lo
- )Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
- )Campus International UCAD-IRD, Dakar, Senegal
| | - B. Fall
- )Hôpital Principal, Dakar, Senegal
| | | | - O. Mediannikov
- )Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
- )Campus International UCAD-IRD, Dakar, Senegal
| | | | - N. Labas
- )Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
| | - N. Faye
- )Université Cheikh Anta Diop de Dakar, Laboratoire de Parasitologie générale, Dakar, Senegal
| | - B. Wade
- )Hôpital Principal, Dakar, Senegal
| | - D. Raoult
- )Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
- )Campus International UCAD-IRD, Dakar, Senegal
- )Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P.-E. Fournier
- )Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
| | - F. Fenollar
- )Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
- )Campus International UCAD-IRD, Dakar, Senegal
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58
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Lo CI, Padhamanabhan R, Fall B, Sambe-Ba B, Mediannikov O, Nguyen TT, Prudent E, Faye N, Wade B, Raoult D, Fournier PE, Fenollar F. Noncontiguous finished genome sequence and description of Necropsobacter massiliensis sp. nov. New Microbes New Infect 2015; 8:41-50. [PMID: 26587237 PMCID: PMC4625094 DOI: 10.1016/j.nmni.2015.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 09/04/2015] [Accepted: 09/07/2015] [Indexed: 11/28/2022] Open
Abstract
Strain FF6(T) was isolated from the cervical abscess of a 4-year-old Senegalese boy, in Dakar, Senegal. MALDI-TOF MS did not provide any identification. This strain exhibited a 95.17% 16S rRNA sequence identity with Necropsobacter rosorum. Using a polyphasic study including phenotypic and genomic analyses, strain FF6(T) was an aero-anaerobic Gram-negative cocobacillus, oxidase positive, and exhibited a genome of 2,493,927 bp (1 chromosome but no plasmid) with a G+C content of 46.2% that coded 2,309 protein-coding and 53 RNA genes. On the basis of these data, we propose the creation of Necropsobacter massiliensis sp. nov.
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Affiliation(s)
- C I Lo
- Faculté de médecine, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France ; Campus International UCAD-IRD, Senegal
| | - R Padhamanabhan
- Faculté de médecine, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France
| | - B Fall
- Hôpital Principal, Senegal
| | | | - O Mediannikov
- Faculté de médecine, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France ; Campus International UCAD-IRD, Senegal
| | - T-T Nguyen
- Faculté de médecine, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France
| | - E Prudent
- Faculté de médecine, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France
| | - N Faye
- Université Cheikh Anta Diop de Dakar, Laboratoire de Parasitologie générale, Dakar, Senegal
| | - B Wade
- Hôpital Principal, Senegal
| | - D Raoult
- Faculté de médecine, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France ; Campus International UCAD-IRD, Senegal ; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P-E Fournier
- Faculté de médecine, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France
| | - F Fenollar
- Faculté de médecine, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France ; Campus International UCAD-IRD, Senegal
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Hugon P, Dufour JC, Colson P, Fournier PE, Sallah K, Raoult D. A comprehensive repertoire of prokaryotic species identified in human beings. THE LANCET. INFECTIOUS DISEASES 2015; 15:1211-1219. [PMID: 26311042 DOI: 10.1016/s1473-3099(15)00293-5] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 02/17/2015] [Accepted: 02/27/2015] [Indexed: 02/07/2023]
Abstract
The compilation of the complete prokaryotic repertoire associated with human beings as commensals or pathogens is a major goal for the scientific and medical community. The use of bacterial culture techniques remains a crucial step to describe new prokaryotic species. The large number of officially acknowledged bacterial species described since 1980 and the recent increase in the number of recognised pathogenic species have highlighted the absence of an exhaustive compilation of species isolated in human beings. By means of a thorough investigation of several large culture databases and a search of the scientific literature, we built an online database containing all human-associated prokaryotic species described, whether or not they had been validated and have standing in nomenclature. We list 2172 species that have been isolated in human beings. They were classified in 12 different phyla, mostly in the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes phyla. Our online database is useful for both clinicians and microbiologists and forms part of the Human Microbiome Project, which aims to characterise the whole human microbiota and help improve our understanding of the human predisposition and susceptibility to infectious agents.
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Affiliation(s)
- Perrine Hugon
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Jean-Charles Dufour
- Assistance Publique des Hôpitaux de Marseille, BioSTIC, Pôle de Santé Publique, Marseille, France; Aix-Marseille Université, UMR912 SESSTIM (AMU-INSERM-IRD), Marseille, France
| | - Philippe Colson
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Pierre-Edouard Fournier
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Kankoe Sallah
- Aix-Marseille Université, UMR912 SESSTIM (AMU-INSERM-IRD), Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
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60
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Bittar F, Bibi F, Ramasamy D, Lagier JC, Azhar EI, Jiman-Fatani AA, Al-Ghamdi AK, Nguyen TT, Yasir M, Fournier PE, Raoult D. Non contiguous-finished genome sequence and description of Bacillus jeddahensis sp. nov. Stand Genomic Sci 2015; 10:47. [PMID: 26380635 PMCID: PMC4572673 DOI: 10.1186/s40793-015-0024-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 05/21/2015] [Indexed: 11/13/2022] Open
Abstract
Strain JCE(T) was isolated from the fecal sample of a 24-year-old obese man living in Jeddah, Saudi Arabia. It is an aerobic, Gram-positive, rod-shaped bacterium. This strain exhibits a 16S rRNA nucleotide sequence similarity of 97.5 % with Bacillus niacini, the phylogenetically closest species with standing nomenclature. Moreover, the strain JCE(T) presents many phenotypic differences, when it is compared to other Bacillus species, and shows a low MALDI-TOF Mass Spectrometry score that does not allow any identification. Thus, it is likely that this strain represents a new species. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,762,944 bp long genome (1 chromosome but no plasmid) contains 4,654 protein-coding and 98 RNAs genes, including 92 tRNA genes. The strain JCE(T) differs from most of the other closely Bacillus species by more than 1 % in G + C content. In addition, digital DNA-DNA hybridization values for the genome of the strain JCE(T) against the closest Bacillus genomes range between 19.5 to 28.1, that confirming again its new species status. On the basis of these polyphasic data made of phenotypic and genomic analyses, we propose the creation of Bacillus jeddahensis sp. nov. that contains the strain JCE(T).
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Affiliation(s)
- Fadi Bittar
- />URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
| | - Fehmida Bibi
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Esam I. Azhar
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- />Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asif A. Jiman-Fatani
- />Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed K. Al-Ghamdi
- />Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ti Thien Nguyen
- />URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
| | - Muhammad Yasir
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Didier Raoult
- />URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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61
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Lo CI, Padhmanabhan R, Mediannikov O, Terras J, Robert C, Faye N, Raoult D, Fournier PE, Fenollar F. High-quality genome sequence and description of Bacillus dielmoensis strain FF4(T) sp. nov. Stand Genomic Sci 2015. [PMID: 26221422 PMCID: PMC4517664 DOI: 10.1186/s40793-015-0019-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Strain FF4T was isolated from the skin flora of a 16-year-old healthy Senegalese female. This strain exhibited a 16S rRNA sequence similarity of 97.5 % with Bacillus fumarioli, the phylogenetically closest species with standing in nomenclature and a poor MALDI-TOF-MS score (1.1 to 1.3) that does not allow any identification. Using a polyphasic study consisting of phenotypic and genomic analyses, strain FF4T was Gram-positive, aerobic, rod-shaped, and exhibited a genome of 4,563,381 bp (1 chromosome but no plasmid) with a G + C content of 40.8 % that coded 4,308 protein-coding and 157 RNA genes (including 5 rRNA operons). On the basis of these data, we propose the creation of Bacillus dielmoensis sp. nov.
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Affiliation(s)
- Cheikh Ibrahima Lo
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France ; Campus International UCAD-IRD, Dakar, Senegal
| | - Roshan Padhmanabhan
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France ; Campus International UCAD-IRD, Dakar, Senegal
| | - Oleg Mediannikov
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France ; Campus International UCAD-IRD, Dakar, Senegal
| | - Jérôme Terras
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France ; Campus International UCAD-IRD, Dakar, Senegal
| | - Catherine Robert
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France ; Campus International UCAD-IRD, Dakar, Senegal
| | - Ngor Faye
- Université Cheikh Anta Diop de Dakar, Laboratoire de Parasitologie générale, Fann, Senegal
| | - Didier Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France ; Campus International UCAD-IRD, Dakar, Senegal ; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France ; Campus International UCAD-IRD, Dakar, Senegal
| | - Florence Fenollar
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France ; Campus International UCAD-IRD, Dakar, Senegal
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The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 2015; 28:237-64. [PMID: 25567229 DOI: 10.1128/cmr.00014-14] [Citation(s) in RCA: 521] [Impact Index Per Article: 57.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.
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Sassi M, Augagneur Y, Mauro T, Ivain L, Chabelskaya S, Hallier M, Sallou O, Felden B. SRD: a Staphylococcus regulatory RNA database. RNA (NEW YORK, N.Y.) 2015; 21:1005-17. [PMID: 25805861 PMCID: PMC4408781 DOI: 10.1261/rna.049346.114] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 02/16/2015] [Indexed: 05/06/2023]
Abstract
An overflow of regulatory RNAs (sRNAs) was identified in a wide range of bacteria. We designed and implemented a new resource for the hundreds of sRNAs identified in Staphylococci, with primary focus on the human pathogen Staphylococcus aureus. The "Staphylococcal Regulatory RNA Database" (SRD, http://srd.genouest.org/) compiled all published data in a single interface including genetic locations, sequences and other features. SRD proposes novel and simplified identifiers for Staphylococcal regulatory RNAs (srn) based on the sRNA's genetic location in S. aureus strain N315 which served as a reference. From a set of 894 sequences and after an in-depth cleaning, SRD provides a list of 575 srn exempt of redundant sequences. For each sRNA, their experimental support(s) is provided, allowing the user to individually assess their validity and significance. RNA-seq analysis performed on strains N315, NCTC8325, and Newman allowed us to provide further details, upgrade the initial annotation, and identified 159 RNA-seq independent transcribed sRNAs. The lists of 575 and 159 sRNAs sequences were used to predict the number and location of srns in 18 S. aureus strains and 10 other Staphylococci. A comparison of the srn contents within 32 Staphylococcal genomes revealed a poor conservation between species. In addition, sRNA structure predictions obtained with MFold are accessible. A BLAST server and the intaRNA program, which is dedicated to target prediction, were implemented. SRD is the first sRNA database centered on a genus; it is a user-friendly and scalable device with the possibility to submit new sequences that should spread in the literature.
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Affiliation(s)
- Mohamed Sassi
- Inserm U835 Biochimie Pharmaceutique, Rennes University, 35043 Rennes, France
| | - Yoann Augagneur
- Inserm U835 Biochimie Pharmaceutique, Rennes University, 35043 Rennes, France
| | - Tony Mauro
- Inserm U835 Biochimie Pharmaceutique, Rennes University, 35043 Rennes, France
| | - Lorraine Ivain
- Inserm U835 Biochimie Pharmaceutique, Rennes University, 35043 Rennes, France
| | | | - Marc Hallier
- Inserm U835 Biochimie Pharmaceutique, Rennes University, 35043 Rennes, France
| | - Olivier Sallou
- Institut de Recherche en Informatique et Systèmes Aléatoires, Rennes University, 35043 Rennes, France
| | - Brice Felden
- Inserm U835 Biochimie Pharmaceutique, Rennes University, 35043 Rennes, France
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Rossi-Tamisier M, Benamar S, Raoult D, Fournier PE. Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species. Int J Syst Evol Microbiol 2015; 65:1929-1934. [PMID: 25736410 DOI: 10.1099/ijs.0.000161] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Modern bacterial taxonomy is based on a polyphasic approach that combines phenotypic and genotypic characteristics, including 16S rRNA sequence similarity. However, the 95 % (for genus) and 98.7 % (for species) sequence similarity thresholds that are currently recommended to classify bacterial isolates were defined by comparison of a limited number of bacterial species, and may not apply to many genera that contain human-associated species. For each of 158 bacterial genera containing human-associated species, we computed pairwise sequence similarities between all species that have names with standing in nomenclature and then analysed the results, considering as abnormal any similarity value lower than 95 % or greater than 98.7 %. Many of the current bacterial species with validly published names do not respect the 95 and 98.7 % thresholds, with 57.1 % of species exhibiting 16S rRNA gene sequence similarity rates ≥98.7 %, and 60.1 % of genera containing species exhibiting a 16S rRNA gene sequence similarity rate <95 %. In only 17 of the 158 genera studied (10.8 %), all species respected the 95 and 98.7 % thresholds. As we need powerful and reliable taxonomical tools, and as potential new tools such as pan-genomics have not yet been fully evaluated for taxonomic purposes, we propose to use as thresholds, genus by genus, the minimum and maximum similarity values observed among species.
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Affiliation(s)
- Morgane Rossi-Tamisier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France
| | - Samia Benamar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France
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Bull CT, Koike ST. Practical benefits of knowing the enemy: modern molecular tools for diagnosing the etiology of bacterial diseases and understanding the taxonomy and diversity of plant-pathogenic bacteria. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:157-80. [PMID: 26002289 DOI: 10.1146/annurev-phyto-080614-120122] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Knowing the identity of bacterial plant pathogens is essential to strategic and sustainable disease management in agricultural systems. This knowledge is critical for growers, diagnosticians, extension agents, and others dealing with crops. However, such identifications are linked to bacterial taxonomy, a complicated and changing discipline that depends on methods and information that are often not used by those who are diagnosing field problems. Modern molecular tools for fingerprinting and sequencing allow for pathogen identification in the absence of distinguishing or conveniently tested phenotypic characteristics. These methods are also useful in studying the etiology and epidemiology of phytopathogenic bacteria from epidemics, as was done in numerous studies conducted in California's Salinas Valley. Multilocus and whole-genome sequence analyses are becoming the cornerstones of studies of microbial diversity and bacterial taxonomy. Whole-genome sequence analysis needs to become adequately accessible, automated, and affordable in order to be used routinely for identification and epidemiology. The power of molecular tools in accurately identifying bacterial pathogenesis is therefore of value to the farmer, diagnostician, phytobacteriologist, and taxonomist.
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Affiliation(s)
- Carolee T Bull
- United States Department of Agriculture, Agricultural Research Service, Salinas, California 93905;
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Keita MB, Padhmananabhan R, Caputo A, Robert C, Delaporte E, Raoult D, Fournier PE, Bittar F. Non-contiguous finished genome sequence and description of Paenibacillus gorillae sp. nov. Stand Genomic Sci 2014; 9:1031-45. [PMID: 25197481 PMCID: PMC4149019 DOI: 10.4056/sigs.5189179] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Strain G1(T) sp. nov. is the type strain of Paenibacillus gorillae a newly proposed species within the genus Paenibacillus. This strain, whose genome is described here, was isolated in France from the fecal sample of a wild western lowland gorilla from Cameroon. P. gorillae is a facultative anaerobic, Gram-negative, rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,257,967 bp long genome (one chromosome but no plasmid) contains 5,856 protein-coding and 62 RNAs genes, including 60 tRNA genes.
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Affiliation(s)
| | | | - Aurélia Caputo
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
| | - Catherine Robert
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
| | | | - Didier Raoult
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
- King Fahad Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | | | - Fadi Bittar
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
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Sassi M, Drancourt M. Genome analysis reveals three genomospecies in Mycobacterium abscessus. BMC Genomics 2014; 15:359. [PMID: 24886480 PMCID: PMC4035080 DOI: 10.1186/1471-2164-15-359] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 04/30/2014] [Indexed: 01/27/2023] Open
Abstract
Background Mycobacterium abscessus complex, the third most frequent mycobacterial complex responsible for community- and health care-associated infections in developed countries, comprises of M. abscessus subsp. abscessus and M. abscessus subsp. bolletii reviously referred as Mycobacterium bolletii and Mycobacterium massiliense. The diversity of this group of opportunistic pathogens is poorly described. Results In-depth analysis of 14 published M. abscessus complex genomes found a pan-genome of 6,153 proteins and core-genome of 3,947 (64.1%) proteins, indicating a non-conservative genome. Analysing the average percentage of amino-acid sequence identity (from 94.19% to 98.58%) discriminates three main clusters C1, C2 and C3: C1 comprises strains belonging to M. abscessus, C2 comprises strains belonging to M. massiliense and C3 comprises strains belonging to M. bolletii; and two sub-clusters in clusters C2 and C3. The phylogenomic network confirms these three clusters. The genome length (from 4.8 to 5.51-Mb) varies from 5.07-Mb in C1, 4.89-Mb in C2A, 5.01-Mb in C2B and 5.28-Mb in C3. The mean number of prophage regions (from 0 to 7) is 2 in C1; 1.33 in C2A; 3.5 in C2B and five in C3. A total of 36 genes are uniquely present in C1, 15 in C2 and 15 in C3. These genes could be used for the detection and identification of organisms in each cluster. Further, the mean number of host-interaction factors (including PE, PPE, LpqH, MCE, Yrbe and type VII secretion system ESX3 and ESX4) varies from 70 in cluster C1, 80 in cluster C2A, 74 in cluster C2B and 93 in clusters C3A and C3B. No significant differences in antibiotic resistance genes were observed between clusters, in contrast to previously reported in-vitro patterns of drug resistance. They encode both penicillin-binding proteins targeted by β-lactam antibiotics and an Ambler class A β-lactamase for which inhibitors exist. Conclusions Our comparative analysis indicates that M. abscessus complex comprises three genomospecies, corresponding to M. abscessus, M. bolletii, and M. massiliense. The genomics data here reported indicate differences in virulence of medical interest; and suggest targets for the refined detection and identification of M. abscessus. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-359) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Michel Drancourt
- Aix Marseille Université, URMITE, UMR63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France.
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Streptomyces leeuwenhoekii sp. nov., the producer of chaxalactins and chaxamycins, forms a distinct branch in Streptomyces gene trees. Antonie van Leeuwenhoek 2014; 105:849-61. [PMID: 24604690 DOI: 10.1007/s10482-014-0139-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 02/11/2014] [Indexed: 10/25/2022]
Abstract
A polyphasic study was carried out to establish the taxonomic status of an Atacama Desert isolate, Streptomyces strain C34(T), which synthesises novel antibiotics, the chaxalactins and chaxamycins. The organism was shown to have chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Streptomyces. Analysis of 16S rRNA gene sequences showed that strain C34(T) formed a distinct phyletic line in the Streptomyces gene tree that was very loosely associated with the type strains of several Streptomyces species. Multilocus sequence analysis based on five house-keeping gene alleles underpinned the separation of strain C34(T) from all of its nearest phylogenetic neighbours, apart from Streptomyces chiangmaiensis TA-1(T) and Streptomyces hyderabadensis OU-40(T) which are not currently in the MLSA database. Strain C34(T) was distinguished readily from the S. chiangmaiensis and S. hyderabadensis strains by using a combination of cultural and phenotypic data. Consequently, strain C34(T) is considered to represent a new species of the genus Streptomyces for which the name Streptomyces leeuwenhoekii sp. nov. is proposed. The type strain is C34(T) (= DSM 42122(T) = NRRL B-24963(T)). Analysis of the whole-genome sequence of S. leeuwenhoekii, with 6,780 predicted open reading frames and a total genome size of around 7.86 Mb, revealed a high potential for natural product biosynthesis.
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Padmanabhan R, Mishra AK, Raoult D, Fournier PE. Genomics and metagenomics in medical microbiology. J Microbiol Methods 2013; 95:415-24. [PMID: 24200711 DOI: 10.1016/j.mimet.2013.10.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 10/08/2013] [Accepted: 10/10/2013] [Indexed: 02/06/2023]
Abstract
Over the last two decades, sequencing tools have evolved from laborious time-consuming methodologies to real-time detection and deciphering of genomic DNA. Genome sequencing, especially using next generation sequencing (NGS) has revolutionized the landscape of microbiology and infectious disease. This deluge of sequencing data has not only enabled advances in fundamental biology but also helped improve diagnosis, typing of pathogen, virulence and antibiotic resistance detection, and development of new vaccines and culture media. In addition, NGS also enabled efficient analysis of complex human micro-floras, both commensal, and pathological, through metagenomic methods, thus helping the comprehension and management of human diseases such as obesity. This review summarizes technological advances in genomics and metagenomics relevant to the field of medical microbiology.
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Affiliation(s)
- Roshan Padmanabhan
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Aix-Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, 27 Bd. Jean Moulin, 13005 Marseille, France
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Keita MB, Diene SM, Robert C, Raoult D, Fournier PE, Bittar F. Non-contiguous finished genome sequence and description of Bacillus massiliogorillae sp. nov. Stand Genomic Sci 2013; 9:93-105. [PMID: 24501648 PMCID: PMC3910557 DOI: 10.4056/sigs.4388124] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Strain G2(T) sp. nov. is the type strain of B. massiliogorillae, a proposed new species within the genus Bacillus. This strain, whose genome is described here, was isolated in France from the fecal sample of a wild western lowland gorilla from Cameroon. B. massiliogorillae is a facultative anaerobic, Gram-variable, rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,431,633 bp long genome (1 chromosome but no plasmid) contains 5,179 protein-coding and 98 RNA genes, including 91 tRNA genes.
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Affiliation(s)
| | - Seydina M Diene
- URMITE, Aix-Marseille Université, Faculté de Médecine, Marseille, France
| | - Catherine Robert
- URMITE, Aix-Marseille Université, Faculté de Médecine, Marseille, France
| | - Didier Raoult
- URMITE, Aix-Marseille Université, Faculté de Médecine, Marseille, France ; King Fahad Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | | | - Fadi Bittar
- URMITE, Aix-Marseille Université, Faculté de Médecine, Marseille, France
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Noncontiguous Genome Sequence of Mycobacterium septicum Strain DSM 44393T. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00574-13. [PMID: 23950116 PMCID: PMC3744672 DOI: 10.1128/genomea.00574-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The rapidly growing Mycobacterium septicum rarely causes pulmonary infections. We report here the draft genome sequence of M. septicum strain DSM 44393T, isolated from catheter-related bacteremia and initially identified as a member of Mycobacterium fortuitum.
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