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Abou Chacra L, Bonnet M, Heredia M, Haddad G, Armstrong N, Alibar S, Bretelle F, Fenollar F. Peptoniphilus genitalis sp. nov. and Mobiluncus massiliensis sp. nov.: Novel Bacteria Isolated from the Vaginal Microbiome. Curr Microbiol 2024; 81:97. [PMID: 38372813 PMCID: PMC10876752 DOI: 10.1007/s00284-023-03584-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/07/2023] [Indexed: 02/20/2024]
Abstract
The strains Marseille-Q7072T (= CSUR Q7072T = CECT 30604 T) and Marseille-Q7826T (= CSUR Q7826T = CECT 30727 T) were isolated from vaginal samples. As MALDI-TOF mass spectrometry failed to identify them, their genomes were directly sequenced to determine their taxogenomic identities. Both strains are anaerobic without any oxidase and catalase activity. C16:0 is the most abundant fatty acid for both strains. Strain Marseille-Q7072T is non-spore-forming, non-motile, Gram-stain-positive, and coccus-shaped, while strain Marseille-Q7826T is non-spore-forming, motile, Gram-stain-variable, and curved rod-shaped. The genomic comparison of the Marseille-Q7072T and Marseille-Q7826T strains showed that all digital DNA-DNA hybridisation (dDDH) and mean orthologous nucleotide identity (OrthoANI) values were below published species thresholds (70% and 95-96%, respectively) with other closely related species with standing in nomenclature. Thus, we conclude that both strains are new bacterial species. Strain Marseille-Q7072T is a new member of the Bacillota phylum, for which the name Peptoniphilus genitalis sp. nov. is proposed, while the Marseille-Q7826T strain is a new member of the Actinomycetota phylum, for which the name Mobiluncus massiliensis sp. nov. is proposed.
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Affiliation(s)
- Linda Abou Chacra
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Marion Bonnet
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Mégane Heredia
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Gabriel Haddad
- IHU-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | | | | | - Florence Bretelle
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- Department of Gynaecology and Obstetrics, Gynépole, La Conception, AP-HM, Marseille, France
| | - Florence Fenollar
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France.
- IHU-Méditerranée Infection, Marseille, France.
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Abou Chacra L, Bonnet M, Heredia M, Haddad G, Armstrong N, Alibar S, Bretelle F, Fenollar F. Cellulomonas endometrii sp. nov.: a novel bacterium isolated from the endometrial microbiota. Arch Microbiol 2023; 205:377. [PMID: 37940730 PMCID: PMC10632280 DOI: 10.1007/s00203-023-03703-9] [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] [Received: 06/02/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023]
Abstract
An isolate of a bacterium recovered from an endometrial biopsy failed to be identified by MALDI-TOF mass spectrometry and was subjected to 16S rRNA sequencing. The obtained sequence was compared by BLASTn against the NCBI database, which revealed that the most closely related species was Cellulomonas hominis and Cellulomonas pakistanensis, with 98.85% and 98.45% identity, respectively. Phenotypic characterisation and genome sequencing were performed. The isolate was facultative anaerobic, gram-positive, motile, non-spore forming, and rod-shaped. Cell wall fatty acid profiling revealed that 12-methyl-tetradecanoic acid was the most abundant fatty acid (36%). The genome size was 4.25 Mbp with a G + C content of 74.8 mol%. Genomic comparison of species closely related to this strain showed that all digital DNA-DNA hybridisation (dDDH) and mean orthologous nucleotide identity (OrthoANI) values were below published species thresholds (70% and 95-96%, respectively). Based on these data, we conclude that this isolate represents a new bacterial species belonging to the family Cellulomonadaceae and the phylum Actinomycetota. We propose the name Cellulomonas endometrii sp. nov. The type strain is Marseille-Q7820T (= CSUR Q7820 = CECT 30716).
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Affiliation(s)
- Linda Abou Chacra
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Marion Bonnet
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Mégane Heredia
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | | | | | | | - Florence Bretelle
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- Department of Gynaecology and Obstetrics, Gynépole, La Conception, AP-HM, Marseille, France
| | - Florence Fenollar
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France.
- IHU-Méditerranée Infection, Marseille, France.
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Anaerococcus ihuae sp. nov. and Mediannikoviicoccus vaginalis gen. nov., sp. nov., two new bacteria isolated from human vaginal samples. Arch Microbiol 2022; 204:508. [PMID: 35859139 PMCID: PMC9300522 DOI: 10.1007/s00203-022-03082-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/11/2022]
Abstract
Strains Marseille-Q5893 (= CSUR Q5893 = CECT 30496) and Marseille-Q5883 (= CSUR Q5883 = CECT 30497) were isolated from vaginal samples using the culturomics approach. The 16S rRNA gene sequences of each strain were sequenced and then compared by BLASTn to the NCBI database. Strains Marseille-Q5893 and Marseille-Q5883 were most closely related to Anaerococcus obesiensis and Finegoldia magna, with identities of 98.5% and 90.0%, respectively. Strain Marseille-Q5893 is strictly anaerobic, while strain Marseille-Q5883 is facultative anaerobic. Both strains are Gram-positive, coccus-shaped, oxidase- and catalase-negative. The most abundant fatty acid for both strains is hexadecanoic acid, followed by 9-octadecenoic acid and tetradecanoic acid. Strain Marseille-Q5893 has a genome size of 1,831,271 bp with a G+C content of 29.4 mol%, whereas strain Marseille-Q5883 has a genome of 1,997,945 bp with a 33.6 mol% G+C content. The genomic comparison of closely related species with strains Marseille-Q5893 and Marseille-Q5883 showed that all digital DNA–DNA hybridization (dDDH) and orthologous average nucleotide identity (OrthoANI) values were lower than the published species thresholds (70% and 95–96%, respectively). Based on these data, we conclude that strain Marseille-Q5893 belongs to a new species in the family Peptoniphilaceae and strain Marseille-Q5883 belongs to a new genus in the family Peptostreptococcaceae. For these two new bacterial species, the names Anaerococcus ihuae sp. nov. and Mediannikoviicoccus vaginalis gen. nov., sp. nov., were proposed.
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Zhang X, Hu Y, Ansari AR, Akhtar M, Chen Y, Cheng R, Cui L, Nafady AA, Elokil AA, Abdel-Kafy ESM, Liu H. Caecal microbiota could effectively increase chicken growth performance by regulating fat metabolism. Microb Biotechnol 2021; 15:844-861. [PMID: 34264533 PMCID: PMC8913871 DOI: 10.1111/1751-7915.13841] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/15/2022] Open
Abstract
It has been established that gut microbiota influences chicken growth performance and fat metabolism. However, whether gut microbiota affects chicken growth performance by regulating fat metabolism remains unclear. Therefore, seven‐week‐old chickens with high or low body weight were used in the present study. There were significant differences in body weight, breast and leg muscle indices, and cross‐sectional area of muscle cells, suggesting different growth performance. The relative abundance of gut microbiota in the caecal contents at the genus level was compared by 16S rRNA gene sequencing. The results of LEfSe indicated that high body weight chickens contained Microbacterium and Sphingomonas more abundantly (P < 0.05). In contrast, low body weight chickens contained Slackia more abundantly (P < 0.05). The results of H & E, qPCR, IHC, WB and blood analysis suggested significantly different fat metabolism level in serum, liver, abdominal adipose, breast and leg muscles between high and low body weight chickens. Spearman correlation analysis revealed that fat metabolism positively correlated with the relative abundance of Microbacterium and Sphingomonas while negatively correlated with the abundance of Slackia. Furthermore, faecal microbiota transplantation was performed, which verified that transferring faecal microbiota from adult chickens with high body weight into one‐day‐old chickens improved growth performance and fat metabolism in liver by remodelling the gut microbiota. Overall, these results suggested that gut microbiota could affect chicken growth performance by regulating fat metabolism.
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Affiliation(s)
- Xiaolong Zhang
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yafang Hu
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Abdur Rahman Ansari
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,Section of Anatomy and Histology, Department of Basic Sciences, College of Veterinary and Animal Sciences (CVAS) Jhang, University of Veterinary and Animal Sciences (UVAS), Lahore, Pakistan
| | - Muhammad Akhtar
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yan Chen
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Ranran Cheng
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Lei Cui
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Abdallah A Nafady
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Abdelmotaleb A Elokil
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,Department of Animal Production, Faculty of Agriculture, Benha University, Moshtohor, 13736, Egypt
| | - El-Sayed M Abdel-Kafy
- Animal Production Research Institute (APRI), Agricultural Research Center (ARC), Ministry of Agriculture, Giza, Egypt
| | - Huazhen Liu
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Mitra M, Nguyen KMAK, Box TW, Berry TL, Fujita M. Isolation and characterization of a heavy metal- and antibiotic-tolerant novel bacterial strain from a contaminated culture plate of Chlamydomonas reinhardtii, a green micro-alga. F1000Res 2021; 10:533. [PMID: 34540203 PMCID: PMC8424464 DOI: 10.12688/f1000research.53779.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/24/2021] [Indexed: 11/04/2023] Open
Abstract
Background:Chlamydomonas reinhardtii, a green micro-alga, is normally cultured in laboratories in Tris-Acetate Phosphate (TAP), a medium which contains acetate as the sole carbon source. Acetate in TAP can lead to occasional bacterial and fungal contamination. We isolated a yellow-pigmented bacterium from a Chlamydomonas TAP plate. It was named Clip185 based on the Chlamydomonas strain plate it was isolated from. In this article we present our work on the isolation, taxonomic identification and physiological and biochemical characterizations of Clip185. Methods: We measured sensitivities of Clip185 to five antibiotics and performed standard microbiological tests to characterize it. We partially sequenced the 16S rRNA gene of Clip185. We identified the yellow pigment of Clip185 by spectrophotometric analyses. We tested tolerance of Clip185 to six heavy metals by monitoring its growth on Lysogeny Broth (LB) media plates containing 0.5 mM -10 mM concentrations of six different heavy metals. Results: Clip185 is an aerobic, gram-positive rod, oxidase-negative, mesophilic, alpha-hemolytic bacterium. It can ferment glucose, sucrose and mannitol. It is starch hydrolysis-positive. It is very sensitive to vancomycin but resistant to penicillin and other bacterial cell membrane- and protein synthesis-disrupting antibiotics. Clip185 produces a C50 carotenoid, decaprenoxanthin, which is a powerful anti-oxidant with a commercial demand. Decaprenoxanthin production is induced in Clip185 under light. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of Clip185 revealed a 99% sequence identity to that of Microbacterium binotii strain PK1-12M and Microbacterium sp. strain MDP6. Clip185 is able to tolerate toxic concentrations of six heavy metals. Conclusions: Our results show that Clip185 belongs to the genus Microbacterium. In the future, whole genome sequencing of Clip185 will clarify if Clip185 is a new Microbacterium species or a novel strain of Microbacterium binotii, and will reveal its genes involved in antibiotic-resistance, heavy-metal tolerance and regulation of decaprenoxanthin biosynthesis.
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Affiliation(s)
- Mautusi Mitra
- Department of Mathematics, Sciences and Technology, University of West Georgia, Carrollton, Georgia, 30118, USA
| | - Kevin Manoap-Anh-Khoa Nguyen
- Department of Mathematics, Sciences and Technology, University of West Georgia, Carrollton, Georgia, 30118, USA
- Department of Mechanical Engineering, Kennesaw State University, Marietta, Georgia, 30060, USA
| | - Taylor Wayland Box
- Department of Mathematics, Sciences and Technology, University of West Georgia, Carrollton, Georgia, 30118, USA
| | - Taylor Lynne Berry
- Carrollton High School, Carrollton, Georgia, 30117, USA
- Department of Chemistry and Biochemistry, University of North Georgia, Dahlonega, Georgia, 30597, USA
| | - Megumi Fujita
- Department of Mathematics, Sciences and Technology, University of West Georgia, Carrollton, Georgia, 30118, USA
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6
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Mitra M, Nguyen KMAK, Box TW, Berry TL, Fujita M. Isolation and characterization of a heavy metal- and antibiotic-tolerant novel bacterial strain from a contaminated culture plate of Chlamydomonas reinhardtii, a green micro-alga. F1000Res 2021; 10:533. [PMID: 34540203 PMCID: PMC8424464 DOI: 10.12688/f1000research.53779.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/27/2021] [Indexed: 11/20/2022] Open
Abstract
Background:Chlamydomonas reinhardtii, a green micro-alga, is normally cultured in laboratories in Tris-Acetate Phosphate (TAP), a medium which contains acetate as the sole carbon source. Acetate in TAP can lead to occasional bacterial and fungal contamination. We isolated a yellow-pigmented bacterium from a Chlamydomonas TAP plate. It was named Clip185 based on the Chlamydomonas strain plate it was isolated from. In this article we present our work on the isolation, taxonomic identification and physiological and biochemical characterizations of Clip185. Methods: We measured sensitivities of Clip185 to five antibiotics and performed standard microbiological tests to characterize it. We partially sequenced the 16S rRNA gene of Clip185. We identified the yellow pigment of Clip185 by spectrophotometric analyses. We tested tolerance of Clip185 to six heavy metals by monitoring its growth on Lysogeny Broth (LB) media plates containing 0.5 mM -10 mM concentrations of six different heavy metals. Results: Clip185 is an aerobic, gram-positive rod, oxidase-negative, mesophilic, alpha-hemolytic bacterium. It can ferment glucose, sucrose and mannitol. It is starch hydrolysis-positive. It is very sensitive to vancomycin but resistant to penicillin and other bacterial cell membrane- and protein synthesis-disrupting antibiotics. Clip185 produces a C50 carotenoid, decaprenoxanthin, which is a powerful anti-oxidant with a commercial demand. Decaprenoxanthin production is induced in Clip185 under light. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of Clip185 revealed a 99% sequence identity to that of Microbacterium binotii strain PK1-12M and Microbacterium sp. strain MDP6. Clip185 is able to tolerate toxic concentrations of six heavy metals. Conclusions: Our results show that Clip185 belongs to the genus Microbacterium. In the future, whole genome sequencing of Clip185 will clarify if Clip185 is a new Microbacterium species or a novel strain of Microbacterium binotii, and will reveal its genes involved in antibiotic-resistance, heavy-metal tolerance and regulation of decaprenoxanthin biosynthesis.
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Affiliation(s)
- Mautusi Mitra
- Department of Mathematics, Sciences and Technology, University of West Georgia, Carrollton, Georgia, 30118, USA
| | - Kevin Manoap-Anh-Khoa Nguyen
- Department of Mathematics, Sciences and Technology, University of West Georgia, Carrollton, Georgia, 30118, USA
- Department of Mechanical Engineering, Kennesaw State University, Marietta, Georgia, 30060, USA
| | - Taylor Wayland Box
- Department of Mathematics, Sciences and Technology, University of West Georgia, Carrollton, Georgia, 30118, USA
| | - Taylor Lynne Berry
- Carrollton High School, Carrollton, Georgia, 30117, USA
- Department of Chemistry and Biochemistry, University of North Georgia, Dahlonega, Georgia, 30597, USA
| | - Megumi Fujita
- Department of Mathematics, Sciences and Technology, University of West Georgia, Carrollton, Georgia, 30118, USA
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Zgheib R, Anani H, Meng MM, Mailhe M, Ricaboni D, Morand A, Caputo A, Traore SI, Fontanini A, Armstrong N, Raoult D, Fournier PE. New human-associated species of the family Atopobiaceae and proposal to reclassify members of the genus Olsenella. Int J Syst Evol Microbiol 2021; 71. [PMID: 34047688 DOI: 10.1099/ijsem.0.004819] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Five novel bacterial strains, Marseille-P1476T (=CSURP1476T=DSM 100642T), Marseille-P3256T (=CSURP3256T=CECT 9977T), Marseille-P2936T (=CSURP2936T=DSM 103159T), Marseille-P2912T (=CSURP2912T=DSM 103345T) and Marseille-P3197T (=CSURP3197T=CCUG 71847T), were isolated from various human specimens. These five strains were not identified at the species level by matrix-assisted laser desorption/ionization time of flight mass spectrometry. Following 16S rRNA gene sequence comparisons with the GenBank database, the highest nucleotide sequence similarities of all studied strains were obtained to members of the paraphyletic genus Olsenella. A polyphasic taxono-genomic strategy (16S rRNA gene-based and core genome-based phylogeny, genomic comparison, phenotypic and biochemical characteristics) enabled us to better classify these strains and reclassify Olsenella species. Among the studied strains, Marseille-P1476T, Marseille-P2936T and Marseille-P3197T belonged to new species of the genus Olsenella for which we propose the names Olsenella massiliensis sp. nov., Olsenella phocaeensis sp. nov. and Olsenella urininfantis sp. nov., respectively. Strains Marseille-P2912T and Marseille-P3256T belonged to a new genus for which the names Thermophilibacter provencensis gen. nov., sp. nov. and Thermophilibacter mediterraneus gen. nov., sp. nov. are proposed, respectively. We also propose the creation of the genera Parafannyhessea gen. nov., Tractidigestivibacter gen. nov. and Paratractidigestivibacter gen. nov. and the reclassification of Olsenella umbonata as Parafannyhessea umbonata comb. nov., Olsenella scatoligenes as Tractidigestivibacter scatoligenes comb. nov., and Olsenella faecalis as Paratractidigestivibacter faecalis comb. nov.
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Affiliation(s)
- Rita Zgheib
- 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 Méditerranéennes (VITROME), Marseille, France
| | - Hussein 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 Méditerranéennes (VITROME), Marseille, France
| | - Marine Makoa Meng
- 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 Méditerranéennes (VITROME), Marseille, France
| | - Morgane Mailhe
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Davide Ricaboni
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Aurélie Morand
- Pédiatrie spécialisée et médecine infantile, Hôpital de la Timone, AP-HM, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Aurelia Caputo
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Sory Ibrahima Traore
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Anthony Fontanini
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Nicholas Armstrong
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Pierre Edouard 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 Méditerranéennes (VITROME), Marseille, France
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8
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Corretto E, Antonielli L, Sessitsch A, Höfer C, Puschenreiter M, Widhalm S, Swarnalakshmi K, Brader G. Comparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance. Front Microbiol 2020; 11:1869. [PMID: 32903828 PMCID: PMC7438953 DOI: 10.3389/fmicb.2020.01869] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/16/2020] [Indexed: 12/11/2022] Open
Abstract
Microbacterium species have been isolated from a wide range of hosts and environments, including heavy metal-contaminated sites. Here, we present a comprehensive analysis on the phylogenetic distribution and the genetic potential of 70 Microbacterium belonging to 20 different species isolated from heavy metal-contaminated and non-contaminated sites with particular attention to secondary metabolites gene clusters. The analyzed Microbacterium species are divided in three main functional clades. They share a small core genome (331 gene families covering basic functions) pointing to high genetic diversity. The most common secondary metabolite gene clusters encode pathways for the production of terpenoids, type III polyketide synthases and non-ribosomal peptide synthetases, potentially responsible of the synthesis of siderophore-like compounds. In vitro tests showed that many Microbacterium strains produce siderophores, ACC deaminase, auxins (IAA) and are able to solubilize phosphate. Microbacterium isolates from heavy metal contaminated sites are on average more resistant to heavy metals and harbor more genes related to metal homeostasis (e.g., metalloregulators). On the other hand, the ability to increase the metal mobility in a contaminated soil through the secretion of specific molecules seems to be widespread among all. Despite the widespread capacity of strains to mobilize several metals, plants inoculated with selected Microbacterium isolates showed only slightly increased iron concentrations, whereas concentrations of zinc, cadmium and lead were decreased.
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Affiliation(s)
- Erika Corretto
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Livio Antonielli
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Angela Sessitsch
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Christoph Höfer
- Institute of Soil Research, Department of Forest- and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Puschenreiter
- Institute of Soil Research, Department of Forest- and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Siegrid Widhalm
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | | | - Günter Brader
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
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9
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Celebi B, Anani H, Zgheib R, Carhan A, Raoult D, Fournier PE. Genomic Characterization of the Novel Bartonella refiksaydamii sp. Isolated from the Blood of a Crocidura suaveolens (Pallas, 1811). Vector Borne Zoonotic Dis 2020; 21:432-440. [PMID: 34077294 DOI: 10.1089/vbz.2020.2626] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bartonella species are reemerging infectious agents that are transmitted by arthropod vectors among animals and/or humans. At least 13 of the 35 currently recognized Bartonella species are pathogenic for humans. Most of the pathogenic species, except Bartonella quintana and Bartonella bacilliformis, are zoonotic agents with animal reservoirs, including cats, dogs, coyotes, foxes, cattle, and rodents. In this study, a novel Bartonella species was isolated from the blood of a Crocidura suaveolens (Pallas, 1811) Lesser shrew that was captured in the Bartın region of Northwestern Turkey. The strain, RSKK 19006, was characterized using whole-genome sequencing and comparison, multilocus sequence typing (gltA, rpoB, ssrA, nuoG, and 16S rRNA) and internal transcribed spacer sequencing, electron microscopy scanning, biochemical tests, and MALDI-TOF MS (matrix assisted laser desorption ionization-time of flight mass spectrometry). This novel Bartonella is a Gram-negative, rod-shaped, microaerophilic bacterium and has neither flagella nor pilus. As a consequence, we propose to name this new species Bartonella refiksaydamii sp. nov. in Bartonella genus. The zoonotic potential of this novel Bartonella species is as yet unknown.
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Affiliation(s)
- Bekir Celebi
- Zoonotic and Vector-Borne Diseases Department, Ministry of Health, General Directorate of Public Health, Ankara, Turkey
| | - Hussein Anani
- UMR VITROME, Aix-Marseille University, Institut pour la Recherche et le Développement, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Rita Zgheib
- UMR VITROME, Aix-Marseille University, Institut pour la Recherche et le Développement, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Ahmet Carhan
- Medical Biology Department, Faculty of Medicine, Yildirim Beyazit University, Ankara, Turkey
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,UMR MEPHI, Aix-Marseille University, Institut pour la Recherche et le Développement, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Pierre-Edouard Fournier
- UMR VITROME, Aix-Marseille University, Institut pour la Recherche et le Développement, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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Abou Abdallah R, Okdah L, Bou Khalil J, Anani H, Fournier PE, Raoult D, Bittar F. Draft genome and description of Chryseobacterium phocaeense sp. nov.: a new bacterial species isolated from the sputum of a cystic fibrosis patient. Arch Microbiol 2019; 201:1361-1368. [DOI: 10.1007/s00203-019-01704-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/21/2019] [Accepted: 07/10/2019] [Indexed: 11/28/2022]
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Anani H, Abdallah RA, Khoder M, Fontanini A, Mailhe M, Ricaboni D, Raoult D, Fournier PE. Colibacter massiliensis gen. nov. sp. nov., a novel Gram-stain-positive anaerobic diplococcal bacterium, isolated from the human left colon. Sci Rep 2019; 9:17199. [PMID: 31748674 PMCID: PMC6868274 DOI: 10.1038/s41598-019-53791-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 11/06/2019] [Indexed: 12/22/2022] Open
Abstract
The gut microbiota is considered to play a key role in human health. As a consequence, deciphering its microbial diversity is mandatory. A polyphasic taxonogenomic strategy based on the combination of phenotypic and genomic analyses was used to characterize a new bacterium, strain Marseille-P2911. This strain was isolated from a left colon sample of a 60-year old man who underwent a colonoscopy for an etiological investigation of iron-deficiency anemia in Marseille, France. On the basis of 16S rRNA sequence comparison, the closest phylogenetic neighbor was Anaeroglobus geminatus (94.59% 16S rRNA gene sequence similarity) within the family Veillonellaceae. Cells were anaerobic, Gram-stain-positive, non-spore-forming, catalase/oxidase negative cocci grouped in pairs. The bacterium was able to grow at 37 °C after 2 days of incubation. Strain Marseille-P2911 exhibited a genome size of 1,715,864-bp with a 50.2% G + C content, and digital DNA-DNA hybridization (dDDH) and OrthoANI values with A. geminatus of only 19.1 ± 4.5% and 74.42%, respectively. The latter value being lower than the threshold for genus delineation (80.5%), we propose the creation of the new genus Colibacter gen. nov., with strain Marseille-P2911T (=DSM 103304 = CSUR P2911) being the type strain of the new species Colibacter massiliensis gen. nov., sp. nov.
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Affiliation(s)
- Hussein Anani
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditeranéennes (VITROME), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Rita Abou Abdallah
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditeranéennes (VITROME), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - May Khoder
- 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
| | - Anthony Fontanini
- 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
| | - Morgane Mailhe
- 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
| | - Davide Ricaboni
- 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
| | - Didier 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 Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditeranéennes (VITROME), Marseille, France. .,Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.
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Anani H, Abou Abdallah R, Chelkha N, Fontanini A, Ricaboni D, Mailhe M, Raoult D, Fournier PE. Draft genome and description of Merdibacter massiliensis gen.nov., sp. nov., a new bacterium genus isolated from the human ileum. Sci Rep 2019; 9:7931. [PMID: 31138831 PMCID: PMC6538751 DOI: 10.1038/s41598-019-44343-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/09/2019] [Indexed: 12/22/2022] Open
Abstract
We used phenotypic, genomic and phylogenetic information following the taxono-genomics approach to demonstrate that strain Marseille–P3254, isolated from an ileal sample of a 76-year old woman who underwent upper and lower digestive tract endoscopy for esophagitis and colonic polyp, is representative of a novel bacterial genus within the family Erysipelotrichaceae in the phylum Firmicutes. It is an anaerobic Gram-negative bacterium without catalase and oxidase activities. The genome of strain Marseille–P3254 is 2,468,496-bp long with a 40.1% G + C content. This new bacterium is most closely related to Eubacterium dolichum, with which it shares 90.7% 16S rRNA sequence similarity. In addition, genomic comparison using the digital DNA–DNA hybridization and OrthoANI analyses between the novel organism and the E. dolichum type strain revealed identities of 25.2 and 68.91%, respectively. The major fatty acids were C16: 0, C18: 1n9 and C18: 0. Based on these data, we propose the creation of the new genus Merdibacter gen. nov., with strain Marseille-P3254T (=CSUR P3254 = DSM 103534) being the type strain of the new species Merdibacter massiliensis gen. nov., sp. nov.
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Affiliation(s)
- Hussein Anani
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Rita Abou Abdallah
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Nisrine Chelkha
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Anthony Fontanini
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Davide Ricaboni
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Morgane Mailhe
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
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Davoust B, Levasseur A, Mediannikov O. Studies of nonhuman primates: key sources of data on zoonoses and microbiota. New Microbes New Infect 2018; 26:S104-S108. [PMID: 30402252 PMCID: PMC6205567 DOI: 10.1016/j.nmni.2018.08.014] [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: 03/02/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 12/11/2022] Open
Abstract
The genetic and morphologic similarities between primates and humans means that much information obtained from primates may be applied to humans, and vice versa. However, habitat loss, hunting and the continued presence of humans have a negative effect on the biology and behaviour of almost all nonhuman primates. Noninvasive methods such as stool collection are among the safest alternative ways to study the multiple aspects of the biology of primates. Many epidemiologic issues (e.g. pathogen detection, microbiota studies) may be easily studied using stool samples from primates. Primates are undoubtedly among the first candidates suspected of becoming the source of one of the next emerging epidemic of zoonotic origin, as has already been observed with HIV, malaria and monkeypox. The Institut Hospitalo-Universitaire Méditerranée Infection in Marseille actively participates in the study, mostly epidemiologic, of nonhuman primates, using mostly stool samples.
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Affiliation(s)
- B Davoust
- Microbes, Evolution, Phylogeny and Infection (MEФI), UMR Aix-Marseille Université, IRD, APHM, IHU Méditerranée Infection, Marseille, France
| | - A Levasseur
- Microbes, Evolution, Phylogeny and Infection (MEФI), UMR Aix-Marseille Université, IRD, APHM, IHU Méditerranée Infection, Marseille, France
| | - O Mediannikov
- Microbes, Evolution, Phylogeny and Infection (MEФI), UMR Aix-Marseille Université, IRD, APHM, IHU Méditerranée Infection, Marseille, France
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Bardet L, Cimmino T, Buffet C, Michelle C, Rathored J, Tandina F, Lagier JC, Khelaifia S, Abrahão J, Raoult D, Rolain JM. Microbial Culturomics Application for Global Health: Noncontiguous Finished Genome Sequence and Description of Pseudomonas massiliensis Strain CB-1T sp. nov. in Brazil. ACTA ACUST UNITED AC 2018. [DOI: 10.1089/omi.2017.0027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lucie Bardet
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, IHU-Méditerranée Infection, Marseille, France
| | - Teresa Cimmino
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, IHU-Méditerranée Infection, Marseille, France
| | - Clémence Buffet
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, IHU-Méditerranée Infection, Marseille, France
| | - Caroline Michelle
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, IHU-Méditerranée Infection, Marseille, France
| | - Jaishriram Rathored
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, IHU-Méditerranée Infection, Marseille, France
| | - Fatalmoudou Tandina
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, IHU-Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, IHU-Méditerranée Infection, Marseille, France
| | - Saber Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, IHU-Méditerranée Infection, Marseille, France
| | - Jônatas Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Didier Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, IHU-Méditerranée Infection, Marseille, France
| | - Jean-Marc Rolain
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, IHU-Méditerranée Infection, Marseille, France
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Description of Chryseobacterium timonianum sp. nov., isolated from a patient with pneumonia. Antonie Van Leeuwenhoek 2017; 110:1121-1132. [PMID: 28509971 DOI: 10.1007/s10482-017-0885-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
Abstract
Using a polyphasic taxonomic strategy, an aerobic, Gram-negative, non-motile, yellow pigmented rod isolated from a sputum sample of a patient with pneumonia was characterised. This bacterial strain, designated G972T, could not be identified by our systematic MALDI-TOF screening on a MicroFlex. This led to the sequencing of the 16S rRNA gene, which shows 98.57% sequence identity with that of Chryseobacterium indologenes 16777T, the phylogenetic closely related type strain of a species with standing in nomenclature, which putatively classifies it as a new species. The major cell fatty acids were identified as 13-methyl-tetradecanoic acid (61%), 3-hydroxy-heptadecanoic acid (16%) and 15-methyl-11-hexadecenoic acid (11%). D-glucose, D-mannose, aesculin, D-maltose, D-trehalose, and gentibiose are the main carbon source. Digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity values (ANI) of the strain G972T against genomes of the type strains of related species ranged between 18.9 and 32.8% and between 71.46 and 83.61%, respectively, thus confirming again the new species status of the strain. Here, we describe the characteristics of this organism, complete genome sequence and annotation. The 5,390,132 bp size genome contains 4867 protein-coding genes, 89 RNAs (three genes are 5S rRNA, one gene is 16S rRNA, one gene is 23S rRNA and 84 tRNAs) with 35.51% GC content. Finally, on the basis of these polyphasic data, consisting of phenotypic and genomic analyses, we conclude that strain strain G972T (= DSM 103388T = CSUR P2233T) represents a novel species for which we propose the name Chryseobacterium timonianum. The 16S rRNA and genome sequences are available in GenBank database under accession numbers LT161886 and FJVD00000000.
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