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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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Boxberger M, Magnien S, Antezack A, Rolland C, Makoa Meng M, Lo CI, La Scola B, Cassir N. Leucobacter manosquensis sp. nov.-A Novel Bacterial Species Isolated from Healthy Human Skin. Microorganisms 2023; 11:2535. [PMID: 37894193 PMCID: PMC10609233 DOI: 10.3390/microorganisms11102535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/22/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Extending our knowledge on human skin microbiota is a challenge to better decipher its role in health and disease. Using the culturomics method, we isolated strain Marseille-Q4368 from the healthy forehead of a 59-year-old woman. We describe here the main characteristics of this bacterium using a taxonogenomic approach. This new bacterial species is Gram-positive, non-motile, and non-spore-forming. Its 16S rRNA sequence exhibited a similarity of 99.59% with Leucobacter chromiiresistens, the most closely related species in terms of nomenclature. However, a digital DNA-DNA hybridization analysis between these two species revealed a maximum identity similarity of only 27.5%. We found phenotypical and genomic differences between strain Marseille-Q4368 and its closely related species. These findings underscore the classification of this bacterium as a distinct species. Hence, we propose the name Leucobacter manosquensis sp. nov. strain Marseille-Q4368 (=CSUR Q4368 = DSM 112403) for this newly identified bacterial species.
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Affiliation(s)
- Manon Boxberger
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (M.B.); (S.M.)
- Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, 19 Boulevard Jean Moulin, 13005 Marseille, France
| | - Sibylle Magnien
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (M.B.); (S.M.)
- Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, 19 Boulevard Jean Moulin, 13005 Marseille, France
| | - Angeline Antezack
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (M.B.); (S.M.)
- Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, 19 Boulevard Jean Moulin, 13005 Marseille, France
- École de Médecine Dentaire, Faculté des Sciences Médicales et Paramédicales, Aix-Marseille Université, Boulevard Jean Moulin, 13385 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Hôpital Timone, Service de Parodontologie, 264, Rue Saint Pierre, 13385 Marseille, France
| | - Clara Rolland
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (M.B.); (S.M.)
- Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, 19 Boulevard Jean Moulin, 13005 Marseille, France
| | - Marine Makoa Meng
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (M.B.); (S.M.)
- Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, 19 Boulevard Jean Moulin, 13005 Marseille, France
| | - Cheikh Ibrahima Lo
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (M.B.); (S.M.)
| | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (M.B.); (S.M.)
- Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, 19 Boulevard Jean Moulin, 13005 Marseille, France
| | - Nadim Cassir
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (M.B.); (S.M.)
- Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Université, 19 Boulevard Jean Moulin, 13005 Marseille, France
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Hammoud A, Medkour H, Zgheib R, Louni M, Diatta G, Bassene H, Sambou M, Gaye M, Haddad G, Fenollar F, Sokhna C, Mediannikov O. Bartonella raoultii sp. nov., isolated from infected rodents ( Mastomys erythroleucus) in Senegal. Int J Syst Evol Microbiol 2023; 73. [PMID: 37578895 DOI: 10.1099/ijsem.0.005888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Abstract
Bartonella species are involved in various human diseases, causing a range of clinical manifestations; animals are considered as the main reservoirs, transmitting diverse species of Bartonella through direct contact and haematophagous insects. Here, we characterize a new species, Bartonella raoultii sp. nov., within the genus Bartonella, using a taxonogenomic polyphasic approach. Strain 094T (= CSUR B1097T=DSM 28004T), isolated from the blood of an infected rodent (Mastomys erythroleucus) in Senegal, is an aerobic and rod-shaped bacterium. The annotated non-contiguous genome sequence is 1 952322 bp long and contains 37.2 mol% G+C content, 1686 protein-coding genes and 50 RNA genes, including seven rRNA genes.
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Affiliation(s)
- Alissa Hammoud
- IHU Méditerranée Infection, 13005 Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Hacène Medkour
- IHU Méditerranée Infection, 13005 Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Rita Zgheib
- IHU Méditerranée Infection, 13005 Marseille, France
- Aix Marseille Univ, IRD, APHM, VITROME, 13005 Marseille, France
| | - Meriem Louni
- IHU Méditerranée Infection, 13005 Marseille, France
- Aix Marseille Univ, IRD, APHM, VITROME, 13005 Marseille, France
- Faculty of Science, M'Hamed Bougara Boumerdès University, Boumerdès 35000, Algeria
| | - Georges Diatta
- VITROME, Campus International IRD-UCAD Hann, Dakar, Senegal
| | - Hubert Bassene
- VITROME, Campus International IRD-UCAD Hann, Dakar, Senegal
| | - Masse Sambou
- VITROME, Campus International IRD-UCAD Hann, Dakar, Senegal
| | - Mapenda Gaye
- IHU Méditerranée Infection, 13005 Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Gabriel Haddad
- IHU Méditerranée Infection, 13005 Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Florence Fenollar
- IHU Méditerranée Infection, 13005 Marseille, France
- Aix Marseille Univ, IRD, APHM, VITROME, 13005 Marseille, France
| | - Cheikh Sokhna
- IHU Méditerranée Infection, 13005 Marseille, France
- Aix Marseille Univ, IRD, APHM, VITROME, 13005 Marseille, France
| | - Oleg Mediannikov
- IHU Méditerranée Infection, 13005 Marseille, France
- Aix Marseille Univ, IRD, APHM, MEPHI, 13005 Marseille, France
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Diouf FS, Beye M, Gaye M, Mbaye B, Alibar S, Sarr M, Dubourg G, Lagier JC, Sokhna C, Fenollar F, Fournier PE, Lo CI. Description of Streptococcus thalassemiae sp. nov., a Bacterium Isolated from Human Blood. Int J Microbiol 2023; 2023:3802590. [PMID: 37559874 PMCID: PMC10409578 DOI: 10.1155/2023/3802590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/13/2023] [Accepted: 05/04/2023] [Indexed: 08/11/2023] Open
Abstract
Blood is a precious biological liquid that is normally sterile. Therefore, bacteria in the bloodstream are shown a priori anomaly. A blood culture is systematically performed to diagnose the cause of the bacteremia. Indeed, a patient received in our service had a thalassemia major and underwent a genoidentical transplant. Then, a blood test was performed to diagnose a four-day fever. In this context, we have isolated strain Marseille-Q2617 from the blood sample. It revealed a new bacterial strain that belongs to the genus Streptococcus. It is a Gram-positive coccus, nonmotile, and nonspore forming. The major fatty acid found is hexadecanoic acid, with 49.5%. A taxonomic method was used to characterize the strain by studying their phenotypic, phylogenetic, and genomic characteristics. In addition, sequence analysis of the 16S rRNA gene shows that the strain Marseille-Q2617 has 99.94% sequence similarity to Streptococcus mitis. Average nucleotide identity (ANI) analysis for strain Marseille-Q2617T showed the highest similarity of 92.9% with S. mitis. The DNA-DNA hybridization value obtained (50.2%) between strain Marseille-Q2607 and S. mitis, its closest related species, was below the recommended threshold (<70%). Strain Marseille-Q2617T has a genome size of 2.02 Mbp with 40.5 mol% of G + C content. Based on these results, we propose a new species of the genus Streptococcus, for which the name Streptococcus thalassemiae sp. nov., Marseille-Q2617T (=CSUR Q2617 = CECT 30109) was proposed.
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Affiliation(s)
- Fatou Samba Diouf
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Mamadou Beye
- IHU-Mediterranean Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Mapenda Gaye
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Babacar Mbaye
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Stephane Alibar
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Mariema Sarr
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Gregory Dubourg
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
| | - Cheikh Sokhna
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Mediterranean Infection, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - Florence Fenollar
- IHU-Mediterranean Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Pierre-Edouard Fournier
- IHU-Mediterranean Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Cheikh Ibrahima Lo
- IHU-Mediterranean Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
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Hamame A, Magdy Wasfy R, Lo CI, Fenollar F, Raoult D, Fournier PE, Houhamdi L. Taxonogenomics of Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. new bacteria isolated from human stool microbiota. Sci Rep 2023; 13:8465. [PMID: 37231091 DOI: 10.1038/s41598-023-35443-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
Two new bacterial strains, Marseille-P2698T (CSUR P2698 = DSM 103,121) and Marseille-P2260T (CSUR P2260 = DSM 101,844 = SN18), were isolated from human stools by the culturomic method. We used the taxonogenomic approach to fully describe these two new bacterial strains. The Marseille-P2698T strain was a Gram-negative, motile, non-spore-forming, rod-shaped bacterium. The Marseille-P2260T strain was a Gram-positive, motile, spore-forming rod-shaped bacterium. Major fatty acids found in Marseille-P2698T were C15:0 iso (63%), C15:0 anteiso (11%), and C17:0 3-OH iso (8%). Those found in Marseille-P2260T strain were C16:00 (39%), C18:1n9 (16%) and C18:1n7 (14%). Strains Marseille-P2698T and Marseille-P2260T had 16S rRNA gene sequence similarities of 91.50% with Odoribacter laneusT, and of 90.98% and 95.07% with Odoribacter splanchnicusT and Eubacterium sulciT, respectively. The exhibited digital DNA-DNA Hybridization values lower than 20.7%, and Orthologous Average Nucleotide Identity values lower than 73% compared to their closest related bacterial species O. splanchnicusT and E. sulciT respectively. Phenotypic, biochemical, phylogenetic, and genomic results obtained by comparative analyses provided sufficient evidence that both of the two studied strains Marseille-P2698T and Marseille-P2260T are two new bacterial species and new bacterial genera for which the names Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. were proposed, respectively.
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Affiliation(s)
- Afaf Hamame
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Reham Magdy Wasfy
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Cheikh Ibrahima Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, Service de Santé Des Armées (SSA), VITROME, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, Service de Santé Des Armées (SSA), VITROME, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, Service de Santé Des Armées (SSA), VITROME, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Linda Houhamdi
- IHU-Méditerranée Infection, Marseille, France.
- Aix Marseille Univ, IRD, AP-HM, Service de Santé Des Armées (SSA), VITROME, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
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Traore SI, Lo CI, Mossaab M, Durand G, Lagier JC, Raoult D, Fournier PE, Fenollar F. Maliibacterium massiliense gen. nov. sp. nov., Isolated from Human Feces and Proposal of Maliibacteriaceae fam. nov. Curr Microbiol 2023; 80:211. [PMID: 37191823 DOI: 10.1007/s00284-023-03301-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 06/30/2021] [Indexed: 05/17/2023]
Abstract
Bacterial strain Marseille-P3954 was isolated from a stool sample of a 35-year-old male patient living in France. It was a gram-positive, rod-shaped anaerobic, non-motile, and non-spore-forming bacterium. C16:0 and C18:1n9 were the major fatty acid, while its genome measured 2,422,126 bp with 60.8 mol% of G+C content. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain Marseille-P3954 had 85.51% of similarity with Christensenella minuta, its closest related species with standing in nomenclature. As this value is very low compared to the recommended threshold, it suggested that the Marseille-P3954 strain belongs to a new bacterial genus, classified in a new family. On the basis of these genomic, phenotypic, and phylogenetic evidences, we propose that strain Marseille-P3954 should be classified as a new genus and species, Maliibacterium massiliense gen. nov., sp. nov. The type strain of M. massiliense sp. nov. is Marseille-P3954 (CSUR P3954 = CECT 9568).
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Affiliation(s)
- Sory Ibrahima Traore
- Aix Marseille University, IRD, AP-HM, MEPHII, Marseille, France
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Cheikh Ibrahima Lo
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Maaloum Mossaab
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
- Laboratory of Biology and Health, Faculty of Sciences Ben M'sik, Hassan II University, Casablanca, Morocco
| | - Guillaume Durand
- Aix Marseille University, IRD, AP-HM, MEPHII, Marseille, France
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Jean Christophe Lagier
- Aix Marseille University, IRD, AP-HM, MEPHII, Marseille, France
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Didier Raoult
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France.
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Description of a moderately acidotolerant and aerotolerant anaerobic bacterium Acidilutibacter cellobiosedens gen. nov., sp. nov. within the family Acidilutibacteraceae fam. nov., and proposal of Sporanaerobacteraceae fam. nov. and Tepidimicrobiaceae fam. nov. Syst Appl Microbiol 2023; 46:126376. [PMID: 36375421 DOI: 10.1016/j.syapm.2022.126376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/17/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022]
Abstract
A Gram-stain positive, moderately thermophilic, acidotolerant and aerotolerant anaerobic bacterium, designated JN-28 T, was isolated from the pit mud of Chinese strong-flavor liquor. Growth was observed at 25-50 °C and pH 5.5-8.0 in the presence of 0-25 g l-1 NaCl (optimally at 45 °C, pH 6.0, without NaCl). Strain JN-28 T was heterotrophic, requiring yeast extract for growth. The major cellular fatty acids were iso-C15:0 and C14:0. The DNA G + C content of genomic DNA was 33.54 mol%. The strain was resistant to vancomycin (10 mg l-1). Genome analysis revealed the presence of genes involved in the response to mild acid stress and oxidative stress, and resistance to vancomycin. 16S rRNA gene-based phylogenetic analysis showed that strain JN-28 T shares ≤ 89.3 % sequence similarity with its closest relatives Sporanaerobacter acetigenes DSM 13106 T and other members in the order Tissierellales. Based on phenotypic and phylogenetic characteristics, Acidilutibacter cellobiosedens gen. nov., sp. nov. is proposed for the new genus and novel species with the type strain JN-28 T (=CCAM 418 T = JCM 39087 T). Further phylogenetic and phylogenomic analyses suggested strain JN-28 T represents a novel family within the order Tissierellales, for which Acidilutibacteraceae fam. nov. is proposed. In addition, the family Tissierellaceae was reclassified, Sporanaerobacteraceae fam. nov. and Tepidimicrobiaceae fam. nov. were formally proposed. Emended description of the family Tissierellaceae is also provided.
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9
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Reclassification of eight Akkermansia muciniphila strains and description of Akkermansia massiliensis sp. nov. and Candidatus Akkermansia timonensis, isolated from human feces. Sci Rep 2022; 12:21747. [PMID: 36526682 PMCID: PMC9758162 DOI: 10.1038/s41598-022-25873-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Akkermansia muciniphila is a human intestinal tract bacterium that plays an important role in the mucus layer renewal. Several studies have demonstrated that it is a modulator for gut homeostasis and a probiotic for human health. The Akkermansia genus contains two species with standing in nomenclature but their genomic diversity remains unclear. In this study, eight new Akkermansia sp. strains were isolated from the human gut. Using the digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) and core genome-based phylogenetic analysis applied to 104 A. muciniphila whole genomes sequences, strains were reclassified into three clusters. Cluster I groups A. muciniphila strains (including strain ATCC BAA-835T as type strain), whereas clusters II and III represent two new species. A member of cluster II, strain Marseille-P6666 differed from A. muciniphila strain ATCC BAA-835T and from A. glycaniphila strain PytT in its ability to grow in microaerophilic atmosphere up to 42 °C, to assimilate various carbon sources and to produce acids from a several compounds. The major fatty acids of strain Marseille-P6666 were 12-methyl-tetradecanoic and pentadecanoic acids. The DNA G + C content of strain Marseille-P6666 was 57.8%. On the basis of these properties, we propose the name A. massiliensis sp. nov. for members of cluster II, with strain Marseille-P6666T (= CSUR P6666 = CECT 30548) as type strain. We also propose the name "Candidatus Akkermansia timonensis" sp. nov. for the members of cluster III, which contains only uncultivated strains, strain Akk0196 being the type strain.
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10
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Bellali S, Haddad G, Pham TPT, Iwaza R, Ibrahim A, Armstrong N, Fadlane A, Couderc C, Diallo A, Sokhna C, Million M, Raoult D, Tidjani Alou M. Draft genomes and descriptions of Urmitella timonensis gen. nov., sp. nov. and Marasmitruncus massiliensis gen. nov., sp. nov., isolated from severely malnourished African children using culturomics. Antonie Van Leeuwenhoek 2022; 115:1349-1361. [PMID: 36149539 PMCID: PMC9584879 DOI: 10.1007/s10482-022-01777-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 08/27/2022] [Indexed: 11/25/2022]
Abstract
Two strains, designated as Marseille-P2918T and Marseille-P3646T, were isolated from a 14-week-old Senegalese girl using culturomics: Urmitella timonensis strain Marseille-P2918T (= CSUR P2918, = DSM 103634) and Marasmitruncus massiliensis strain Marseille-P3646T (= CSUR P3646, = CCUG72353). Both strains were rod-shaped, anaerobic, spore forming motile bacteria. The 16S rRNA gene sequences of strains Marseille-P2918T (LT598554) and Marseille-P3646T (LT725660) shared 93.25% and 94.34% identity with Tissierella praeacuta ATCC 25539T and Anaerotruncus colihominis CIP 107754T, their respective phylogenetically closest species with standing in nomenclature. Therefore, strain Marseille-P2918T is classified within the family Tissierellaceae and order Tissierellales whereas strain Marseille-P3646T is classified within the family Oscillospiraceae and order Eubacteriales. The genome of strain Marseille-P2918T had a size of 2.13 Mb with a GC content of 50.52% and includes six scaffolds and six contigs, and that of strain Marseille-P3646T was 3.76 Mbp long consisting of five contigs with a 50.04% GC content. The genomes of both strains presented a high percentage of genes encoding enzymes involved in genetic information and processing, suggesting a high growth rate and adaptability. These new taxa are extensively described and characterised in this paper, using the concept of taxono-genomic description.
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Affiliation(s)
- Sara Bellali
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Gabriel Haddad
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
| | - Thi-Phuong-Thao Pham
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Rim Iwaza
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
| | - Ahmad Ibrahim
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
| | - Nicholas Armstrong
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Amael Fadlane
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Carine Couderc
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | | | - Cheikh Sokhna
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Matthieu Million
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Didier Raoult
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
| | - Maryam Tidjani Alou
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France.
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11
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Weizmannia faecalis sp. nov., isolated from a human stool sample. Arch Microbiol 2022; 204:612. [DOI: 10.1007/s00203-022-03229-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 11/02/2022]
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12
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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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13
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Raoultibacter phocaeensis sp. nov., A New Bacterium Isolated from a Patient with Recurrent Clostridioides difficile Infection. Curr Microbiol 2022; 79:263. [PMID: 35857140 DOI: 10.1007/s00284-022-02959-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/27/2022] [Indexed: 11/03/2022]
Abstract
Strain Marseille-P8396T is a new species isolated from a patient with recurrent Clostridioides difficile infection. Its optimal growth condition was observed at pH of 7.5, at a temperature of 37 °C after 72 h of incubation on Columbia agar (BioMérieux, France) with 5% sheep blood, under an anaerobic atmosphere. Strain Marseille-P8396T cells are Gram-positive rods, nonspore-forming, and nonmotile. 9-Octadecenoic acid (41.9%), hexadecanoic acid (22.5%), and 11-Octadecenoic acid (11.0%) represent the major fatty acid of strain Marseille-P8396T. The optimal growth condition of strain Marseille-P8396T was observed at 37 °C after 72 h of incubation under an anaerobic atmosphere, pH ranging from 6.5 to 8.5, and salinity of 0.5 to 7.5%. Its genome (Genbank Accession Number NZ_CABDUX000000000) size was 3.86 Mb with 59.4 mol% of G+C content, and 3,124 protein-coding genes. The 16S rRNA gene sequence (Genbank accession number NR_148574.1) of strain Marseille-P8396T shared a similarity of 98.71% with Raoultibacter timonensis strain Marseille-P3277T (Genbank accession number NR_148574.1), currently the most closely related species. However, the OrthoANI and digital DNA-DNA hybridization values with Raoultibacter timonensis strain Marseille-P3277T (Genbank accession number OEPT01000000) were 80.15% and 24.6 ± 4.8%, respectively. Taken together, these results clearly demonstrate that strain Marseille-P8396T represents a new species within the genus Raoultibacter described here as Raoultibacter phocaeensis sp. nov. (type strain: Marseille-P8396T=CSUR8396T=CECT 30202T).
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14
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Iwaza R, Abou Chacra L, Ibrahim A, Pham TPT, Lo CI, Tidjani Alou M, Sokhna C, Raoult D, Lagier JC. Description of Ornithinibacillus massiliensis sp. nov., Isolated from a Child with Marasmus. Curr Microbiol 2022; 79:262. [PMID: 35852643 DOI: 10.1007/s00284-022-02955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/24/2022] [Indexed: 11/29/2022]
Abstract
A Gram-positive, aerobic, motile, endospore-forming, rod-shaped bacterium was isolated from a stool sample of a child with marasmus. The 16S rRNA gene showed that strain Marseille-P3601T exhibited 98.68% sequence identity with Ornithinibacillus scapharcae strain TW25. The genomic DNA G+C contents of this strain was 36.9 mol%. The fatty acid profiles of the strain were iso/anteiso branched structures. The highest DDH value was 20.6%, shared with O. californiensis, amongst its closest strain phylogenetically. Based on the phylogenetic position and the genomic, morphological, and biochemical properties, strain Marseille-P3601T (=CSUR P3601=CCUG 71291) represents a novel species in the genus Ornithinibacillus, for which the name Ornithinibacillus massiliensis sp. nov. is proposed.
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Affiliation(s)
- Rim Iwaza
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Linda Abou Chacra
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Ahmad Ibrahim
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Thi Phuong Thao Pham
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Cheikh Ibrahima Lo
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Maryam Tidjani Alou
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Cheikh Sokhna
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Campus Communication, UCAD-IRD of Hann, Dakar, Senegal
| | - Didier Raoult
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Jean-Christophe Lagier
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France. .,IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.
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15
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Shang C, Li Y, Zhang J, Gan S. Analysis of Bacterial Diversity in Different Types of Daqu and Fermented Grains From Danquan Distillery. Front Microbiol 2022; 13:883122. [PMID: 35865918 PMCID: PMC9295720 DOI: 10.3389/fmicb.2022.883122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial communities in high-temperature Daqu and fermented grains are important for brewing Jiang-flavor Baijiu such as Danquan Baijiu. Daqu is a saccharifying and fermenting agent, which has a significant impact on the flavor of Baijiu. However, bacterial communities in three different types of samples from the Danquan distillery (dqjq_ck, dqjqcp, and dqjp3) were still unclear, which limited further development of Danquan Baijiu. “dqjq_ck” and “dqjqcp” indicate high-temperature Daqu at days 45 and 135, respectively. “dqjp3” indicates fermented grains. In this study, the bacterial communities of three samples were analyzed by Illumina Miseq high-throughput sequencing. The bacterial communities of three samples primarily composed of thermophilic bacteria and bacteria with stress resistance. The most abundant species in dqjq_ck, dqjqcp, and dqjp3 were Comamonas, Bacillus, and unclassified Lactobacillales, respectively. The main bacteria included Bacillus, Comamonas, Myroides, Paenibacillus, Acetobacter, Kroppenstedtia, Staphylococcus, Saccharopolyspora, Planifilum, Lactobacillus, Acinetobacter, Oceanobacillus, Enterococcus, Thermoactinomyces, Lactococcus, Streptomyces, Saccharomonospora, Tepidimicrobium, Anaerosalibacter, unclassified_Lactobacillales, unclassified_Thermoactinomycetaceae_1, unclassified_Bacillaceae_2, unclassified_Bacillales, unclassified_Microbacteriaceae, unclassified_Rhodobacteraceae, unclassified_Actinopolysporineae, and unclassified_Flavobacteriaceae in three samples (percentage was more than 1% in one of three samples). In our study, the succession of microbiota in three samples representing three important stages of Danquan Baijiu brewing was revealed. This article lays a good foundation for understanding the fermentation mechanism and screening some excellent indigenous bacteria to improve the quality of Danquan Baijiu in future.
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Affiliation(s)
- Changhua Shang
- College of Life Sciences, Guangxi Normal University, Guilin, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin (Guangxi Normal University), Guilin, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Changhua Shang
| | - Yujia Li
- College of Life Sciences, Guangxi Normal University, Guilin, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
| | - Jin Zhang
- College of Life Sciences, Guangxi Normal University, Guilin, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
| | - Shanling Gan
- College of Life Sciences, Guangxi Normal University, Guilin, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
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16
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Ketsub N, Whatmore P, Abbasabadi M, Doherty WOS, Kaparaju P, O'Hara IM, Zhang Z. Effects of pretreatment methods on biomethane production kinetics and microbial community by solid state anaerobic digestion of sugarcane trash. BIORESOURCE TECHNOLOGY 2022; 352:127112. [PMID: 35381335 DOI: 10.1016/j.biortech.2022.127112] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Solid state anaerobic digestion (SS-AD) of lignocellulose is effective in improving biomethane productivity but is limited by low biomass digestibility and lack of substrate-specific working microorganisms. In this study, the effects of different pretreatment methods on biomethane production by SS-AD of sugarcane trash were studied. The biomethane production, fitted to a modified Gompertz's model, predicted a maximum methane yield of 214.2 L/kg volatile solids (VS) and productivity of 6.9 L/kg VS/day from KOH-pretreated trash, respectively. Microbial community analysis showed that bacterial community was significantly associated with volatile acids and pretreatment types while archaeal community was significantly associated with methane yield. Microbial community dynamics was revealed in SS-AD. Main genera related to pretreatment method were identified and discussed. This study generated important information on SS-AD of lignocellulosic biomass pretreated by different methods, which is useful for developing bioaugmentation strategies to improve biomethane production by SS-AD.
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Affiliation(s)
- Napong Ketsub
- Centre for Agriculture and the Bioeconomy, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia; School of Mechanical, Medical and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Paul Whatmore
- Bioinformatics Research Officer, Division of Research & Innovation, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Mahsa Abbasabadi
- Centre for Agriculture and the Bioeconomy, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia; School of Biology and Environmental Sciences, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - William O S Doherty
- Centre for Agriculture and the Bioeconomy, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia; School of Mechanical, Medical and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Prasad Kaparaju
- School of Engineering and Built Environment, Griffith University, Brisbane, Queensland 4111, Australia
| | - Ian M O'Hara
- Centre for Agriculture and the Bioeconomy, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia; School of Mechanical, Medical and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, Queensland 4000, Australia; ARC Centre of Excellence in Synthetic Biology, QUT, Brisbane, QLD 4000, Australia
| | - Zhanying Zhang
- Centre for Agriculture and the Bioeconomy, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia; School of Mechanical, Medical and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, Queensland 4000, Australia; ARC Centre of Excellence in Synthetic Biology, QUT, Brisbane, QLD 4000, Australia.
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17
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Yacouba A, Sissoko S, Saha OLFT, Haddad G, Dubourg G, Gouriet F, Alou MT, Alibar S, Million M, Lagier JC, Raoult D, Fenollar F, Fournier PE, Lo CI. Description of Acinetobacter ihumii sp. nov., Microbacterium ihumii sp. nov., and Gulosibacter massiliensis sp. nov., three new bacteria isolated from human blood. FEMS Microbiol Lett 2022; 369:6572836. [PMID: 35460225 PMCID: PMC9126734 DOI: 10.1093/femsle/fnac038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/16/2022] [Accepted: 04/21/2022] [Indexed: 11/19/2022] Open
Abstract
Blood is precious tissue that is normally sterile. With the aim of diagnosing the cause
of bacteremia, three bacterial strains were isolated from three different individuals.
Strains Marseille-P7157T and Marseille-Q2854T are Gram-stain
positive, non-spore-forming rod-shaped bacteria, while strain Marseille-P8049T
is a Gram-stain negative, motile, non-spore-forming and rod-shaped bacterium. The major
fatty acids found (>30%) were hexadecanoic acid for strain Marseille-P8049T
and 12-methyl tetradecanoic acid for both strains Marseille-P7157T and
Marseille-Q2854T. The 16S rRNA gene sequence analysis shows that strains
Marseille-P8049 and Marseille-Q2854T have sequence similarity of 96.8%, 99.04%,
and 98.3% with Acinetobacter ursingii strain LUH3792 (NR_025392.1),
Gulosibacter faecalis strain B187 (NR_041812.1), and Schaalia
canis strain CCUG 41706 (NR_025366.1), respectively. In addition, strains
Marseille-Q2854T, Marseille-P8049T and Marseille-P7157T
shared with their closely related species cited above the following DDH values: 19.5%,
24.4%, and 20.2%, respectively. Based on these phenotypic and genomic findings, we
consider that strains Marseille-P8049T (= CSUR P8049 = CECT 30350),
Marseille-P2854T ( = CSUR Q2854 = CECT 30120) and Marseille-P7157T
( = CSUR P7157 = CECT 30048) are new bacterial species, for which the names
Acinetobacter ihumii sp. nov., Microbacterium ihumii
sp. nov., and Gulosibacter massiliensis sp. nov., are proposed.
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Affiliation(s)
- Abdourahamane Yacouba
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Université Abdou Moumouni, Niamey, Niger
| | - Sibiri Sissoko
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | | | - Gabriel Haddad
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Grégory Dubourg
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Frédérique Gouriet
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Maryam Tidjani Alou
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Stéphane Alibar
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Matthieu Million
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Cheikh Ibrahima Lo
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
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18
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Brachybacterium epidermidis Sp. Nov., a Novel Bacterial Species Isolated from the Back of the Right Hand, in a 67-Year-Old Healthy Woman. Int J Microbiol 2022; 2022:2875994. [PMID: 35392139 PMCID: PMC8983266 DOI: 10.1155/2022/2875994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 11/22/2022] Open
Abstract
Knowledge on human skin microbiota composition has been expanding in recent years. Its role in human health and disease represents an active area of investigation. As part of our culturomics project that consists of exploring the human microbiota by isolating bacteria through innovative culture-dependent methods, we isolated a new bacterial strain from the back of the right hand, in a 67-year-old healthy woman. Here, we characterize the strain Marseille-Q2903 by the taxonogenomic approach. Marseille-Q2903 exhibits a 99.5% 16S rRNA sequence similarity with Brachybacterium murisT but with only 92% of coverage. The closest species based on a 100% coverage of the 16S sequence is Brachybacterium timonenseT with an identity similarity of 97.63%. Furthermore, digital DNA-DNA hybridization reveals a maximum identity similarity of only 31.5% and an OrthoANI parameter provided a value of 86.95% between Marseille-Q2903 and Brachybacterium murisT. Marseille-Q2903 is a yellowish-pigmented, Gram-positive, coccoid shaped, and facultative aerobic bacterium, and belonging to the Dermabacteraceae family. The major fatty acids detected are 12-methyl-tetradecanoic acid (69%), 14-methyl-hexadecanoic acid (16%), and 14-methyl-pentadecanoic acid (7%). Marseille-Q2903 genome size is of 3,073,790 bp, with a 70.43% G + C content. Taken altogether, these results confirm the status of this strain as a new member of the Brachybacterium genus for which the name of Brachybacterium epidermidis sp. strain Marseille-Q2903T is proposed (=CSURQ2903T = CECT30363).
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19
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Sarr M, Tall ML, Ben Khedher M, Pham TPT, Mbaye B, Camara A, Armstrong N, Chartier C, Fadlane A, Sokhna C, Raoult D, Tidjani Alou M, Million M. Konateibacter massiliensis gen. nov. sp. nov. and Paenibacillus faecalis sp. nov., Two New Species Isolated from the Stool Samples of Infants Suffering from Marasmus. Curr Microbiol 2022; 79:68. [DOI: 10.1007/s00284-021-02757-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 12/30/2021] [Indexed: 11/28/2022]
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20
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Zgheib R, Hasni I, Mbaye B, Anani H, Haddad G, Armstrong N, Chartier C, Caputo A, Raoult D, Fenollar F, Fournier PE. Buttiauxella massiliensis sp. nov., Isolated from a Human Bone Infection. Curr Microbiol 2022; 79:41. [PMID: 34982239 DOI: 10.1007/s00284-021-02714-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/08/2021] [Indexed: 11/25/2022]
Abstract
Strain Marseille-P9829 was isolated from a bone sample collected from an open right fibula fracture from a 46-years old patient. Strain Marseille-P9829 (= CSUR P9829 = DSM 110695) was a Gram-negative, non-spore-forming and non-motile bacterium. This strain had a positive catalase activity but was oxidase-negative. The major fatty acids methyl esters were hexadecanoic acid (45.6%) and 9-hexadecenoic acid (28.4%). Matrix Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry analysis suggested that this strain belongs to the species Buttiauxella gaviniae. Since there were few reports of clinical infections with this species in humans, whole genome sequencing was performed and a polyphasic taxono-genomic approach was followed in order to verify the classification of strain Marseille-P9829. The 16S rRNA gene sequence BLAST against the NCBI database yielded the highest similarity of 99.8% with Buttiauxella agrestis, suggesting that strain Marseille-P9829 belongs to this species. However, genomic comparison by digital DNA-DNA hybridization showed that values between strain Marseille-P9829 and other validly published Buttiauxella species were all lower than 70%. Furthermore, all average nucleotide identities were lower than 95-96%. Therefore, these results confirmed that strain Marseille-P9829 belonged to a new Buttiauxella species for which we propose the name Buttiauxella massiliensis sp. nov., with strain Marseille-P9829 as type strain.
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Affiliation(s)
- Rita Zgheib
- Aix Marseille Université, 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
- Institut Méditerranée-Infection, Marseille, France
| | - Issam Hasni
- Institut Méditerranée-Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Babacar Mbaye
- Institut Méditerranée-Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Hussein Anani
- Aix Marseille Université, 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
- Institut Méditerranée-Infection, Marseille, France
| | - Gabriel Haddad
- Institut Méditerranée-Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | | | | | - Aurélia Caputo
- Institut Méditerranée-Infection, Marseille, France
- 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
- Institut Méditerranée-Infection, Marseille, France
- 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
| | - Florence Fenollar
- Aix Marseille Université, 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
- Institut Méditerranée-Infection, Marseille, France
| | - Pierre-Edouard Fournier
- Aix Marseille Université, 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.
- Institut Méditerranée-Infection, Marseille, France.
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21
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Zgheib R, Ibrahim A, Anani H, Ndongo S, Bilen M, Armstrong N, Richez M, Raoult D, Fournier PE. Neglectibacter timonensis gen. nov., sp. nov. and Scatolibacter rhodanostii gen. nov., sp. nov., two anaerobic bacteria isolated from human stool samples. Arch Microbiol 2021; 204:45. [DOI: 10.1007/s00203-021-02712-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 12/18/2022]
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22
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Olowo-Okere A, Ibrahim YKE, Lo CI, Olayinka BO, Yimagou EK, Yacouba A, Mohammed Y, Nabti LZ, Ragueh AA, Lupande D, Raoult D, Rolain JM, Diene SM. Bhargavaea massiliensis sp. nov. and Dietzia massiliensis sp. nov., Novel Bacteria Species Isolated from Human Urine Samples in Nigeria. Curr Microbiol 2021; 79:18. [PMID: 34905116 DOI: 10.1007/s00284-021-02721-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/13/2021] [Indexed: 10/19/2022]
Abstract
Two novel bacteria species designated Marseille-Q1000T and Marseille-Q0999T were isolated from urine samples of patients in Sokoto, Northwest-Nigeria. They were Gram-positive bacteria and belong to two different genera, Bhargavaea and Dietzia. The genome size and G + C content of Marseille-Q1000T and Marseille-Q0999T were 3.07 and 3.51 Mbp with 53.8 and 71.0 mol% G + C content, respectively. The strains exhibited unique phenotypic and genomic features that are substantially different from previously known bacterial species with standing in nomenclature. On the basis of the phenotypic, phylogenetic and genomic characteristics, strains Marseille-Q0999T (= CSURQ0999 = DSM 112394) and Marseille-Q1000T (= CSURQ1000 = DSM 112384) were proposed as the type strains of Bhargavaea massiliensis sp. nov., and Dietzia massiliensis sp. nov., respectively.
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Affiliation(s)
- Ahmed Olowo-Okere
- Department of Pharmaceutics and Pharmaceutical Microbiology, Usmanu Danfodiyo University, Sokoto, Nigeria
| | | | - Cheikh Ibrahima Lo
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Busayo Olalekan Olayinka
- Department of Pharmaceutics and Pharmaceutical Microbiology, Ahmadu Bello University, Zaria, Nigeria
| | - Edmond Kuete Yimagou
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Abdourahamane Yacouba
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Yahaya Mohammed
- Department of Medical Microbiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Larbi Zakaria Nabti
- Faculté des Sciences, Département de Biochimie et Microbiologie, Université Mohamed Boudiaf, BP 166, 28000, M'sila, M'sila, Algeria
| | - Ayan Ali Ragueh
- Department of Medical Microbiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - David Lupande
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | | | - Jean-Marc Rolain
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Seydina M Diene
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France. .,Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.
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23
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Antezack A, Boxberger M, Rolland C, Ben Khedher M, Monnet-Corti V, La Scola B. Isolation and characterization of Campylobacter massiliensis sp. nov., a novel Campylobacter species detected in a gingivitis subject. Int J Syst Evol Microbiol 2021; 71. [PMID: 34751644 DOI: 10.1099/ijsem.0.005039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative bacterium, designated strain Marseille-Q3452T, was isolated from subgingival dental plaque of a subject suffering from dental plaque biofilm-induced gingivitis on an intact periodontium in Marseille, France. The strain was characterized by 16S rRNA and atpA gene sequence analysis and by conventional phenotypic and chemotaxonomic testing. The average nucleotide identity (ANI) and core genome phylogeny were determined using whole-genome sequences. Although strain Marseille-Q3452T showed 99.72 % 16S rRNA gene sequence similarity with Campylobacter showae strain ATCC 51146T, atpA and ANI analyses revealed divergence between the two strains. The two species could also be distinguished phenotypically on the basis of the absence of flagella and nitrate reduction. On the basis of the results from phenotypic, chemotaxonomic, genomic and phylogenetic analyses and data, we concluded that strain Marseille-Q3452T represents a novel species of the genus Campylobacter, for which the name Campylobacter massiliensis sp. nov. is proposed (=CSUR Q3452=CECT 30263).
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Affiliation(s)
- Angéline Antezack
- Aix-Marseille Université, Faculté des Sciences Médicales et Paramédicales, Ecole de Médecine Dentaire, 27 boulevard Jean Moulin, 13385 Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), Hôpital Timone, Service de Parodontologie, 264, rue Saint Pierre, 13385 Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Manon Boxberger
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Clara Rolland
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Mariem Ben Khedher
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Virginie Monnet-Corti
- Aix-Marseille Université, Faculté des Sciences Médicales et Paramédicales, Ecole de Médecine Dentaire, 27 boulevard Jean Moulin, 13385 Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), Hôpital Timone, Service de Parodontologie, 264, rue Saint Pierre, 13385 Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Bernard La Scola
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
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24
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Ben Khedher M, Diouf FS, Lo CI, Alibar S, Durand G, Raoult D, Fournier PE, Fenollar F. Collinsella ihumii sp. nov., a new anaerobic bacterium isolated from human stool. Arch Microbiol 2021; 203:6315-6322. [DOI: 10.1007/s00203-021-02562-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
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25
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Antezack A, Boxberger M, Ben Khedher M, La Scola B, Monnet-Corti V. Isolation and description of Selenomonas timonae sp. nov., a novel Selenomonas species detected in a gingivitis patient. Int J Syst Evol Microbiol 2021; 71. [PMID: 34612809 DOI: 10.1099/ijsem.0.005040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative bacterium, designated strain Marseille-Q3039T, was isolated from subgingival dental plaque of a woman with gingivitis in Marseille, France. Strain Marseille-Q3039T was found to be an anaerobic, motile and spore-forming crescent-shaped bacterium that grew at 25-41.5 °C (optimum, 37 °C), pH 5.5-8.5 (optimum, pH 7.5) and salinity of 5.0 g l-1 NaCl. The results of 16S rRNA gene sequence analysis revealed that strain Marseille-Q3039T was closely related to Selenomonas infelix ATCC 43532T (98.42 % similarity), Selenomonas dianae ATCC 43527T (97.25 %) and Centipedia periodontii DSM 2778T (97.19 %). The orthologous average nucleotide identity and digital DNA-DNA hybridization relatedness between strain Q3039T and its closest phylogenetic neighbours were respectively 84.57 and 28.2 % for S. infelix ATCC 43532T and 83.93 and 27.2 % for C. periodontii DSM 2778T. The major fatty acids were identified as C13 : 0 (27.7 %), C15 : 0 (24.4 %) and specific C13 : 0 3-OH (12.3 %). Genome sequencing revealed a genome size of 2 351 779 bp and a G+C content of 57.2 mol%. On the basis of the results from phenotypic, chemotaxonomic, genomic and phylogenetic analyses and data, we concluded that strain Marseille-Q3039T represents a novel species of the genus Selenomonas, for which the name Selenomonas timonae sp. nov. is proposed (=CSUR Q3039=CECT 30128).
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Affiliation(s)
- Angéline Antezack
- Aix-Marseille Université, Faculté des Sciences Médicales et Paramédicales, Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), Hôpital Timone, Service de Parodontologie, 264, Rue Saint Pierre, 13385 Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Manon Boxberger
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Mariem Ben Khedher
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Bernard La Scola
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Virginie Monnet-Corti
- Aix-Marseille Université, Faculté des Sciences Médicales et Paramédicales, Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), Hôpital Timone, Service de Parodontologie, 264, Rue Saint Pierre, 13385 Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
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26
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Lo CI, Dione N, Mbaye A, Gómez PFM, Ngom II, Valles C, Alibar S, Lagier JC, Fenollar F, Fournier PE, Raoult D, Diene SM. Limosilactobacillus caccae sp. nov., a new bacterial species isolated from the human gut microbiota. FEMS Microbiol Lett 2021; 368:6373442. [PMID: 34549292 DOI: 10.1093/femsle/fnab128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/17/2021] [Indexed: 11/14/2022] Open
Abstract
Strain Marseille-P3519T isolated from the fecal flora of a 25-year-old healthy French woman was a Gram-positive anaerobic bacterium, non-motile and non-spore forming. The 16S rRNA gene sequence of Marseille-P3519 showed 97.73% of sequence similarity with Limosilactobacillus reuteri DSM 20016, the closest species, phylogenetically. Furthermore, the average nucleotide identity of strain Marseille-3519 with its closest related species was 75.8% that was very below the recommended threshold (>95-96%). Its genome had 2 237 367 bp with 45.42 mol% of G + C content. Major fatty acids were C16:0 (50.8%), C18:1n9 (18.0%), C18:2n6 (9.8%) and C19:1n9 (8.9%). It was catalase negative and fermented glycerol, glucose, fructose, D-maltose, lactose and mannose. These findings support that strain Marseille-P3519 ( = CSURP3519 = CECT 30110) is a new member of the genus Limosilactobacillus for which the name Limosilactobacillus caccae sp. nov., is proposed.
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Affiliation(s)
- Cheikh Ibrahima Lo
- Aix Marseille Uni versity, IRD, AP-HM, SSA, VITROME, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Niokhor Dione
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Aminata Mbaye
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Patricia Fernández-Mellado Gómez
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Issa Isaac Ngom
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Camille Valles
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Stéphane Alibar
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Jean-Christophe Lagier
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Florence Fenollar
- Aix Marseille Uni versity, IRD, AP-HM, SSA, VITROME, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Pierre-Edouard Fournier
- Aix Marseille Uni versity, IRD, AP-HM, SSA, VITROME, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Seydina M Diene
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
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27
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Kieu HT, Garrigou N, Fadlane A, Brechard L, Armstrong N, Decloquement P, Yasir M, Azhar EI, Al-Masaudi SB, Lagier JC, Tidjani Alou M, Raoult D. Clostridium culturomicium sp. nov. and Clostridium jeddahitimonense sp. nov., novel members of the Clostridium genus isolated from the stool of an obese Saudi Arabian. Curr Microbiol 2021; 78:3586-3595. [PMID: 34297170 DOI: 10.1007/s00284-021-02616-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/15/2021] [Indexed: 11/26/2022]
Abstract
Taxono-genomics is an innovative concept coined for the description of new bacterial species. Phenotypic characteristics were combined with a genomic approach to describe two new species within the Clostridium senso stricto genus: Clostridium culturomicium strain CL-6T and Clostridium jeddahitimonense strain CL-2T, both isolated from the gut microbiota of an obese man from Saudi Arabia. Strains CL-6T and CL-2T shared a similarity of 98.4% with the 16S rRNA gene of Clostridium subterminale strain JCM 1417T (accession number NR113027) and 98% with that of Clostridium disporicum strain DS1T (accession number NR026491), respectively. The highest OrthoANI values were shared with Clostridium punense for strain CL-6T (70.8%) and with Clostridium disporicum for strain CL-2T (87.1%). Additionally, strain CL-6T and strain CL-2T shared a 16S rRNA similarity of 91.4%. Both strains were anaerobic, spore-forming and Gram-stain-positive non-motile bacilli. The genome of Clostridium culturomicium strain CL-6T is 4,325,182 bp long with 32.2% GC content. As for Clostridium jeddahitimonense strain CL-2T, the genome is 4,074,758 bp long with 29.2% GC content.
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Affiliation(s)
- Hoang Thong Kieu
- Aix Marseille University, RD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | | | | | | | | | | | - Muhammad Yasir
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Saad B Al-Masaudi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Jean-Christophe Lagier
- Aix Marseille University, RD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | | | - Didier Raoult
- Aix Marseille University, RD, AP-HM, MEPHI, Marseille, France.
- IHU-Méditerranée Infection, Marseille, France.
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28
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Sarr M, Diouf FS, Lo CI, Tidjani Alou M, Alibar S, Million M, Sokhna C, Fenollar F. Taxonogenomics description of Bacillus marasmi sp. nov., a new species isolated from the stool sample. New Microbes New Infect 2021; 42:100906. [PMID: 34188938 PMCID: PMC8220230 DOI: 10.1016/j.nmni.2021.100906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/05/2022] Open
Abstract
Using the culturomics method, two strains were isolated, identified, and characterised following the taxonogenomics concept. Bacillus marasmi sp. nov. strain Marseille-P3556 (= CSURP3556) is isolated from a 13-month-old girl living in Niger. The phylogenetic tree, phenotypic criteria, and genomic analysis described here clearly show that this bacterium is different from previously known bacterial species withstanding in nomenclature and new members of Bacillus genus.
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Affiliation(s)
- M Sarr
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - F S Diouf
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - C I Lo
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - M Tidjani Alou
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - S Alibar
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - M Million
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - C Sokhna
- IHU-Méditerranée Infection, Marseille, France.,Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - F Fenollar
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
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29
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Konate S, Camara A, Lo C, Tidjani Alou M, Hamidou Togo A, Niare S, Armstrong N, Djimdé A, Thera M, Fenollar F, Raoult D, Million M. Virgibacillus doumboii sp. nov., a halophilic bacterium isolated from the stool of a healthy child in Mali. New Microbes New Infect 2021; 42:100890. [PMID: 34258018 PMCID: PMC8255231 DOI: 10.1016/j.nmni.2021.100890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/20/2021] [Accepted: 04/20/2021] [Indexed: 01/09/2023] Open
Abstract
A moderately halophilic and strictly aerobic bacterium was isolated from a human stool as part of a study on the diagnosis of childhood malnutrition in Mali. Strain Marseille-Q1616T is a Gram-stain-positive, rod-shaped, catalase-positive and oxidase-negative bacterium. It has a genome size of 3.91 Mbp with 39.79% G+C content, which contains 3954 protein-coding genes including genes encoding phosphomycin resistance and Listeria monocytogenes, 16 rRNA genes and 64 tRNA genes. Strain Marseille-Q1616T exhibited a 96.3% 16S rRNA gene sequence similarity and shared an OrthoANI value of 70.64% (the highest observed) with Virgibacillus kekensis, the phylogenetically closest validly published species. Based on phenotypic and phylogenetic evidence and genomic average nucleotide identity values, we suggest the creation of a new species within the Virgibacillus genus, named Virgibacillus doumboii sp. nov., type strain Marseille-Q1616T (= CSURQ1616).
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Affiliation(s)
- S. Konate
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - A. Camara
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - C.I. Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - M. Tidjani Alou
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - A. Hamidou Togo
- Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - S. Niare
- Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - N. Armstrong
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - A. Djimdé
- Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - M.A. Thera
- Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - F. Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - M. Million
- Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
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30
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Ndongo S, Maaloum M, Richez M, Saile R, Fournier PE, Lagier JC, Raoult D, Khelaifia S. Vitreoscilla massiliensis sp. nov., Isolated From the Stool of an Amazonian Patient. Curr Microbiol 2021; 78:3313-3320. [PMID: 34165609 PMCID: PMC8289809 DOI: 10.1007/s00284-021-02577-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 06/15/2021] [Indexed: 11/30/2022]
Abstract
Strain SN6T is a non-motile and non-spore-forming gram-negative bacterium which was isolated from the stool sample of an Amazonian patient. The optimum growth was observed at 37 °C, pH 7, and 0–5 g/l of NaCl. Based on the 16S rRNA gene sequence similarity, the strain SN6T exhibited 97.5% identity with Vitreoscilla stercoraria strain ATCC_15218 (L06174), the phylogenetically closest species with standing in nomenclature. The predominant fatty acid was hexadecenoic acid (31%). The genomic DNA G + C content of the strain SN6T was 49.4 mol %. After analysis of taxonogenomic data, phenotypic and biochemical characteristics, we concluded that strain SN6T represents a new species of the genus Vitreoscilla for which the name Vitreoscilla massiliensis sp.nov is proposed. The type strain is SN6T (=CSUR P2036 = LN870312 = DSM 100958).
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Affiliation(s)
- Sokhna Ndongo
- IHU-Méditerranée Infection, Marseille, France.,IRD, MEPHI, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Mossaab Maaloum
- IHU-Méditerranée Infection, Marseille, France.,IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Aix Marseille Univ, Marseille, France.,Laboratory of Biology and Health, Faculty of Sciences Ben M'sik, Hassan II University, Casablanca, Morocco
| | | | - Rachid Saile
- Laboratory of Biology and Health, Faculty of Sciences Ben M'sik, Hassan II University, Casablanca, Morocco
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Marseille, France.,IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Aix Marseille Univ, Marseille, France
| | - Jean Christophe Lagier
- IHU-Méditerranée Infection, Marseille, France.,IRD, MEPHI, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France.,IRD, MEPHI, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Saber Khelaifia
- IHU-Méditerranée Infection, Marseille, France. .,IRD, MEPHI, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Aix Marseille Univ, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
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31
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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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32
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Kangale LJ, Raoult D, Ghigo E, Fournier PE. Chryseobacterium schmidteae sp. nov. a novel bacterial species isolated from planarian Schmidtea mediterranea. Sci Rep 2021; 11:11002. [PMID: 34040129 PMCID: PMC8155073 DOI: 10.1038/s41598-021-90562-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/13/2021] [Indexed: 02/07/2023] Open
Abstract
Marseille-P9602T is a Chryseobacterium-like strain that we isolated from planarian Schmidtea mediterranea and characterized by taxono-genomic approach. We found that Marseille-P9602T strain exhibits a 16S rRNA gene sequence similarity of 98.76% with Chryseobacterium scophthalmum LMG 13028T strain, the closest phylogenetic neighbor. Marseille-P9602T strain was observed to be a yellowish-pigmented, Gram-negative, rod-shaped bacterium, growing in aerobic conditions and belonging to the Flavobacteriaceae family. The major fatty acids detected are 13-methyl-tetradecanoic acid (57%), 15-methylhexadecenoic acid (18%) and 12-methyl-tetradecanoic acid (8%). Marseille-P9602 strain size was found from genome assembly to be of 4,271,905 bp, with a 35.5% G + C content. The highest values obtained for Ortho-ANI and dDDH were 91.67% and 44.60%, respectively. Thus, hereby we unravel that Marseille-P9602 strain is sufficiently different from other closed related species and can be classified as a novel bacterial species, for which we propose the name of Chryseobacterium schmidteae sp. nov. Type strain is Marseille-P9602T (= CSUR P9602T = CECT 30295T).
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Affiliation(s)
- Luis Johnson Kangale
- IRD, AP-HM, SSA, VITROME, Aix-Marseille Univ, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, IHU-Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée Infection, IHU-Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
- IRD, AP-HM, MEPHI, Aix-Marseille Univ, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Eric Ghigo
- Institut Hospitalo-Universitaire Méditerranée Infection, IHU-Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.
- TechnoJouvence, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.
| | - Pierre-Edouard Fournier
- IRD, AP-HM, SSA, VITROME, Aix-Marseille Univ, Marseille, France.
- Institut Hospitalo-Universitaire Méditerranée Infection, IHU-Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.
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33
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Khare M, Sinha D, Zgheib R, Traore SI, Lagier JC, Raoult D, Edouard FP. Genomic description and characterization of Nigeribacterium massiliense gen. nov., sp. nov., isolated from the human gut. Microbes Infect 2021; 23:104842. [PMID: 34020025 DOI: 10.1016/j.micinf.2021.104842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/23/2021] [Accepted: 05/08/2021] [Indexed: 02/07/2023]
Abstract
Strain Marseille-P1302 was isolated from the stool of a 2-year-old Nigerian boy suffering from Kwashiorkor, a form of severe acute malnutrition. The strain grows in aerobic atmosphere and bacterial cells are Gram-positive cocci ranging in diameter from 0.8 to 1 μm. Strain Marseille-P1302 exhibits a 16S rRNA sequence similarity of 94.97% with Brevilactibacter flavus strain VG341T, but phylogenetically-closest species with standing in nomenclature is Brevilactibacter sinopodophylli strains KCTC 33808Twith the sequence similarity of 93.41%. The draft genome of strain Marseille-P1302 is 2,934,258bp-long with a 70.38% G+C content, and contains 2,704 protein-coding genes and 55 RNAs that includes 9 rRNA genes. On the basis of these data, we propose the creation of the new genus Nigeribacterium gen. nov., with strain Marseille-P1302T (= CSUR P1302 = DSM 29084) being the type strain of new species Nigeribacterium. massiliense gen. nov., sp. nov.
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Affiliation(s)
- Mudra Khare
- Aix Marseille University, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, UMR Vecteurs Infections Tropicales et Méditerranéennes. (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France
| | - Dhiraj Sinha
- Aix Marseille University, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, UMR Vecteurs Infections Tropicales et Méditerranéennes. (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France
| | - Rita Zgheib
- Aix Marseille University, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, UMR Vecteurs Infections Tropicales et Méditerranéennes. (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France
| | - Sory Ibrahima Traore
- Institut Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Dévelopement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Jean-Christophe Lagier
- Institut Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Dévelopement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Institut Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Dévelopement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Fournier Pierre Edouard
- Institut Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Dévelopement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.
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34
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Metabacillus schmidteae sp. nov., Cultivated from Planarian Schmidtea mediterranea Microbiota. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12020021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Taxonogenomics combines phenotypic assays and genomic analysis as a means of characterizing novel strains. We used this strategy to study Marseille-P9898T strain, an aerobic, motile, Gram-negative, spore-forming, and rod-shaped bacterium isolated from planarian Schmidtea mediterranea. Marseille-P9898T is catalase-positive and oxidase-negative. The major fatty acids detected are 12-methyl-tetradecanoic acid, 13-methyl-tetradecanoic acid, and hexadecanoic acid. Marseille-P9898T strain shared more than 98% sequence similarity with the Metabacillus niabensis strain 4T19T (98.99%), Metabacillus halosaccharovorans strain E33T (98.75%), Metabacillus malikii strain NCCP-662T (98.19%), and Metabacillus litoralis strain SW-211T (97.15%). Marseille-P9898 strain belongs to Metabacillus genus. Genomic analysis revealed the highest similarities with Ortho-ANI and dDDH, 85.76% with Metabacillus halosaccharovorans, and 34.20% with Bacillus acidicola, respectively. These results show that the Marseille-P9898T strain is a novel bacterial species from Metabacillus genus, for which we propose the name of Metabacillus schmidteae sp. nov. (Type strain Marseille-P9898T = CSUR P9898T = DSM 111480T).
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Pedobacter ghigonii sp. nov., Isolated from the Microbiota of the Planarian Schmidtea mediterranea. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12020019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The planarian S. mediterranea is a platyhelminth with worldwide distribution that can regenerate any part of its body after amputation and has the capacity to eliminate a large spectrum of human bacterial pathogens. Surprisingly, the microbiota of S. mediterranea remains poorly investigated. Using the culturomics strategy to study the bacterial component of planarians, we isolated a new bacterial strain, Marseille-Q2390, which we characterized with the taxono-genomic approach that associates phenotypic assays and genome sequencing and analysis. Strain Marseille-Q2390 exhibited a 16S rRNA sequence similarity of 99.36% with Pedobacter kyungheensis strain THG-T17T, the closest phylogenetic neighbor. It is a white-pigmented, Gram-negative, and rod-shaped bacterium. It grows in aerobic conditions and belongs to the family Sphingobacteriaceae. The genome of strain Marseille-Q2390 is 5,919,359 bp-long, with a G + C content of 40.3%. By comparing its genome with other closely related strains, the highest Orthologous Average Nucleotide Identity (Ortho-ANI) and digital DNA-DNA hybridization (dDDH) values were 85.71% and 30.50%, respectively, which were found with Pedobacter soli strain 15-51T. We conclude that strain Marseille-Q2390T is sufficiently different from other nearby species to be classified within a new species for which we propose the name Pedobacter ghigonii sp. nov.
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Isolation and Description of Catonella massiliensis sp. nov., a Novel Catonella Species, Isolated from a Stable Periodontitis Subject. Pathogens 2021; 10:pathogens10030367. [PMID: 33808593 PMCID: PMC8003473 DOI: 10.3390/pathogens10030367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/11/2021] [Accepted: 03/16/2021] [Indexed: 11/18/2022] Open
Abstract
The genus Catonella currently counts a unique species, C. morbi, isolated from periodontal pockets and associated with periodontitis and endodontic infections. This study contributed to the taxonomical and clinical knowledge of this genus by describing a novel species isolated from a saliva sample from a man in clinical gingival health following successful treatment of periodontitis. Morphological and chemotaxonomic characteristics were investigated using different growth conditions, pH, and temperature. Cellular fatty acid methyl ester (FAME) analysis was conducted by gas chromatography/mass spectrometry (GC/MS). Phylogenetic analysis based on 16S rRNA, orthologous average nucleotide identity (OrthoANI), and digital DNA-DNA hybridization (dDDH) relatedness were performed. Strain Marseille-Q4567T was found to be an anaerobic and non-spore-forming rod-shaped bacterium that grew at 28–41.5 °C (optimum 37 °C), pH 6.5–8.5 (optimum pH 7.5), and 5–10 g/L of NaCl (optimum 5 g/L). The predominant cellular fatty acid was C16:0 (64.2%), followed by unsaturated structures C18:1n9 (12.5%) and C18:2n6 (7.8%). Based on 16S rRNA sequence comparison, the closest phylogenetic neighbor was C. morbi ATCC 51271T (98.23% similarity). The OrthoANI and dDDH values between strain Q4567T and C. morbi ATCC 51271T were respectively 79.43% and 23.8%. Therefore, we concluded that strain Marseille-Q4567T represents a novel species of the genus Catonella, for which the name Catonella massiliensis sp. nov. is proposed (= CSUR Q4567).
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Naud S, Bellali S, Anani H, Lo C, Yacouba A, Tidjani Alou M, Armstrong N, Bonvalet M, Zitvogel L, Raoult D, Lagier JC. Luxibacter massiliensis gen. nov., sp. nov., a new bacterium isolated from the human gut microbiota. New Microbes New Infect 2021; 40:100850. [PMID: 33732473 PMCID: PMC7941043 DOI: 10.1016/j.nmni.2021.100850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/22/2022] Open
Abstract
An anaerobic facultative Gram-stain positive bacterium was isolated from human gut microbiota. Strain Marseille-P5551T was considered to be a new genus within the phylum Firmicutes, as it exhibits a 91.87% similarity level with Faecalicatena orotica (NR_117129.1), the phylogenetically closest related species. The draft genome size of strain Marseille-P5551T is 4 142 938 bp with 44.4% of G + C content. We hereby suggest the creation of Luxibacter massiliensis gen. nov., sp. nov., as a new bacterial genus.
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Affiliation(s)
- S. Naud
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - S. Bellali
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - H. Anani
- IHU-Méditerranée Infection, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - C.I. Lo
- IHU-Méditerranée Infection, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - A. Yacouba
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - M. Tidjani Alou
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
| | - N. Armstrong
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - M. Bonvalet
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
| | - L. Zitvogel
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
| | - D. Raoult
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
| | - J.-C. Lagier
- Aix-Marseille Université, IRD, AP-HM, MEФI, France
- IHU-Méditerranée Infection, France
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Isolation and Characterization of Kingella bonacorsii sp. nov., A Novel Kingella Species Detected in a Stable Periodontitis Subject. Pathogens 2021; 10:pathogens10020240. [PMID: 33669894 PMCID: PMC7923279 DOI: 10.3390/pathogens10020240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 11/24/2022] Open
Abstract
Members of the genus Kingella are mostly commensals of the oral cavity, but some of them are involved in invasive infections, especially in young children. This study provides new knowledge on the diversity of this genus by describing a novel species of Kingella isolated from a dental plaque sample from a 51-year-old man with a history of periodontitis. Morphological and chemotaxonomic characteristic were investigated using different growth conditions, pH and temperature. Cellular fatty acid methyl ester (FAME) analysis was performed by gas chromatography/mass spectrometry (GC/MS). Phylogenetic analysis based on 16S rRNA, orthologous average nucleotide identity (OrthoANI) and digital DNA–DNA hybridization (dDDH) relatedness were also performed. Strain Marseille-Q4569T was found to be a facultative aerobic, nonmotile and non-spore-forming rod-shaped bacterium that grows at 28–41.5 °C (optimum 37 °C), pH 5.5–8.5 (optimum pH 7.5) and 5–15 g/L of NaCl. The major fatty acids were Hexadecanoic acid (32.7%), 11-Octadecenoic acid (26.1 %) and 9-Hexadecenoic acid (21.3 %). Despite high 16S rRNA gene sequence similarity (98.72%) between strain Marseille-Q4569T and Kingella oralis strain UB-38T, the degree of OrthoANI was at the limit of the cutoff (95.83%), and the degree of dDDH was lower (63.6%) than thresholds used to delineate prokaryotic species. Therefore, it is proposed that strain Marseille-Q4569T represents a novel species of the genus Kingella, for which the name Kingella bonacorsii sp. nov. is proposed (=CSUR Q4569).
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Negativibacillus massiliensis gen. nov., sp. nov., a New Bacterial Genus Isolated from a Human Left Colon Sample. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12010004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A new genus, a member of the Ruminococcaceae family, was isolated from the left colon of a healthy woman. Strain Marseille P3213 was a non-motile, spore-forming, Gram-stain negative, rod-shaped bacterium. This strictly anaerobic species reached optimal growth after an incubation of 72 h at 37 °C. The 16S rRNA gene sequence of this strain shared a 93.52% similarity level with Harryflintia acetispora strain V20-281a, its closest phylogenetic neighbor with standing in the nomenclature. Its genome had a size of 2.87 Mb, with a 45.81% G + C content. We hereby propose the creation of Negativibacillus massiliensis strain P3213T as the 43rd genus within the Ruminococcaceae family.
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Morand A, Tall ML, Kuete Yimagou E, Ngom II, Lo CI, Cornu F, Tsimaratos M, Lagier JC, Levasseur A, Raoult D, Fournier PE. Anaerococcus urinimassiliensis sp. nov., a new bacterium isolated from human urine. Sci Rep 2021; 11:2684. [PMID: 33514860 PMCID: PMC7846727 DOI: 10.1038/s41598-021-82420-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 10/20/2020] [Indexed: 12/22/2022] Open
Abstract
To date there are thirteen species validly assigned to the genus Anaerococcus. Most of the species in this genus are anaerobic and of human origin. Anaerococcus urinimassiliensis sp. nov., strain Marseille-P2143T is member of family Peptoniphilaceae, which was isolated from the urine of a 17-year-old boy affected by autoimmune hepatitis and membranoproliferative glomerulonephritis using the culturomic approach. In the current study, a taxono-genomics method was employed to describe this new species. The strain Marseille-P2143T was gram positive cocci with translucent colonies on blood agar. Its genome was 2,189,509 bp long with a 33.5 mol% G + C content and exhibited 98.48% 16S rRNA similarity with Anaerococcus provencensis strain 9,402,080. When Anaerococcus urinomassiliensis strain Marseill-P2143T is compared with closely related species, the values ranged from 71.23% with A. hydrogenalis strain DSM 7454T (NZ_ABXA01000052.1) to 90.64% with A. provencensis strain 9402080T (NZ_HG003688.1). This strain has implemented the repertoire of known bacteria of the human urinary tract.
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Affiliation(s)
- Aurélie Morand
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. .,Pédiatrie Spécialisée Et Médecine Infantile, Hôpital de La Timone, AP-HM, Marseille, France.
| | - Mamadou Lamine Tall
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Edmond Kuete Yimagou
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Issa Isaac Ngom
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Cheikh Ibrahima Lo
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Florent Cornu
- Pédiatrie Multidisciplinaire, Hôpital de La Timone, AP-HM, Marseille, France
| | - Michel Tsimaratos
- Pédiatrie Multidisciplinaire, Hôpital de La Timone, AP-HM, Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Anthony Levasseur
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Institut Universitaire de France (IUF), Paris, France
| | - Didier Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Pierre-Edouard Fournier
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
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Proteomics and Lipidomics Investigations to Decipher the Behavior of Willaertia magna C2c Maky According to Different Culture Modes. Microorganisms 2020; 8:microorganisms8111791. [PMID: 33207645 PMCID: PMC7696429 DOI: 10.3390/microorganisms8111791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 11/17/2022] Open
Abstract
Willaertia magna C2c Maky is a free-living amoeba that has demonstrated its ability to inhibit the intracellular multiplication of some Legionella pneumophila strains, which are pathogenic bacteria inhabiting the aquatic environment. The Amoeba, an industry involved in the treatment of microbiological risk in the water and plant protection sectors, has developed a natural biocide based on the property of W. magna to manage the proliferation of the pathogen in cooling towers. In axenic liquid medium, amoebas are usually cultivated in adhesion on culture flask. However, we implemented a liquid culture in suspension using bioreactors in order to produce large quantities of W. magna. In order to investigate the culture condition effects on W. magna, we conducted a study based on microscopic, proteomics and lipidomics analyzes. According to the culture condition, amoeba exhibited two different phenotypes. The differential proteomics study showed that amoebas seemed to promote the lipid metabolism pathway in suspension culture, whereas we observed an upregulation of the carbohydrate pathway in adherent culture. Furthermore, we observed an over-regulation of proteins related to the cytoskeleton for W. magna cells grown in adhesion. Regarding the lipid analysis, suspension and adhesion cell growth showed comparable lipid class compositions. However, the differential lipid analysis revealed differences that confirmed cell phenotype differences observed by microscopy and predicted by proteomics. Overall, this study provides us with a better insight into the biology and molecular processes of W. magna in different culture lifestyles.
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42
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Zou Y, Sun Y, Qi H, Liu D, Tian H, Wang N, Li X. Streptococcus xiaochunlingii sp. nov. E24 Isolated From the Oropharynx of Healthy Chinese Children. Front Microbiol 2020; 11:563213. [PMID: 33133039 PMCID: PMC7550633 DOI: 10.3389/fmicb.2020.563213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/08/2020] [Indexed: 11/13/2022] Open
Abstract
A Gram-positive, α-hemolytic, catalase-negative, facultative anaerobic and non-motile coccus was isolated form throat swabs taken from the oropharynx of healthy children. The genome was shown to be 1.950,659 bp long and contained 42.03 mol% G + C bases with 1,942 protein-coding and 53 RNA coding genes. The results of 16S rRNA gene sequencing strongly suggested that the strain is a member of the Streptococcus genus, with 98.04, 98.11, and 97.34% similarities to Streptococcus australis ATCC 700641T, Streptococcus rubneri LMG 27207T and Streptococcus parasanguinis ATCC 15912T, respectively. A sodA gene comparison exhibited a sequence identity of 92.6% with the closest strain Streptococcus australis ATCC 700641T. In silico DNA-DNA hybridization showed a highest DNA similarity value of 52% with Streptococcus australis ATCC 700641T. Comparing 18 biochemical traits, the similarities of the Streptococcus strain E24 were 72% with Streptococcus rubneri LMG 27207T, 78% with Streptococcus australis ATCC 700641T and 44% with Streptococcus parasanguinis ATCC 15912T. We suggest that based on the genotypic and phenotypic results that the strain E24 is a novel species of the Streptococcus genus and propose the name Streptococcus xiaochunlingii sp. nov. E24.
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Affiliation(s)
- Yang Zou
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - Ye Sun
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - He Qi
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - Defeng Liu
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - Han Tian
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - Nan Wang
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - Xinming Li
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
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43
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Camara A, Konate S, Lo C, Kuete E, Sarr M, Amsrtong N, Niare S, Thera M, Fenollar F, Raoult D, Million M. Virgibacillus ihumii sp. nov., a new bacterium isolated from the stool of healthy African children. New Microbes New Infect 2020; 38:100790. [PMID: 33294190 PMCID: PMC7695897 DOI: 10.1016/j.nmni.2020.100790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 11/30/2022] Open
Abstract
During a case–control study on severe acute malnutrition, strain Marseille-Q1233 was isolated. It is a Gram-positive, rod-shaped and halophilic bacillus isolated from a stool sample of Malian child under the age of 5. The fatty acid profile of the strain consisted of C15:0-anteiso and C14:0-iso as major components. Digital DNA-DNA hybridization and average nucleotide identity calculation showed 23.10% and 80.81% similarity respectively between strain Marseille-Q1233 and Virgibacillus siamensis strain Marseille-P2607, the phylogenetically closely related species with standing in nomenclature. On the basis of these results, we report the description of Virgibacillus ihumii sp. nov. strain Marseille-Q1233 as a new bacterial species.
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Affiliation(s)
- A. Camara
- Aix-Marseille Université, IRD, APHM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - S. Konate
- Aix-Marseille Université, IRD, APHM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - C.I. Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, APHM, SSA, VITROME, Marseille, France
| | - E. Kuete
- Aix-Marseille Université, IRD, APHM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - M. Sarr
- Aix-Marseille Université, IRD, APHM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - N. Amsrtong
- Aix-Marseille Université, IRD, APHM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - S. Niare
- Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - M.A. Thera
- Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - F. Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, APHM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, APHM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - M. Million
- Aix-Marseille Université, IRD, APHM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- Corresponding author: M. Million, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
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Bordigoni A, Lo C, Yimagou EK, Nicaise B, Diop K, Raoult D, Desnues C, Fenollar F. Two new bacteria isolated from vagina of a patient with vaginosis: Atopobium massiliense sp. nov. and Butyricimonas vaginalis sp. nov. New Microbes New Infect 2020; 38:100771. [PMID: 33204431 PMCID: PMC7652708 DOI: 10.1016/j.nmni.2020.100771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/09/2020] [Accepted: 09/27/2020] [Indexed: 12/21/2022] Open
Abstract
Two new bacterial strains, Marseille-P4126 (=CSURP4126) and Marseille-P4593 (=CSURP4593), were isolated from the vaginal sample of a French woman with vaginosis. These strains were identified and characterized using the taxonogenomics method. The findings from phylogenetic tree interpretation, phenotypic criteria and genomic analysis provided here distinctly display that Atopobium massiliense sp. nov. and Butyricimonas vaginalis sp. nov. are new members of the genus Atopobium and Butyricimonas, respectively.
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Affiliation(s)
- A. Bordigoni
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - E. Kuete Yimagou
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - B. Nicaise
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - K. Diop
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C. Desnues
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - F. Fenollar
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
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45
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Ngom I, Hasni I, Senghor B, Lo C, Armstrong N, Sokhna C, Raoult D, Fournier PE, Lagier JC. Description of Gracilibacillus phocaeensis sp. nov., a new halophilic bacterium isolated from Senegalian human stool. New Microbes New Infect 2020; 38:100799. [PMID: 33294194 PMCID: PMC7695981 DOI: 10.1016/j.nmni.2020.100799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/05/2020] [Accepted: 10/19/2020] [Indexed: 10/24/2022] Open
Abstract
Using the taxonogenomics method, we describe Gracilibacillus phocaeensis strain Marseille-P3801, a new species previously isolated from a salty stool of a 20-year-old man from N'Diop, Senegal. It is a Gram-positive, aerobic and motile bacillus. The major fatty acids are C15:0-anteiso (59%), C16:0 (16%) and C17:0-anteiso (11%). Strain Marseille-P3801 exhibits a 98.45% sequence similarity with Gracilibacillus thailandensis strain TP2-8, the phylogenetically closest species. Its genome is 4.66 Mb with 39.6 mol% G + C content.
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Affiliation(s)
- I.I. Ngom
- Aix-Marseille Université, IRD, APHM, MEPHI, France
- IHU-Méditerranée Infection, France
| | - I. Hasni
- Aix-Marseille Université, IRD, APHM, MEPHI, France
- IHU-Méditerranée Infection, France
- Amoeba R&D Department, Chassieu, France
| | - B. Senghor
- Aix-Marseille Université, IRD, APHM, MEPHI, France
- IHU-Méditerranée Infection, France
| | - C.I. Lo
- IHU-Méditerranée Infection, France
- Aix-Marseille Université, IRD, APHM, SSA, VITROME, Marseille, France
| | - N. Armstrong
- Aix-Marseille Université, IRD, APHM, MEPHI, France
- IHU-Méditerranée Infection, France
| | - C. Sokhna
- IHU-Méditerranée Infection, France
- Aix-Marseille Université, IRD, APHM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, France
- IHU-Méditerranée Infection, France
| | - P.-E. Fournier
- IHU-Méditerranée Infection, France
- Aix-Marseille Université, IRD, APHM, SSA, VITROME, Marseille, France
| | - J.-C. Lagier
- Aix-Marseille Université, IRD, APHM, MEPHI, France
- IHU-Méditerranée Infection, France
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46
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State of the Art in the Culture of the Human Microbiota: New Interests and Strategies. Clin Microbiol Rev 2020; 34:34/1/e00129-19. [PMID: 33115723 DOI: 10.1128/cmr.00129-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The last 5 years have seen a turning point in the study of the gut microbiota with a rebirth of culture-dependent approaches to study the gut microbiota. High-throughput methods have been developed to study bacterial diversity with culture conditions aimed at mimicking the gut environment by using rich media such as YCFA (yeast extract, casein hydrolysate, fatty acids) and Gifu anaerobic medium in an anaerobic workstation, as well as media enriched with rumen and blood and coculture, to mimic the symbiosis of the gut microbiota. Other culture conditions target phenotypic and metabolic features of bacterial species to facilitate their isolation. Preexisting technologies such as next-generation sequencing and flow cytometry have also been utilized to develop innovative methods to isolate previously uncultured bacteria or explore viability in samples of interest. These techniques have been applied to isolate CPR (Candidate Phyla Radiation) among other, more classic approaches. Methanogenic archaeal and fungal cultures present different challenges than bacterial cultures. Efforts to improve the available systems to grow archaea have been successful through coculture systems. For fungi that are more easily isolated from the human microbiota, the challenge resides in the identification of the isolates, which has been approached by applying matrix-assisted laser desorption ionization-time of flight mass spectrometry technology to fungi. Bacteriotherapy represents a nonnegligible avenue in the future of medicine to correct dysbiosis and improve health or response to therapy. Although great strides have been achieved in the last 5 years, efforts in bacterial culture need to be sustained to continue deciphering the dark matter of metagenomics, particularly CPR, and extend these methods to archaea and fungi.
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47
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Traore S, Ngom I, Lo C, Di Pinto F, Sokhna C, Fournier PE, Raoult D, Fenollar F. Detailed description of Senegalia massiliensis strain SIT17 T , a bacterium isolated from the human gut. New Microbes New Infect 2020; 37:100700. [PMID: 32793352 PMCID: PMC7414013 DOI: 10.1016/j.nmni.2020.100700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/30/2020] [Accepted: 05/15/2020] [Indexed: 11/21/2022] Open
Abstract
Strain SIT17T was isolated from the stool of a healthy 13-month-old Senegalese boy. It is a Gram-positive, anaerobic, rod-shaped, non-spore-forming and mobile bacterium. It exhibited 92.74% 16S rRNA gene sequence similarity with the Brassicibacter thermophilus strain Cel2f, the phylogenetically most closely related species. Its genome is about 2.87 Mb long with 27.39 mol% G + C content. We provide more details of Senegalia massiliensis strain SIT17T (= CSURP2130 = DSM 103071), the creation of which was previously announced.
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Affiliation(s)
- S.I. Traore
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - I.I. Ngom
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - F. Di Pinto
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C. Sokhna
- IHU-Méditerranée Infection, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - P.-E. Fournier
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix Marseille Univ, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - F. Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
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48
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Konate S, Lo CI, Kuete E, Sarr M, Amsrtong N, Levasseur A, Caputo A, Thera MA, Raoult D, Million M. Halobacillus ihumii sp. nov., a new bacterium isolated from stool of healthy children living in Mali. New Microbes New Infect 2020; 37:100708. [PMID: 32793353 PMCID: PMC7408719 DOI: 10.1016/j.nmni.2020.100708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/02/2022] Open
Abstract
Strain Marseille-Q1234T is a new species from the genus Halobacillus that was isolated in 2019 from a stool sample in a healthy Malian child <5 years old. Cells are Gram-positive and strictly halophilic bacilli. Strain Marseille-Q1234T exhibits 98.46% 16S rRNA gene sequence similarity to Halobacillus naozhouensis strain JSM 071068T (NR_116505.1), the phylogenetically closely related species with standing in nomenclature. Based on the phenotypic and phylogenetic evidence, OrthoANI values and results of the biochemical tests, the new species is named Halobacillus ihumii sp. nov., for which strain Marseille-Q1234T (= CSURQ1234) is proposed as the type strain.
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Affiliation(s)
- S Konate
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - C I Lo
- IHU-Méditerranée Infection, Marseille, France.,Université des Sciences, des Techniques et des Technologies de Bamako, Mali
| | - E Kuete
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - M Sarr
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - N Amsrtong
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - A Levasseur
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - A Caputo
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - M A Thera
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - M Million
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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49
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Diop K, Cadoret F, Nguyen TT, Baudoin JP, Armstrong N, Raoult D, Bretelle F, Fournier PE, Fenollar F. Vaginimicrobium propionicum gen. nov., sp. nov., a novel propionic acid bacterium derived from human vaginal discharge. Int J Syst Evol Microbiol 2020; 70:4091-4097. [PMID: 32628103 DOI: 10.1099/ijsem.0.004106] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A Gram-stain-positive anaerobic rod-shaped bacterium, designated strain Marseille-P3275T, was isolated using culturomics from the vaginal discharge of healthy French woman. Marseille-P3275T was non-motile and did not form spores. Cells had neither catalase nor oxidase activity. The major fatty acids were C16 : 0 (29 %), C18:1ω9 (18 %), and iso-C15 : 0 (17 %). The genomic DNA G+C content was 50.64 mol%. The phylogenetic analysis based on 16S rRNA gene sequence indicated that Marseille-P3275T was related to members of the family Propionibacteriaceae (between 90.32-92.92 % sequence similarity) with formation of a clade with the monospecific genus Propionimicrobium (type species Propionimicrobium lymphophilum). On the basis of these phylogenetic and phenotypic differences, Marseille-P3275T was classified in a novel genus, Vaginimicrobium, as Vaginimicrobium propionicum gen. nov., sp. nov. The type strain is Marseille-P3275T (=CSUR P3275T=CECT 9677T).
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Affiliation(s)
- Khoudia Diop
- IHU-Méditerranée Infection, Marseille, France.,Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Frederic Cadoret
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Thi Tien Nguyen
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Jean-Pierre Baudoin
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Nicholas Armstrong
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Florence Bretelle
- Department of Gynecology and Obstetrics, Gynépole, Hôpital Nord, AP-HM, Marseille, France.,Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Marseille, France.,Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Florence Fenollar
- Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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50
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Ndongo S, Beye M, Labas N, Di Pinto F, Richez M, Lagier JC, Fournier PE, Raoult D, Bittar F. Gorillibacterium timonense sp. nov., isolated from an obese patient. Arch Microbiol 2020; 202:1223-1229. [PMID: 32103285 DOI: 10.1007/s00203-020-01834-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/28/2019] [Accepted: 02/11/2020] [Indexed: 01/15/2023]
Abstract
A Gram-negative and facultative anaerobic bacterium, designated strain SN4T, was isolated from the stool sample of an obese Amazonian patient. The new isolate was characterized by the taxonogenomics approach. The strain SN4T was beige-colored, circular and not haemolytic. Cells are rod shaped and motile with several flagella. Strain SN4T grows optimally at pH 7 and can survive in the presence of a saline concentration of up to 75 g/l NaCl. The 16S ribosomal RNA gene sequence analysis of the novel strain SN4T showed 95.28% similarity in nucleotide sequence with Gorillibacterium massiliense G5T, the phylogenetically closest neighbor and the type species of this genus. Anteiso-C15:0, iso-C15:0 and C16:0 were found as the major components in the cellular fatty acid analysis of this isolate. The genomic draft of strain SN4T is 5,263,742 bp long with 53.33% of G+C content. The differences in physiological, biochemical characteristics and phylogenetic and genomic data make it possible to clearly distinguish the strain SN4T from G. massiliense G5T. Based on the taxonogenomic description and the phenotypic and biochemical characteristics of this bacterium presented in this article, we propose the SN4T strain (= CSUR P2011 = DSM 100,698) as a new species, Gorillibacterium timonense sp. nov.
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Affiliation(s)
- Sokhna Ndongo
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Mamadou Beye
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Noémie Labas
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Fabrizio Di Pinto
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Magali Richez
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Jean-Christophe Lagier
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Fadi Bittar
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France.
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
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