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Yuvarajan S, Hameed A, Bhagwath Arun A, Kanekar S, Rekha PD. Urease-negative uropathogen Kalamiella piersonii YU22 metabolizes urea by urea carboxylase and allophanate hydrolase enzyme system. Microbiol Res 2022; 263:127142. [DOI: 10.1016/j.micres.2022.127142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022]
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Siebor E, Neuwirth C. Overview of Salmonella Genomic Island 1-Related Elements Among Gamma-Proteobacteria Reveals Their Wide Distribution Among Environmental Species. Front Microbiol 2022; 13:857492. [PMID: 35479618 PMCID: PMC9035990 DOI: 10.3389/fmicb.2022.857492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/28/2022] [Indexed: 11/29/2022] Open
Abstract
The aim of this study was to perform an in silico analysis of the available whole-genome sequencing data to detect syntenic genomic islands (GIs) having homology to Salmonella genomic island 1 (SGI1), analyze the genetic variations of their backbone, and determine their relatedness. Eighty-nine non-redundant SGI1-related elements (SGI1-REs) were identified among gamma-proteobacteria. With the inclusion of the thirty-seven backbones characterized to date, seven clusters were identified based on integrase homology: SGI1, PGI1, PGI2, AGI1 clusters, and clusters 5, 6, and 7 composed of GIs mainly harbored by waterborne or marine bacteria, such as Vibrio, Shewanella, Halomonas, Idiomarina, Marinobacter, and Pseudohongiella. The integrase genes and the backbones of SGI1-REs from clusters 6 and 7, and from PGI1, PGI2, and AGI1 clusters differed significantly from those of the SGI1 cluster, suggesting a different ancestor. All backbones consisted of two parts: the part from attL to the origin of transfer (oriT) harbored the DNA recombination, transfer, and mobilization genes, and the part from oriT to attR differed among the clusters. The diversity of SGI1-REs resulted from the recombination events between GIs of the same or other families. The oriT appeared to be a high recombination site. The multi-drug resistant (MDR) region was located upstream of the resolvase gene. However, most SGI1-REs in Vibrio, Shewanella, and marine bacteria did not harbor any MDR region. These strains could constitute a reservoir of SGI1-REs that could be potential ancestors of SGI1-REs encountered in pathogenic bacteria. Furthermore, four SGI1-REs did not harbor a resolvase gene and therefore could not acquire an integron. The presence of mobilization genes and AcaCD binding sites indicated that their conjugative transfer could occur with helper plasmids. The plasticity of SGI1-REs contributes to bacterial adaptation and evolution. We propose a more relevant classification to categorize SGI1-REs into different clusters based on their integrase gene similarity.
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Affiliation(s)
- Eliane Siebor
- Laboratory of Bacteriology, University Hospital of Dijon, Dijon, France
- UMR-CNRS 6249 Chrono-Environnement, University of Burgundy - Franche-Comté, Besançon, France
| | - Catherine Neuwirth
- Laboratory of Bacteriology, University Hospital of Dijon, Dijon, France
- UMR-CNRS 6249 Chrono-Environnement, University of Burgundy - Franche-Comté, Besançon, France
- *Correspondence: Catherine Neuwirth,
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Hameed A, Shahina M, Lin SY, Chen WM, Hsu YH, Lai WA, Young CC. Description of Gemmobacter aestuarii sp. nov., isolated from estuarine surface water and reclassification of Cereibacter changlensis as Gemmobacter changlensis Chen et al. 2013. Arch Microbiol 2020; 202:1035-1042. [DOI: 10.1007/s00203-020-01809-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 12/17/2019] [Accepted: 01/03/2020] [Indexed: 10/25/2022]
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Chen C, Han S, Zhu Z, Fu G, Wang R, Zhang Q, Ye Y, Ren Y, Yan C, Xu L, Wu M. Idiomarina mangrovi sp. nov., isolated from rhizosphere soil of a mangrove Avicennia marina forest. Int J Syst Evol Microbiol 2019; 69:1662-1668. [PMID: 30942686 DOI: 10.1099/ijsem.0.003372] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining negative, aerobic, motile and rod-shaped bacterium, designated ZQ330T, was isolated from rhizosphere soil of a mangrove (Avicennia marina) forest of Zhangzhou, Fujian Province, China. The growth range of NaCl concentration was 0.5-10.0 % (w/v), with an optimum at 2.5-3.0 % (w/v), the temperature range for growth was 10-40 °C, with an optimum at 28-30 °C, the pH range for growth was pH 6.0-9.5, with an optimum at pH 7.5. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ZQ330T exhibited less than 97.0 % sequence similarity to all type strains with validly published names and revealed that strain ZQ330T formed a distinct lineage in the genus Idiomarina. The average nucleotide identity, and in silico DNA-DNA hybridization values between strain ZQ330T and the reference strains were 64.8-69.9 % and 27.5-28.4 %, respectively. Chemotaxonomic analysis indicated that the main respiratory quinone was Q-8, the predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0, summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1ω9c), iso-C15 : 1F, C16 : 0, C18 : 0, summed feature 3 (C16 : 1ω8c and/or iso-C16 : 1 2-OH) and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified glycolipid, an unidentified aminolipid, an unidentified phospholipid and two unidentified lipids. Based on the genotypic, phenotypic, chemotaxonomic and phylogenetic features, strain ZQ330T is considered to represent a novel species, for which the name Idiomarina mangrovi sp. nov. is proposed. The type strain is ZQ330T (=MCCC 1K03495T=KCTC 62455T).
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Affiliation(s)
- Can Chen
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Shuaibo Han
- 2College of Life Sciences, Zhejiang University, Hangzhou 310000, PR China
| | - Zhimin Zhu
- 3Key Laboratory of Submarine Geosciences, State Oceanic Administration, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Geyi Fu
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Ruijun Wang
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Qin Zhang
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Yanghui Ye
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Yanhu Ren
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Cen Yan
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Lin Xu
- 4College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310000, PR China
| | - Min Wu
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
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