scholarly journals Comparative genomic analysis and characterization of Staphylococcus sp. AOAB, isolated from a notoriously invasive Mnemiopsis leidyi gut revealed multiple antibiotic resistance determinants

2021 ◽  
Author(s):  
Richard M. Mariita ◽  
Mohammad J. Hossain ◽  
Anthony G. Moss
Keyword(s):  
Sequence Similarity ◽  
Genomic Analysis ◽  
Mnemiopsis Leidyi ◽  
Comparative Genomic ◽  
Marker Genes ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Isolation And Characterization ◽  
Taxonomic Approach

AbstractHere, we describe the isolation and characterization of a coagulase-negative, vancomycin and oxacillin-susceptible novel bacterium of the genus Staphylococcus. Staphylococcus sp. strain AOAB was isolated from the stomodeum (gut) of the Mnemiopsis leidyi from Mobile Bay, Alabama USA. A polyphasic taxonomic approach comprised of phenotypic, chemotaxonomic and genotypic characteristics was used for analysis. The dominant respiratory quinone detected was MK-7 (100%). Major cellular fatty acids were anteiso-C15:0 (40.52%), anteiso-C17:0 (13.04 %), C-18:0 (11.53%) and C-20:0 (10.45%). The polar lipid profile consisted of glycolipid, phospholipid, phosphatidylglycerol and diphosphatidylglycerol. Although strain AOAB had a 16SrRNA gene sequence similarity of 99% with S. warneri SG1, S. pasteuri, S. devriesei KS-SP_60, S. lugdunensis HKU09-01, S. epidermidis RP62A, S. haemolyticus JCSC1435 and S. hominis DM 122, it was be distinguished from those species based on Multi-Locus Sequence Analysis (MLSA) using 6 marker genes (16S rRNA, hsp60, rpoB, dnaJ, sodA and tuf). MLSA revealed strain AOAB to be closely related to S. warneri SG1 and S. pasteuri SP1 but distinct from two hitherto known species. These results were confirmed by Average Nucleotide Identity (closest ANI of 84.93% and 84.58% identity against S. warneri SG1 and S. pasteuri SP1 respectively). In-silico DNA-DNA hybridization was <70% (33.1 % and 32.8% against S. warneri SG1 and S. pasteuri SP1 respectively), which further confirmed that the strain was a potential novel Staphylococcus species.

Rheinheimera tilapiae sp. nov., isolated from a freshwater culture pond

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1457-1463 ◽  
Author(s):  
Wen-Ming Chen ◽  
Shwu-Harn Yang ◽  
Chiu-Chung Young ◽  
Shih-Yi Sheu
Keyword(s):  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Cichlid Fish ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Approach

A bacterial strain designated Ruye-90T was isolated from a freshwater tilapiine cichlid fish culture pond in Taiwan and characterized using a polyphasic taxonomic approach. Strain Ruye-90T was Gram-negative, aerobic, yellow-coloured, rod-shaped, and motile by means of a single polar flagellum. Growth occurred at 4–30 °C (optimum, 20–30 °C), at pH 7.0–9.0 (optimum, pH 8.0–9.0) and with 0–2 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Ruye-90T belonged to the genus Rheinheimera and its most closely related neighbour was Rheinheimera tangshanensis JA3-B52T with sequence similarity of 97.5 %. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 41.3 %), C16 : 0 (19.3 %), C18 : 1ω7c (8.4 %) and C12 : 0 3-OH (7.0 %). The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 49.0 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, aminolipid and two uncharacterized phospholipids. The DNA–DNA relatedness of strain Ruye-90T with respect to recognized members of the genus Rheinheimera was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Ruye-90T represents a novel species in the genus Rheinheimera , for which the name Rheinheimera tilapiae sp. nov. is proposed. The type strain is Ruye-90T ( = LMG 26339T = BCRC 80263T = KCTC 23315T).

scholarly journals Isolation and Characterization of a Novel Phage for Controlling Multidrug-Resistant Klebsiella pneumoniae

2020 ◽  
Vol 8 (4) ◽  
pp. 542 ◽  
Author(s):  
Qin Peng ◽  
Meng Fang ◽  
Xushan Liu ◽  
Chunling Zhang ◽  
Yue Liu ◽  
...  
Keyword(s):  
Bacterial Pathogens ◽  
Physical Stability ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Comparative Genomic ◽  
High Antibacterial Activity ◽  
Isolation And Characterization ◽  
Hospital Sewage ◽  
Siphoviridae Family

The emergence of multidrug-resistant bacterial pathogens has severely threatened global health. A phage with the ability to efficiently and specifically lyse bacteria is considered an alternative for controlling multidrug-resistant bacterial pathogens. The discovery of novel agents for controlling the infections caused by K. pneumoniae is urgent due to the broad multidrug-resistance of K. pneumoniae. Only a few phage isolates have been reported to infect multidrug-resistant K. pneumoniae. In this study, by using the multidrug-resistant K. pneumoniae strain as an indicator, a novel phage called vB_KleS-HSE3, which maintains high antibacterial activity and high physical stability, was isolated from hospital sewage. This phage infected one of four tested multidrug-resistant K. pneumoniae strains. This phage belongs to the Siphoviridae family and a comparative genomic analysis showed that this phage is part of a novel phage lineage among the Siphoviridae family of phages that infect strains of Klebsiella. Based on its features, the vB_KleS-HSE3 phage has potential for controlling infections caused by multidrug-resistant K. pneumoniae.

Gemmobacter lanyuensis sp. nov., isolated from a freshwater spring

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4039-4045 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Yu-Wen Shiau ◽  
Yan-Ting Wei ◽  
Wen-Ming Chen
Keyword(s):  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Freshwater Spring ◽  
Taxonomic Approach

A bacterial strain designated Orc-4T was isolated from a freshwater spring in Taiwan and characterized using the polyphasic taxonomic approach. Cells of strain Orc-4T were facultatively anaerobic, Gram-reaction-negative, poly-β-hydroxybutyrate-accumulating, non-motile rods surrounded by a thick capsule and forming cream–white colonies. Growth occurred at 15–40 °C (optimum, 25–30 °C), at pH 6.0–9.0 (optimum, pH 7.0) and with 0–1 % NaCl (optimum, 0–0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Orc-4T belonged to the genus Gemmobacter within the family Rhodobacteraceae of the class Alphaproteobacteria and its most closely related neighbour was Gemmobacter fontiphilus JS43T with sequence similarity of 97.8 %. Strain Orc-4T contained C18 : 1ω7c as the predominant fatty acid. The major respiratory quinone was Q-10. The DNA G+C content of the genomic DNA was 63.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one uncharacterized aminolipid and several uncharacterized phospholipids. The DNA–DNA relatedness of strain Orc-4T with respect to recognized species of the genus Gemmobacter was less than 48 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Orc-4T represents a novel species of the genus Gemmobacter , for which the name Gemmobacter lanyuensis sp. nov. is proposed. The type strain is Orc-4T ( = BCRC 80378T = LMG 26667T = KCTC 23714T).

scholarly journals Characterization of a Deep Sea Bacillus toyonensis Isolate: Genomic and Pathogenic Features

2021 ◽  
Vol 11 ◽  
Author(s):  
Jing-chang Luo ◽  
Hao Long ◽  
Jian Zhang ◽  
Yan Zhao ◽  
Li Sun
Keyword(s):  
Deep Sea ◽  
Mammalian Cells ◽  
Acute Infection ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Circular Chromosome ◽  
Isolation And Characterization ◽  
High Concentrations ◽  
Bacillus Toyonensis

Bacillus toyonensis is a group of Gram-positive bacteria belonging to the Bacillus cereus group and used in some cases as probiotics or biocontrol agents. To our knowledge, B. toyonensis from the deep sea (depth &gt;1,000 m) has not been documented. Here, we report the isolation and characterization of a B. toyonensis strain, P18, from a deep sea hydrothermal field. P18 is aerobic, motile, and able to grow at low temperatures (4°C) and high concentrations of NaCl (8%). P18 possesses a circular chromosome of 5,250,895 bp and a plasmid of 536,892 bp, which encode 5,380 and 523 genes, respectively. Of these genes, 2,229 encode hypothetical proteins that could not be annotated based on the COG database. Comparative genomic analysis showed that P18 is most closely related to the type strain of B. toyonensis, BCT-7112T. Compared to BCT-7112T, P18 contains 1,401 unique genes, 441 of which were classified into 20 COG functional categories, and the remaining 960 genes could not be annotated. A total of 319 putative virulence genes were identified in P18, including toxin-related genes, and 24 of these genes are absent in BCT-7112T. P18 exerted strong cytopathic effects on fish and mammalian cells that led to rapid cell death. When inoculated via injection into fish and mice, P18 rapidly disseminated in host tissues and induced acute infection and mortality. Histopathology revealed varying degrees of tissue lesions in the infected animals. Furthermore, P18 could survive in fish and mouse sera and possessed hemolytic activity. Taken together, these results provide the first evidence that virulent B. toyonensis exists in deep sea environments.

scholarly journals Epilithonimonas psychrotolerans sp. nov., isolated from alpine permafrost

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3777-3781 ◽  
Author(s):  
Liang Ge ◽  
Qi Zhao ◽  
Hongmei Sheng ◽  
Jianmin Wu ◽  
Lizhe An
Keyword(s):  
Sequence Similarity ◽  
Rrna Gene ◽  
Culturable Bacteria ◽  
The Novel ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Dna Reassociation ◽  
Taxonomic Approach ◽  
Reference Strains ◽  
Good Agreement

A bacterial strain, designated TSBY 57T, was isolated during a study on the phylogenetic diversity of culturable bacteria from alpine permafrost in Tianshan Mountains, China, and was classified by means of a polyphasic taxonomic approach. The novel strain was found to belong to the genus Epilithonimonas and was distinguished from recognized species of this genus. Strain TSBY 57T grew aerobically, at 0–30 °C, with 0–1.5 % (w/v) NaCl and at pH 6–8.Cells were Gram-stain-negative, non-motile, non-spore-forming rods. Compared with the reference strains, the novel strain was psychrotolerant. The predominant fatty acids were summed feature 3 (consisting of C16 : 1ω7c and/or C16 : 1ω6c), anteiso-C15 : 0 and iso-C15 : 0.The sole respiratory quinone was MK-6.Phosphatidylethanolamine was predominant in the polar lipid profile of strain TSBY 57T. These chemotaxonomic traits were in good agreement with the characteristics of the genus Epilithonimonas. On the basis of 16S rRNA gene sequence similarity, strain TSBY 57T was a member of the genus Epilithonimonas and was closely related to Epilithonimonas tenax DSM 16811T (99.0 %), Epilithonimonas ginsengisoli DCY78T (98.6 %) and Epilithonimonas lactis H1T (98.5 %). However, DNA–DNA reassociation values between strain TSBY 57T and E. tenax DSM 16811T, E. ginsengisoli DCY78T and E. lactis H1T were 39.5 ± 2.6, 37.7 ± 1.0 and 37.3 ± 1.1 %, respectively. The G+C content of the DNA was 34.4 ± 0.2 mol%. Based on data from this polyphasic taxonomic study, strain TSBY 57T represents a novel species of the genus Epilithonimonas, for which the name Epilithonimonas psychrotolerans sp. nov. is proposed. The type strain is TSBY 57T ( = NRRL B-51307T = CCTCC AB 207182T).

scholarly journals Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas sp. AAP5

2021 ◽  
Vol 9 (4) ◽  
pp. 768
Author(s):  
Karel Kopejtka ◽  
Yonghui Zeng ◽  
David Kaftan ◽  
Vadim Selyanin ◽  
Zdenko Gardian ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Close Phylogenetic Relationship

An aerobic, yellow-pigmented, bacteriochlorophyll a-producing strain, designated AAP5 (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Tyrolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus Sphingomonas and has the highest pairwise 16S rRNA gene sequence similarity with Sphingomonas glacialis (98.3%), Sphingomonas psychrolutea (96.8%), and Sphingomonas melonis (96.5%). Its genomic DNA G + C content is 65.9%. Further, in silico DNA-DNA hybridization and calculation of the average nucleotide identity speaks for the close phylogenetic relationship of AAP5 and Sphingomonas glacialis. The high percentage (76.2%) of shared orthologous gene clusters between strain AAP5 and Sphingomonas paucimobilis NCTC 11030T, the type species of the genus, supports the classification of the two strains into the same genus. Strain AAP5 was found to contain C18:1ω7c (64.6%) as a predominant fatty acid (>10%) and the polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, six unidentified glycolipids, one unidentified phospholipid, and two unidentified lipids. The main respiratory quinone was ubiquinone-10. Strain AAP5 is a facultative photoheterotroph containing type-2 photosynthetic reaction centers and, in addition, contains a xathorhodopsin gene. No CO2-fixation pathways were found.

scholarly journals Spirosoma telluris sp. nov. and Spirosoma arboris sp. nov. isolated from soil and tree bark, respectively

2020 ◽  
Vol 70 (10) ◽  
pp. 5355-5362 ◽  
Author(s):  
Heeyoung Kang ◽  
Inseong Cha ◽  
Haneul Kim ◽  
Kiseong Joh
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Sequence Similarity ◽  
Polar Lipids ◽  
Tree Bark ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

Two novel strains (HMF3257T and HMF4905T), isolated from freshwater and bark samples, were investigated to determine their relationships within and between species of the genus Spirosoma by using a polyphasic approach. They were aerobic, Gram-stain-negative, non-motile and rod-shaped bacteria. The major fatty acids (>10%) in both strains were identified as summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 1 ω5c, while strains HMF3257T and HMF4905T contained a moderately high amount of C16 : 0 and iso-C15 : 0, respectively. The predominant respiratory quinone was MK-7 for both strains. In addition to phosphatidylethanolamine and one unidentified glycolipid, the polar lipid profile of strain HMF3257T consisted of three unidentified aminophospholipids, one unidentified aminolipid and two unidentified polar lipids, and that of strain HMF4905T consisted of one unidentified aminophospholipid, two unidentified aminolipids and three unidentified polar lipids. The DNA G+C contents of strains HMF3257T and HMF4905T were 47.2 and 46.4 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains HMF3257T and HMF4905T are closely related to Spirosoma migulaei 15J9-8T (97.0 % sequence similarity), while sharing 97.4 % sequence similarity with each other. The average nucleotide identity value between strains HMF3257T and HMF4905T was 81.1 %, and the digital DNA–DNA hybridization value between these two strains was 24.4 %. Based on the above data, strains HMF3257T and HMF4905T represent two novel members within the genus Spirosoma , for which the names Spirosoma telluris sp. nov. and Spirosoma arboris sp. nov. are proposed, respectively. The type strain of S. telluris is HMF3257T (=KCTC 62463T=NBRC 112670T) and type strain of S. arboris is HMF4905T (=KCTC 72779T=NBRC 114270T).

scholarly journals Isolation and Characterization of the Gene Coding for the Amidinotransferase Involved in the Biosynthesis of Phaseolotoxin in Pseudomonas syringae pv. phaseolicola

2001 ◽  
Vol 14 (4) ◽  
pp. 545-554 ◽  
Author(s):  
Gustavo Hernández-Guzmán ◽  
Ariel Alvarez-Morales
Keyword(s):  
Aspartic Acid ◽  
Pseudomonas Syringae ◽  
Sequence Similarity ◽  
Insertion Mutant ◽  
Halo Blight ◽  
Streptomyces Spp ◽  
Isolation And Characterization ◽  
Gene Coding ◽  
Blight Disease

Pseudomonas syringae pv. phaseolicola is the causal agent of the “halo blight” disease of beans. A key component in the development of the disease is a nonhost-specific toxin, Nδ-(N'-sulphodiaminophosphinyl)-ornithyl-alanyl-homoarginine, known as phaseolotoxin. The homoarginine residue in this molecule has been suggested to be the product of Larginine:lysine amidinotransferase activity, previously detected in extracts of P. syringae pv. phaseolicola grown under conditions of phaseolotoxin production. We report the isolation and characterization of an amidinotransferase gene (amtA) from P. syringae pv. phaseolicola coding for a polypeptide of 362 residues (41.36 kDa) and showing approximately 40% sequence similarity to Larginine:inosamine-phosphate amidinotransferase from three species of Streptomyces spp. and 50.4% with an Larginine:glycine amidinotransferase from human mitochondria. The cysteine, histidine, and aspartic acid residues involved in substrate binding are conserved. Furthermore, expression of the amtA and argK genes and phaseolotoxin production occurs at 18°C but not at 28°C. An amidinotransferase insertion mutant was obtained that lost the capacity to synthesize homoarginine and phaseolotoxin. These results show that the amtA gene isolated is responsible for the amidinotransferase activity detected previously and that phaseolotoxin production depends upon the activity of this gene.

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