-
International Journal of Systematic and... Dec 2020A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated strain IMCC25678, was isolated from an artificial freshwater...
A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated strain IMCC25678, was isolated from an artificial freshwater reservoir, Chungju Lake, in the Republic of Korea. The 16S rRNA gene sequence analysis indicated that strain IMCC25678 belongs to the genus with ≤98.7 % sequence similarities to species. Whole genome sequencing of strain IMCC25678 revealed a 3.9 Mbp genome size with a DNA G+C content of 42.2 mol%. The IMCC25678 genome shared ≤89.7 % average nucleotide identity and ≤21.4 % digital DNA-DNA hybridization values with closely related species of the genus , indicating that the strain represents a novel species. Summed feature 3 (C 6 and/or C 7), iso-C and iso-C 3-OH were found to be the predominant cellular fatty acid constituents in the strain. The major respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine, one unidentified phosphoglycolipid, one unidentified sphingolipid and three unidentified polar lipids. Based on the phylogenetic and phenotypic characteristics, strain IMCC25678 was considered to represent a novel species within the genus , for which the name sp. nov. is proposed. The type strain is IMCC25678 (=KACC 19485=NBRC 113130).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Lakes; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phylogeny; RNA, Ribosomal, 16S; Republic of Korea; Sequence Analysis, DNA; Species Specificity; Sphingobacterium; Water Microbiology
PubMed: 33054902
DOI: 10.1099/ijsem.0.004507 -
International Journal of Systematic and... Mar 2020A Gram-stain-negative, rod-shaped, non-motile and non-spore-forming bacterium, designated HAL-9, was isolated from oil-contaminated soil in Daqing oilfield, Heilongjiang...
A Gram-stain-negative, rod-shaped, non-motile and non-spore-forming bacterium, designated HAL-9, was isolated from oil-contaminated soil in Daqing oilfield, Heilongjiang Province, PR China. Strain HAL-9 was able to degrade quizalofop--ethyl and diclofop-methyl. Growth was observed at 10-35 °C (optimum, 30 °C), pH 6.0-10.0 (optimum, pH 7.0) and salinity of 0 %-5.0 % (w/v; optimum 1.0 %). The results of phylogenetic analysis based on the 16S rRNA gene indicated that strain HAL-9 belongs to the genus and showed the highest sequence similarity (98.3 %) to Y3L14, followed by DSM 11724 (95.1 %) and DSM 22361 (95.1 %). Menaquinone-7 (MK-7) was the only isoprenoid quinone. The predominant cellular fatty acids were summed feature 3 (C 7 and/or C 6), iso-C and iso-C 3-OH. The major polar lipids were phosphatidylethanolamine, three phosphoglycolipids and three unidentified lipids. The draft genome of strain HAL-9 was 5.41 Mb. The G+C content of strain HAL-9 was 40.6 mol%. Furthermore, the average nucleotide identity and DNA-DNA hybridization values between strain HAL-9 and Y3L14 were 86.2 % and 32.8 %, respectively, which were below the standard thresholds for species differentiation. On the basis of phenotypic, genotypic and phylogenetic evidence, strain HAL-9 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is HAL-9 (=ACCC 61581=CCTCC AB 2019176=KCTC 72287).
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Glycolipids; Nucleic Acid Hybridization; Petroleum Pollution; Phosphatidylethanolamines; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Sphingobacterium; Vitamin K 2
PubMed: 31967955
DOI: 10.1099/ijsem.0.004000 -
International Journal of Systematic and... Jan 2022An investigation of the diversity of 1-aminocyclopropane-1-carboxylate deaminase producing bacteria associated with camel faeces revealed the presence of a novel...
An investigation of the diversity of 1-aminocyclopropane-1-carboxylate deaminase producing bacteria associated with camel faeces revealed the presence of a novel bacterial strain designated C459-1. It was Gram-stain-negative, short-rod-shaped and non-motile. Strain C459-1 was observed to grow optimally at 35 °C, at pH 7.0 and in the presence of 0 % NaCl on Luria-Bertani agar medium. The cells were found to be positive for catalase and oxidase activities. The major fatty acids (>10 %) were identified as iso-C, summed feature 3 (C 6 and/or C 7) and iso-C 3-OH. The predominant menaquinone was MK-7. The major polar lipids consisted of phosphatidylethanolamine, one sphingophospholipid, two unknown aminophospholipids, three unknown glycolipids and five unknown lipids. The genomic DNA G+C content was 40.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C459-1 was affiliated with the genus and had the highest sequence similarity to h337 (97.0 %) and HER1398 (95.6 %). The average nucleotide identity and digital DNA-DNA hybridization values between strain C459-1 and h337 were 83.8 and 33.8 %, respectively. Phenotypic characteristics including enzyme activities and carbon source utilization differentiated strain C459-1 from other species. Based on its phenotypic, chemotaxonomic and phylogenetic properties, strain C459-1 represents a novel species of the genus , for which the name sp. nov. is proposed, with strain is C459-1 (CGMCC 1.18716=KCTC 82381) as the type strain.
Topics: Animals; Bacterial Typing Techniques; Base Composition; Camelus; Carbon-Carbon Lyases; DNA, Bacterial; Fatty Acids; Feces; Glycolipids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sphingobacterium
PubMed: 35100101
DOI: 10.1099/ijsem.0.005215 -
Microbiology Spectrum Dec 2022sp. is a yellowish Gram-negative bacterium that is usually characterized by high concentrations of sphingophospholipids as lipid components. As microbial enzymes have...
sp. is a yellowish Gram-negative bacterium that is usually characterized by high concentrations of sphingophospholipids as lipid components. As microbial enzymes have been in high demand in industrial fields in the past few decades, this study hopes to provide significant information on lipase activities of sp., since limited studies have been conducted on the sp. lipase. A microbe from one collected Artic soil sample, ARC4, was identified as psychrotolerant sp., and it could grow in temperatures ranging from 0°C to 24°C. The expression of sp. lipase was successfully performed through an efficient approach of utilizing mutated group 3 late embryogenesis abundant (G3LEA) proteins developed from Polypedilum vanderplanki. Purified enzyme was characterized using a few parameters, such as temperature, pH, metal ion cofactors, organic solvents, and detergents. The expressed enzyme is reported to be cold adapted and has the capability to work efficiently under neutral pH (pH 5.0 to 7.0), cofactors like Na ion, and the water-like solvent methanol. Addition of nonionic detergents greatly enhanced the activity of purified enzyme. The mechanism of action of LEA proteins has remained unknown to many; in this study we reveal their presence and improved protein expression due to the molecular shielding effect reported by others. This paper should be regarded as a useful example of using such proteins to influence an existing expression system to produce difficult-to-express proteins.
Topics: Lipase; Sphingobacterium; Detergents; Temperature; Solvents; Peptides; Hydrogen-Ion Concentration; Phylogeny
PubMed: 36314920
DOI: 10.1128/spectrum.01422-21 -
Current Microbiology Feb 2022A novel bacterium designated WQ 366 was isolated from the faeces of Bos taurus, foraging on the slopes of the Baima Snow Mountain in Yunnan, China. The isolate grew...
A novel bacterium designated WQ 366 was isolated from the faeces of Bos taurus, foraging on the slopes of the Baima Snow Mountain in Yunnan, China. The isolate grew optimally at 30 ℃ and pH 7.0-8.0 without NaCl. The cells were Gram-stain-negative, aerobic, rod-shaped, non-gliding, catalase-positive, and produced yellow color colonies on Columbia Agar. A polyphasic study was applied to clarify its taxonomic position through 16S rRNA gene and genome sequence analysis, and other extensive biological typing. Phylogenetic analysis revealed that the isolate was affiliated to the genus Sphingobacterium and its 16S rRNA gene sequence was closely related to Sphingobacterium bovisgrunnientis YK2 (97.3%), Sphingobacterium composti T5-12 (96.4%), and Sphingobacterium cavernae 5.0403-2 (96.4%). The calculated whole genome average nucleotide identity (ANI) and the digital DNA-DNA hybridization values between strain WQ 366 and the three related strains were 78.3, 78.6, 73.9 and 21.2, 21.2, 21.0%, respectively. The predominant fatty acids (>10%) were iso-C, iso-C 3-OH, Summed Feature 3 (C ω7c and/or C ω6c), and Summed feature 9 (iso-C ω9c and 10-methyl C). The main polar lipids were PE, GPL, GL, and PL. MK-7 was the major menaquinone. The genome size and the G + C content of WQ 366 was 4.1 Mb and 34.6%, respectively. All these results indicated that strain WQ 366 represents a novel species of the Sphingobacterium genus. Therefore, the name Sphingobacterium bovistauri sp. nov. is proposed, and the type strain is WQ 366 (= CCTCC AA 2020029 = KCTC 82395).
Topics: Animals; Bacterial Typing Techniques; Cattle; China; DNA, Bacterial; Fatty Acids; Feces; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sphingobacterium; Vitamin K 2
PubMed: 35129696
DOI: 10.1007/s00284-022-02763-2 -
International Journal of Systematic and... Feb 2018A novel Gram-negative, rod shaped, non-motile bacterium, designated strain YK2, was isolated from yak milk from Leh, India. The strain was positive for oxidase- and...
A novel Gram-negative, rod shaped, non-motile bacterium, designated strain YK2, was isolated from yak milk from Leh, India. The strain was positive for oxidase- and catalase-activities and negative for starch hydrolysis, nitrate reduction, citrate utilization, urease, lysine decarboxylase and ornithine decarboxylase activities. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C17 : 1ω9c and C16 : 1ω7c and/or C16 : 1ω6c and/or iso-C15 : 0 2-OH (summed feature 3). The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid and six unidentified lipids. The DNA G+C content of the strain was 38.9 mol%. The 16S rRNA gene sequence analysis indicated that strain YK2 was a member of the genus Sphingobacterium and closely related to Sphingobacterium alimentarium and Sphingobacterium composti with pair-wise sequence similarity of 98.3 and 97.9 %, respectively. The sequence similarity to other members of the genus Sphingobacterium was between 92.6 to 96.3 %. Phylogenetic analysis showed that strain YK2 clustered with Sphingobacterium alimentarium and together clustered with Sphingobacterium composti. DNA-DNA hybridization of strain YK2 with Sphingobacterium alimentarium WCC 4521 and Sphingobacterium composti T5-12 showed a relatedness of only 38 and 54 %, respectively. Based on the phenotypic characteristics and on phylogenetic inference, it appears that strain YK2 represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium bovisgrunnientis sp. nov. is proposed. The type strain of Sphingobacterium bovisgrunnientis sp. nov. is YK2 (=MTCC 12631=KCTC 52685=JCM 31951).
Topics: Animals; Bacterial Typing Techniques; Base Composition; Cattle; DNA, Bacterial; Fatty Acids; India; Milk; Nucleic Acid Hybridization; Phosphatidylethanolamines; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sphingobacterium
PubMed: 29388539
DOI: 10.1099/ijsem.0.002562 -
Archives of Microbiology Dec 2020A bacterial strain designated NYYP31 was isolated from the leaves of an annual halophytes, Suaeda corniculata Bunge, collected from the southern edge of the...
A bacterial strain designated NYYP31 was isolated from the leaves of an annual halophytes, Suaeda corniculata Bunge, collected from the southern edge of the Gurbantunggut desert, north-west China. Strain NYYP31 was Gram-staining negative, strictly aerobic, rod-shaped, non-motile, and non-spore-forming. Growth was observed at 4-42 °C, at pH 5.0-10.0, in the presence of up to 8% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences and coding sequences of 92 protein clusters showed that strain NYYP31 should be assigned to the genus Sphingobacterium. 16S rRNA gene sequence similarity analysis showed that strain NYYP31 was most closely related to the type strain of Sphingobacterium daejeonense (97.9%) and Sphingobacterium lactis (97.7%). The predominant isoprenoid quinone was MK-7. The major fatty acids were identified as iso-C, iso-C 3-OH and summed feature 3 (C ω7c and/or C ω6c). The polar lipids were phosphatidylethanolamine, two unidentified phospholipids, three unidentified lipids, three unidentified amino phospholipids, and two unidentified glycolipids. The genomic DNA G + C content was 36.4 mol%. The average nucleotide identity (ANI) values for strain NYYP31 to the type strains of S. daejeonense and S. lactis were 77.9 and 74.1%, respectively, which were below the cut-off level (95-96%) for species delineation. Based on the above results, strain NYYP31 represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium endophyticum sp. nov. is proposed. The type strain is NYYP31 (= CGMCC 1.16979 = NBRC 114258).
Topics: Bacterial Typing Techniques; Base Composition; Chenopodiaceae; China; DNA, Bacterial; Endophytes; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Plant Leaves; RNA, Ribosomal, 16S; Salt-Tolerant Plants; Sequence Analysis, DNA; Soil Microbiology; Sphingobacterium; Vitamin K 2
PubMed: 32737542
DOI: 10.1007/s00203-020-02000-z -
International Journal of Systematic and... Jul 2019One Gram-stain negative, aerobic, non-motile bacterial strain, 2c-3, was isolated from symptomatic canker bark tissue of Populus × euramericana. It was studied by the...
One Gram-stain negative, aerobic, non-motile bacterial strain, 2c-3, was isolated from symptomatic canker bark tissue of Populus × euramericana. It was studied by the genome sequence-derived average nucleotide identity (ANI), phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics. 16S rRNA gene data revealed that the novel isolate shares the greatest sequence similarity to Sphingobacterium populi 7Y-4 (97.0 %). The ANI values between the novel isolate and S. populi 7Y-4 was 81.19 %, lower than the proposed species boundary ANI cut-off (95-96 %). The major fatty acids are iso-C15 : 0, C16 : 1ω7c and iso-C17 : 0 3-OH. The polar lipids of the novel isolate included phosphatidylethanolamine, phospholipid, aminophospholipid and unknown lipids (L1-10). The menaquinone of the novel isolate was MK-7. The DNA G+C content was 41.96 mol %. Based on phenotypic and genotypic characteristics, the isolate represents a novel species within the genus Sphingobacterium, for which the name Sphingobacterium corticibacter is proposed. The type strain is 2c-3 (=CFCC 11898=KCTC 52798).
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Phospholipids; Phylogeny; Plant Bark; Populus; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sphingobacterium; Vitamin K 2
PubMed: 31091182
DOI: 10.1099/ijsem.0.003148 -
European Journal of Case Reports in... 2019We present the case of a 75-year-old woman admitted to hospital because of an infected pressure ulcer. Cultures revealed that the responsible bacterium was , which was...
UNLABELLED
We present the case of a 75-year-old woman admitted to hospital because of an infected pressure ulcer. Cultures revealed that the responsible bacterium was , which was successfully eradicated with ciprofloxacin. Over the last few years, there have been reports of new cases of infection caused by bacteria previously not thought to be harmful to humans, like . Previous cases were reported mostly in immunosuppressed patients and the present report is, to our knowledge, the first describing a pressure ulcer infected by this bacterium.
LEARNING POINTS
Bacteria previously not thought to be harmful to humans can cause disease. should be considered a potential cause of pressure ulcer infection.As may be resistant to many antibiotics, complete susceptibility testing should be mandatory.
PubMed: 31583212
DOI: 10.12890/2019_001214 -
International Journal of Systematic and... Nov 2019A bacterial strain M05W1-28 was isolated from a well that collected water for irrigation from a deep aquifer at a depth of 400 m. Cells were observed to be rod-shaped,...
A bacterial strain M05W1-28 was isolated from a well that collected water for irrigation from a deep aquifer at a depth of 400 m. Cells were observed to be rod-shaped, non-motile, aerobic, stained Gram-negative. Optimal growth was obtained at pH 7.0 (range: 6.0-9.0), 28 °C (range: 15-37 °C) and 0 % NaCl (range: 0-1.5 %, w/v) in modified tryptic soy broth (mTSB) without added NaCl and R2A. The cells were found to be positive for catalase and oxidase activities. The major fatty acids (>10 %) were identified as summed feature 3 (C 7 / C 6) and iso-C. The major polar lipids were phosphatidylethanolamine, glycolipid, phosphoglycolipids, phospholipids, and unidentified lipids. The major respiratory quinone was menaquinone-7 (MK-7). The genomic G+C content of strain M05W1-28 was 40.7 %. Based on similarities of 16S rRNA gene sequences, strain M05W1-28 was affiliated with the genus , exhibiting the highest sequence similarities with LMG 8342 (97.5 %), THG07 (97.1 %) and less than 97.0 % to other members of the genus. The average nucleotide identity (ANI) and digital DNA-DNA hybridisation values (dDDH) between M05W1-28 and LMG 8342 were 78.1 and 22.5 %, respectively. Phenotypic characteristics including enzyme activities and carbon source utilisation differentiated the strain from other species. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain M05W1-28 represented a novel species within the genus , for which the name sp. nov. is proposed. The type strain is M05W1-28 (=CGMCC 1.13711=KCTC 72027).
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Groundwater; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sphingobacterium; Vitamin K 2
PubMed: 31502948
DOI: 10.1099/ijsem.0.003521