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International Journal of Systematic and... Jul 2017A Gram-stain-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated YIM X0211T, was isolated from a soil sample of Shiling...
A Gram-stain-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated YIM X0211T, was isolated from a soil sample of Shiling County, Yunnan Province, south-west China. The new isolate was characterized taxonomically by using a polyphasic approach. The strain grew optimally at 30 °C, at pH 7.0 and with 0-3 % (w/v) NaCl. It was positive for catalase and oxidase but negative for H2S production. Comparative 16S rRNA gene sequence analysis showed that strain YIM X0211T fell within the cluster comprising Sphingobacterium species and clustered with Sphingobacterium mizutaii DSM 11724T (97.93 % similarity). The G+C content of the genomic DNA was 41.2 mol%. The predominant respiratory quinone was menaquinone MK-7. The major fatty acids were iso-C15 : 0 2-OH, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). The polar lipids consisted of phosphatidylethanolamine, sphingolipid, and several unknown phospholipids or lipids. The DNA-DNA hybridization value between strain YIM X0211T and S. mizutaii DSM 11724T was 42.3±0.4 %, which is below the 70 % limit for species delineation. These chemotaxonomic data supported the affiliation of strain YIM X0211T to the genus Sphingobacterium. Based on the recorded phenotypic and genotypic characteristics, it is determined that the isolate represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium soli sp. nov. is proposed. The type strain is YIM X0211T (=KCTC 42696T=CGMCC 1.15966T).
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Sphingobacterium; Vitamin K 2
PubMed: 28699577
DOI: 10.1099/ijsem.0.001946 -
International Journal of Systematic and... Mar 2012A Gram-negative, non-motile, non-spore-forming, non-flagellated rod capable of degrading cypermethrin, designated LQY-18(T), was isolated from activated sludge of a...
A Gram-negative, non-motile, non-spore-forming, non-flagellated rod capable of degrading cypermethrin, designated LQY-18(T), was isolated from activated sludge of a wastewater treatment plant in China. Strain LQY-18(T) grew at 8-40 °C (optimum 30 °C), at pH 5.0-10.0 (optimum pH 7.0) and with 0-5% (w/v) NaCl (optimum 1%). The predominant menaquinone was MK-7 (97%) and the major fatty acids were summed feature 3 (comprising C(16:1)ω6c and/or C(16:1)ω7c), iso-C(15:0) and iso-C(17:0) 3-OH. The DNA G+C content was 40.3 mol%. Phylogenetic analysis revealed that the isolate belonged to the genus Sphingobacterium of the phylum Bacteroidetes and showed low 16S rRNA gene sequence similarity with recognized members of the genus Sphingobacterium. The closest neighbour was Sphingobacterium mizutaii ATCC 33299(T) (92.9% 16S rRNA gene sequence similarity). On the basis of phenotypic, genetic and phylogenetic data, strain LQY-18(T) (=ACCC 05410(T)=CCTCC AB 2010005(T)=KCTC 23009(T)) should be classified as a representative of a novel species of the genus Sphingobacterium, for which the name Sphingobacterium wenxiniae sp. nov. is proposed.
Topics: Bacterial Typing Techniques; Base Composition; China; Cluster Analysis; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Hydrogen-Ion Concentration; Molecular Sequence Data; Phylogeny; Pyrethrins; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sewage; Sodium Chloride; Sphingobacterium; Temperature; Vitamin K 2
PubMed: 21551333
DOI: 10.1099/ijs.0.033118-0 -
International Journal of Systematic and... Sep 2008A Gram-negative bacterium, designated strain CW 186(T), was isolated from forest soil in Anhui province, China. Cells of strain CW 186(T) were strictly aerobic,...
A Gram-negative bacterium, designated strain CW 186(T), was isolated from forest soil in Anhui province, China. Cells of strain CW 186(T) were strictly aerobic, non-motile and rod-shaped. The strain grew optimally at 25-30 degrees C and pH 6.0-8.0. The major cellular fatty acids of strain CW 186(T) were iso-C(15:0) (32.2%), iso-C(17:0) 3-OH (9.8%) and summed feature 3 (iso-C(15:0) 2-OH and/or C(16:1)omega7c; 33.7%). The predominant isoprenoid quinone was MK-7. The G+C content of the genomic DNA was 36.3 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain CW 186(T) formed a monophyletic cluster with Sphingobacterium daejeonense LMG 23402(T), Sphingobacterium composti LMG 23401(T), Sphingobacterium composti DSM 18850(T), Sphingobacterium mizutaii ATCC 33299(T) and Sphingobacterium spiritivorum ATCC 33861(T). Sequence similarities were less than 94% (the maximal similarity was about 93.9% to S. composti LMG 23401(T)) to Sphingobacterium species with validly published names. A polyphasic taxonomic study including chemotaxonomic and phylogenetic analyses demonstrated that strain CW 186(T) should be classified as representing a novel species of the genus Sphingobacterium, for which the name Sphingobacterium anhuiense sp. nov. is proposed. The type strain is CW 186(T) (=KCTC 22209(T)=CCTCC AB 207197(T)).
Topics: Aerobiosis; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Genes, rRNA; Hydrogen-Ion Concentration; Locomotion; Molecular Sequence Data; Phylogeny; Quinones; RNA, Bacterial; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sequence Homology, Nucleic Acid; Soil Microbiology; Sphingobacterium; Temperature; Trees
PubMed: 18768611
DOI: 10.1099/ijs.0.65864-0 -
International Journal of Systematic and... Mar 2013A novel Gram-staining-negative bacterial strain, designated XH4(T), was isolated from soil of a Populus euphratica forest in the Hotan River valley, Xinjiang Uyghur...
Sphingobacterium hotanense sp. nov., isolated from soil of a Populus euphratica forest, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium shayense.
A novel Gram-staining-negative bacterial strain, designated XH4(T), was isolated from soil of a Populus euphratica forest in the Hotan River valley, Xinjiang Uyghur autonomous region, PR China. The cells were strictly aerobic, non-motile, short rods. The isolate grew optimally at 37 °C and at pH 7.0-8.0. Based on 16S rRNA gene sequence analysis, strain XH4(T) belonged to the genus Sphingobacterium and was closely related to Sphingobacterium mizutaii ATCC 33299(T) (96.1 % sequence similarity). The DNA G+C content was 41.2 mol%. The major polar lipid of strain XH4(T) was phosphatidylethanolamine, and several unidentified polar lipids were also present. Strain XH4(T) showed the typical chemotaxonomic features of the genus Sphingobacterium, with the presence of ceramide phosphorylethanolamine 2 (CerPE-2) as the major ceramide. The major cellular fatty acids of strain XH4(T) were iso-C15 : 0 (34.0 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 20.7 %) and iso-C17 : 0 3-OH (14.7 %). The predominant isoprenoid quinone was MK-7. On the basis of phenotypic data and phylogenetic inference, strain XH4(T) represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium hotanense sp. nov. is proposed. The type strain is XH4(T) ( = NRRL B-59204(T) = CCTCC AB 209007(T)). Emended descriptions of Sphingobacterium daejeonense and Sphingobacterium shayense are also given.
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Phosphatidylethanolamines; Phylogeny; Populus; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Sphingobacterium; Sphingomyelins; Trees; Vitamin K 2
PubMed: 22611196
DOI: 10.1099/ijs.0.030155-0 -
Toxics Apr 2023To effectively carry out the bioremediation of a Pb polluted environment, a lead-tolerant strain named D1 was screened from the activated sludge of a factory in Hefei,...
To effectively carry out the bioremediation of a Pb polluted environment, a lead-tolerant strain named D1 was screened from the activated sludge of a factory in Hefei, and its lead removal in a solution with Pb concentration of 200 mg/L could reach 91% under optimal culture conditions. Morphological observation and 16S rRNA gene sequencing were used to identify D1 accurately, and its cultural characteristics and lead removal mechanism were also preliminarily studied. The results showed that the D1 strain was preliminarily identified as the strain. The experiments conducted via orthogonal test showed that the optimal conditions for the growth of strain D1 were pH 7, inoculum volume 6%, 35 °C, and rotational speed 150 r/min. According to the results of scanning electron microscopy and energy spectrum analysis before and after the D1 exposure to lead, it is believed that the lead removal mechanism of D1 is surface adsorption. The Fourier transform infrared spectroscopy (FTIR) results revealed that multiple functional groups on the surface of the bacterial cells are involved in the Pb adsorption process. In conclusion, the D1 strain has excellent application prospects in the bioremediation of lead-contaminated environments.
PubMed: 37235227
DOI: 10.3390/toxics11050412 -
International Journal of Systematic and... Sep 2006A Gram-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated TR6-04(T), was isolated from compost and characterized...
A Gram-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated TR6-04(T), was isolated from compost and characterized taxonomically by using a polyphasic approach. The organism grew optimally at 30 degrees Celsius and at pH 6.5-7.0. The isolate was positive for catalase and oxidase tests but negative for gelatinase, indole and H(2)S production. Comparative 16S rRNA gene sequence analysis showed that strain TR6-04(T) fell within the radiation of the cluster comprising Sphingobacterium species and clustered with Sphingobacterium mizutaii ATCC 33299(T) (96.7 % sequence similarity); the similarity to sequences of other species within the family Sphingobacteriaceae was less than 92.0 %. The G+C content of the genomic DNA was 38.7 mol%. The predominant respiratory quinone was MK-7. The major fatty acids were iso-C(15 : 0), iso-C(17 : 0) 3-OH and summed feature 4 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c). These chemotaxonomic data supported the affiliation of strain TR6-04(T) to the genus Sphingobacterium. However, on the basis of its phenotypic properties and phylogenetic distinctiveness, strain TR6-04(T) (=KCTC 12579(T)=LMG 23402(T)=CCUG 52468(T)) should be classified as the type strain of a novel species, for which the name Sphingobacterium daejeonense sp. nov. is proposed.
Topics: Bacterial Typing Techniques; Base Composition; Base Sequence; DNA, Bacterial; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Sphingobacterium
PubMed: 16957095
DOI: 10.1099/ijs.0.64406-0 -
Biochimica Et Biophysica Acta Dec 2003The unique feature of the genus Sphingobacterium is the presence of sphingophospholipids and ceramides, besides diacylglycerophospholipids. As major cellular lipid...
The unique feature of the genus Sphingobacterium is the presence of sphingophospholipids and ceramides, besides diacylglycerophospholipids. As major cellular lipid components, five kinds of sphingophospholipids were purified from Sphingobacterium spiritivorum ATCC 33861(T), the type species of genus Sphingobacterium. They were identified as ceramide phosphorylethanolamines (CerPE-1 and CerPE-2), ceramide phosphoryl-myo-inositols (CerPI-1 and CerPI-2), and ceramide phosphorylmannose (CerPM-1). The ceramide of CerPE-1, CerPI-1, and CerPM-1 was composed of 15-methylhexadecasphinganine (isoheptadeca sphinganine, iso-C17:0) and 13-methyltetradecanoic acid (isopentadecanoic acid, iso-C15:0), whereas that of CerPE-2 and CerPI-2 was composed of isoheptadeca sphinganine and 2-hydroxy-13-methyltetradecanoic acid (2-hydroxy isopentadecanoic acid, 2-OH iso-C15:0). These sphingophospholipids were also found in cellular lipids of Sphingobacterium multivorum ATCC 33613(T), Sphingobacterium mizutaii ATCC 33299(T), Sphingobacterium faecium IFO 15299(T), Sphingobacterium thalpophilum ATCC 43320(T), and Sphingobacterium antarcticum ATCC 51969(T). To our knowledge, the existence of CerPM-1 is a novel sphingophospholipid through eukaryotic and prokaryotic cells.
Topics: Ceramides; Chromatography, Thin Layer; Fatty Acids; Magnetic Resonance Spectroscopy; Molecular Structure; Phospholipids; Solubility; Spectrometry, Mass, Fast Atom Bombardment; Spectrophotometry, Infrared; Sphingobacterium; Sphingolipids
PubMed: 14729071
DOI: 10.1016/j.bbalip.2003.10.010 -
Scientific Reports May 2022Peptic ulcer disease (PUD) and chronic gastritis are prevalent in developing countries. The role of oxidative stress in the pathogenesis of gastrointestinal mucosal...
Peptic ulcer disease (PUD) and chronic gastritis are prevalent in developing countries. The role of oxidative stress in the pathogenesis of gastrointestinal mucosal disorders is well recognized. In PUD, the gastric mucosa and its associated microbiome are subject to diet and stress-induced oxidative perturbations. Tissue redox potential (ORP) measurement can quantify oxidative stress, reflecting the balance between prooxidants and antioxidants. This study hypothesizes that the oxidative stress quantified by tissue ORP will be associated with characteristic changes in the mucosa-associated microbiome in PUD and gastritis. In addition, we propose using relative microbial abundance as a quantitative marker of mucosal health. Endoscopy was performed to obtain gastric mucosal biopsies from ten PUD and ten non-ulcer dyspepsia (NUD) patients. The tissue ORP was measured directly with a microelectrode using a biopsy specimen. A second specimen from an adjacent site was subjected to 16s rRNA gene sequencing. From the OTUs, the relative abundance of the microbial taxon in each of the samples was derived. We analyzed the genome of the predominant species for genes encoding the utilization of oxygen as an electron acceptor in respiration and for the presence of antioxidant defense mechanisms. The organisms were then grouped based on their established and inferred redox traits. Shannon diversity index and Species richness were calculated on rarefied data. The relative abundance of organisms that prefer high ORP over those that favor low ORP is conceived as the "Microbial Redox Index (MRI)," an indicator of mucosal health. In the gastric mucosa, aerobic species predominate and are more diverse than the anaerobes. The predominant aerobes are Helicobacter pylori and Sphingobacterium mizutaii. The abundance of these two species had an inverse correlation with the abundance of low ORP preferring anaerobes. Their relative abundance ratio (Microbial Redox Index) correlated with the tissue oxidation-reduction potential (ORP), a direct measure of oxidative stress. Correlation analysis also revealed that the abundance of all anaerobes inversely correlated with the dominant aerobic taxa. In addition, Shannon and Species richness diversity indices, the probable indicators of mucosal health, were negatively correlated with Microbial Redox Index. Using PUD as a prototype mucosal disease, this article describes a generalized approach to infer and quantify mucosal oxidative stress by analyzing the relative abundance of microorganisms that preferentially grow at the extremes of the tissue redox potential. This ratiometric Microbial Redox Index can also be assessed using simple qPCR without the need for sequencing. The approach described herein may be helpful as a widely applicable quantitative measure of mucosal health with prognostic and therapeutic implications.
Topics: Gastric Mucosa; Gastritis; Helicobacter Infections; Helicobacter pylori; Humans; Microbiota; Oxidation-Reduction; Peptic Ulcer; RNA, Ribosomal, 16S
PubMed: 35589904
DOI: 10.1038/s41598-022-12431-x -
Microorganisms Oct 2022Polyhydroxyalkanoate (PHA), a biodegradable and plastic-like biopolymer, has been receiving research and industrial attention due to severe plastic pollution, resource...
Polyhydroxyalkanoate (PHA), a biodegradable and plastic-like biopolymer, has been receiving research and industrial attention due to severe plastic pollution, resource depletion, and global waste issues. This has spurred the isolation and characterisation of novel PHA-producing strains through cultivation and non-cultivation approaches, with a particular interest in genes encoding PHA synthesis pathways. Since sea sponges and sediment are marine benthic habitats known to be rich in microbial diversity, sponge tissues ( and ) and sediment samples were collected in this study from Redang and Bidong islands located in the Malaysian Coral Triangle region. PHA synthase () genes were identified from sediment-associated bacterial strains using a cultivation approach and from sponge-associated bacterial metagenomes using a non-cultivation approach. In addition, phylogenetic diversity profiling was performed for the sponge-associated bacterial community using 16S ribosomal ribonucleic acid (16S rRNA) amplicon sequencing to screen for the potential presence of PHA-producer taxa. A total of three genes from the bacterial metagenome of and three genes from sediment isolates ( UMTKB-6, UMTKB-7, UMTKB-8) were identified. Produced PHA polymers were shown to be composed of 5C to C monomers, with previously unreported PHA-producing ability of the strain, as well as a 3-hydroxyvalerate-synthesising ability without precursor addition by the strain.
PubMed: 36296332
DOI: 10.3390/microorganisms10102057