Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:6.3.4.6 (urease)
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Strain SN-82(T) was isolated from the sea-surface microlayer at Keelung on the north-east coast of Taiwan. Sequence analysis of the D1/D2 domain of the 26S rDNA of strain SN-82(T) suggested that this strain is related to the aerius clade in the Filobasidiales. Phenotypic characteristics such as the absence of sexual structures and ballistoconidia, the assimilation of myo-inositol and d-glucuronate, the inability to ferment glucose, the possession of coenzyme Q-10 and positive Diazonium blue B and urease reactions also indicated that this strain belongs to the genus Cryptococcus. However, divergences of more than 3.6 % were observed in the D1/D2 domain when compared with other described Cryptococcus species, which indicated that the isolated yeast represents a previously unrecognized member of this genus. Therefore, the novel yeast species Cryptococcus keelungensis sp. nov. is proposed, with strain SN-82(T) (=CBS 10876(T) =BCRC 23107(T) =JCM 14893(T)) as the type strain.
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PMID:Cryptococcus keelungensis sp. nov., an anamorphic basidiomycetous yeast isolated from the sea-surface microlayer of the north-east coast of Taiwan. 1906 91

During a survey of yeast strains having high conversion efficiency to ethanol from cellobiose, 'Ogataea pini' ATCC 28781 and 'Pichia pini' NBRC 1794 were found to be distinct from any known species and from each other by a BLAST homology search using the D1/D2 LSU rRNA gene sequences. The D1/D2 phylogeny showed that 'O. pini' ATCC 28781 and 'P. pini' NBRC 1794 belonged to the Ogataea cluster, whereas a comparison of the ITS 1 and 2 regions sequences showed that the ATCC and NBRC strains each formed a species distinct from O. ganodermae, O. pini, O. henricii, and P. zsoltii, based on the D1/D2 sequence divergence. The ATCC and NBRC strains formed two to four hat-shaped ascospores and two to four, or more ones per deliquescent ascus, respectively, were negative for DBB and urease reactions, assimilated methanol slowly and nitrate not at all, and had the major ubiquinone system Q-7. These characteristics coincided basically with the definition of Ogataea proposed by Yamada et al. in 1994, excluding the number of ascospores. On the other hand, the ATCC and NBRC strains differed not only from each other but from relatives in various phenotypic characteristics. These differences suggest that two new yeasts of Ogataea be described as novel. The new species and their type strains are as follows: O. neopini ATCC 28781(T); and O. corticis NBRC 1794(T). In addition, the emendation of the genus Ogataea is made; besides, we propose the transfer of P. zsoltii, P. dorogensis, and P. trehaloabstinens, which were placed in the Ogataea cluster based on the D1/D2 sequence analysis, to the genus Ogataea as O. zsoltii comb. nov., O. dorogensis comb. nov., and O. trehaloabstinens comb. nov.
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PMID:Ogataea neopini sp. nov. and O. corticis sp. nov., with the emendation of the ascomycete yeast genus Ogataea, and transfer of Pichia zsoltii, P. dorogensis, and P. trehaloabstinens to it. 1916 78

A Gram-negative, aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated TR6-06(T), was isolated from a compost sample in South Korea and characterized taxonomically by using a polyphasic approach. The organism grew optimally at 30 degrees C and pH 6.5-7.0. The isolate was positive for catalase and oxidase tests, but negative for gelatinase and urease and for indole and H(2)S production. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain TR6-06(T) was most closely affiliated with members of the genus Pedobacter of the family Sphingobacteriaceae. Strain TR6-06(T) exhibited 16S rRNA gene sequence similarity values of 89.9-93.5 % to the type strains of species of the genus Pedobacter. The G+C content of the genomic DNA of strain TR6-06(T) was 41.9 mol%. The predominant respiratory quinone was MK-7. The major fatty acids were iso-C(15 : 0), iso-C(17 : 0) 3-OH, C(16 : 1)omega7c and anteiso-C(15 : 0). These chemotaxonomic data support the affiliation of strain TR6-06(T) to the genus Pedobacter. However, on the basis of its phenotypic properties and phylogenetic distinctiveness, strain TR6-06(T) (=KCTC 12638(T)=LMG 23490(T)) should be classified as the type strain of a novel species, for which the name Pedobacter composti sp. nov. is proposed.
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PMID:Pedobacter composti sp. nov., isolated from compost. 1919 76

Three strains of a novel anamorphic yeast species were isolated from natural samples collected in Thailand, including strain EF10 isolated from sediment in a mangrove forest, strain ST-473 from rotten wood, and strain ST-479 from a wild mushroom (Hygrophorus sp.). Analysis of the D1/D2 domains of the large-subunit rRNA gene sequence revealed that the sequence of strain EF10 differed from the other two strains (ST-473 and ST-479), which had identical sequences, by only one nucleotide (nt) substitution in 535 nt. The closest species in terms of pairwise sequence similarity was Saturnispora mendoncae, with 32 nt substitutions and seven gaps in 535 nt. Phylogenetic analysis demonstrated that the three strains form a cluster with S. mendoncae and the other eight species in the Saturnispora clade. Phenotypic characteristics of the three strains were the same including proliferation by multilateral budding, absence of ascospores and negative diazonium blue B and urease reactions. The major ubiquinone was Q-7. On this basis, the three strains were assigned to a single novel species of the genus Candida, for which the name Candida siamensis sp. nov. is proposed. The type strain is EF10(T) (=BCC 29901(T)=NBRC 104878(T)=CBS 11022(T)).
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PMID:Candida siamensis sp. nov., an anamorphic yeast species in the Saturnispora clade isolated in Thailand. 1923 99

A novel, non-pigmented, slow-growing mycobacterium was identified on the basis of biochemical and nucleic acid analyses, as well as growth characteristics. Three isolates were cultured from clinical samples (two from sputum and one from pus in lymph nodes) obtained from three immunocompetent patients with infections. Bacterial growth occurred at 28-42 degrees C on Middlebrook 7H11-OADC agar. The isolates showed negative results for Tween hydrolysis, nitrate reductase, semiquantitative catalase, urease activity, 3 day arylsulfatase activity, pyrazinamidase, tellurite reduction and niacin accumulation tests, but positive results for 14 day arylsulfatase activity and heat-stable catalase tests. The isolates contained alpha-, keto-, and dicarboxymycolates in their cell walls. Sequence analysis revealed that all isolates had identical, unique 16S rRNA sequences. Phylogenetic analysis of the 16S rRNA, rpoB, hsp65 and sodA gene sequences confirmed that these isolates are unique but closely related to Mycobacterium celatum. DNA-DNA hybridization of the isolates demonstrated less than 50 % reassociation with M. celatum and Mycobacterium branderi. On the basis of these findings, a novel species designated Mycobacterium kyorinense sp. nov. is proposed. The type strain is KUM 060204(T) (=JCM 15038(T)=DSM 45166(T)).
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PMID:Mycobacterium kyorinense sp. nov., a novel, slow-growing species, related to Mycobacterium celatum, isolated from human clinical specimens. 1950 12

Three Arcobacter isolates, recovered from mussels (genus Mytilus), and one isolate from brackish water in Catalonia (north-east Spain) showed a novel pattern using a recently described identification method for members of the genus Arcobacter, 16S rRNA gene RFLP. Enterobacterial repetitive intergenic consensus PCR fingerprinting demonstrated that the three isolates from mussels belonged to two genotypes and that the fourth isolate from water belonged to a third genotype. Analysis of the 16S rRNA and rpoB gene sequences showed that the new isolates formed a separate lineage within the genus Arcobacter. This was also confirmed by the low DNA-DNA relatedness values (16-30 %) of the isolates with the type strains of recognized Arcobacter species. Hydrolysis of indoxyl acetate, a characteristic trait for all species of the genus Arcobacter, was negative for the novel isolates. The susceptibility of the novel isolates to cefoperazone, together with the lack of urease production and nitrate reduction, further enabled them to be differentiated from recognized Arcobacter species based on physiological characteristics. Genotypic and phenotypic characteristics indicated that the new isolates represent a novel species of the genus Arcobacter, for which the name Arcobacter mytili sp. nov. is proposed, with the type strain F2075(T) (=CECT 7386(T) =LMG 24559(T)). The DNA G+C content of strain F2075(T) was 26.9 mol%.
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PMID:Arcobacter mytili sp. nov., an indoxyl acetate-hydrolysis-negative bacterium isolated from mussels. 1950 22

A collection of 12 strains, isolated from diseased tortoises and tentatively identified as [Pasteurella] testudinis-like based on phenotypic characters, was compared with three reference strains of [P.] testudinis. All strains could be separated from the reference strains with respect to 16S rRNA gene sequences, partial sequences of the rpoB housekeeping gene and by phenotypic characters. Based upon differences in 16S rRNA and rpoB gene sequences, the new isolates are suggested to represent a novel species in a new genus of the family Pasteurellaceae Pohl 1981, for which the name Chelonobacter oris gen. nov., sp. nov. is proposed. The type strain is 1662(T) (=CCUG 55632(T)=DSM 21392(T)). beta-Haemolysis and acid production from (+)-l-arabinose, dulcitol, (-)-d-mannitol, (+)-d-mannose, trehalose and salicin separated the new strains from members of existing genera of the family Pasteurellaceae, in addition to the beta-galactosidase, urease and alpha-glucosidase reactions. Differences in indole production, phosphatase, beta-glucosidase and production of acid from dulcitol and trehalose separated C. oris from [P.] testudinis. Several phenotypic characters separated C. oris from Bisgaard's taxa 14 and 32.
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PMID:Comparative studies on [Pasteurella] testudinis and [P.] testudinis-like bacteria and proposal of Chelonobacter oris gen. nov., sp. nov. as a new member of the family Pasteurellaceae. 1957 48

The Mycobacterium avium complex (MAC) consists of four recognized species, Mycobacterium avium, Mycobacterium colombiense, Mycobacterium intracellulare and Mycobacterium chimaera, and a variety of other strains that may be members of undescribed taxa. We report on two isolates of a scotochromogenic, slowly growing, non-tuberculous Mycobacterium species within the M. avium complex from a lymph node and an infected wound after a dogbite of separate patients in The Netherlands. The extrapulmonary infections in immunocompetent patients suggested a high level of virulence. These isolates were characterized by a unique nucleotide sequence in the 16S rRNA gene, 99% similar to Mycobacterium colombiense, and the MAC-Q 16S-23S internal transcribed spacer (ITS) sequence. Sequence analyses of the hsp65 gene revealed 97% similarity to M. avium. The rpoB gene sequence was 98% similar to M. colombiense. Phenotypically, the scotochromogenicity, positive semi-quantitative catalase and heat-stable catalase tests, negative tellurite reductase and urease tests and susceptibility to hydroxylamine and oleic acid set these isolates apart from related species. High-performance liquid chromatography analysis of cell-wall mycolic acid content revealed a unique pattern, related to that of M. avium and M. colombiense. Together, these findings supported a separate species status within the Mycobacterium avium complex. We propose elevation of scotochromogenic M. avium complex strains sharing this 16S gene and MAC-Q ITS sequence to separate species status, for which the name Mycobacterium vulneris sp. nov. is proposed. The type strain is NLA000700772T (=DSM 45247T=CIP 109859T).
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PMID:Proposal to elevate Mycobacterium avium complex ITS sequevar MAC-Q to Mycobacterium vulneris sp. nov. 1962 Mar 76

During a Danish study on the prevalence of campylobacteria in pig abortions and food of animal origin, eight Gram-negative, slightly curved, rod-shaped, non-spore-forming bacteria were clustered by using amplified fragment length polymorphism analysis in a distinct phenon within the genus Arcobacter. In the present study, numerical analysis of whole-cell protein profiles also showed that all isolates clustered in a single group distinct from other recognized Arcobacter species. DNA-DNA hybridization among two representative strains exhibited a mean DNA-DNA relatedness value of 79 %. DNA-DNA hybridization with the type strains of recognized Arcobacter species revealed levels of DNA-DNA relatedness of 41 % or less. The DNA G+C content of the type strain was 28.5 mol%. Pairwise comparison of the 16S rRNA gene sequences with those of the type strains of established species identified Arcobacter cryaerophilus (97.9 %), Arcobacter cibarius (97.5 %) and Arcobacter skirrowii (97.2 %) as the nearest phylogenetic neighbours. The isolates could be distinguished from other Arcobacter species by means of the following biochemical tests: activities of catalase and urease, reduction of nitrate and growth on minimal medium, lack of growth at 37 degrees C under standardized aerobic and microaerobic conditions, in 4 % NaCl and 1 % glycine media. Finally, DNA fingerprints obtained by using enterobacterial repetitive intergenic consenus-PCR showed that the eight isolates represent eight strains of a single novel Arcobacter species, for which the name Arcobacter thereius sp. nov. is proposed. The type strain is LMG 24486(T) (=CCUG 56902(T)).
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PMID:Arcobacter thereius sp. nov., isolated from pigs and ducks. 1962 51

Slowly growing, scotochromogenic bacteria of a novel Mycobacterium species were isolated from lymph node samples in two children and pulmonary samples in two elderly patients from different regions in the Netherlands as well as from a surface water sample in Zambia. Its 16S rRNA gene, 16S-23S internal transcribed spacer (ITS), hsp65 and rpoB gene sequences are unique in comparison with other mycobacteria. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that these micro-organisms are most closely related to Mycobacterium scrofulaceum ATCC 19981(T) (8 differences; 0.6 % divergence). The hsp65 sequence shows 96 % similarity to that of Mycobacterium saskatchewanense MB54784 and the rpoB sequence shows 95 % similarity to that of Mycobacterium chimaera CIP 107892(T). The 16S-23S ITS sequence places these micro-organisms within the Mycobacterium avium complex, as a novel ITS sequevar. This is not supported by analysis of the 16S rRNA, hsp65 or rpoB gene sequences. Their scotochromogenicity, combined with mostly positive urease, positive semiquantitative catalase and negative tellurite reduction tests, set these isolates apart from related species. The mycolic acid patterns, obtained by HPLC, are similar to that of Mycobacterium scrofulaceum, though the peak heights and distribution present minor differences. We propose the name Mycobacterium mantenii sp. nov. for this novel species. The type strain, isolated from a lymph node biopsy sample, is strain 04-1474(T) (=NLA000401474(T) =CIP 109863(T) =DSM 45255(T)).
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PMID:Mycobacterium mantenii sp. nov., a pathogenic, slowly growing, scotochromogenic species. 1962 25


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