Isolation and characterization of a novel facultatively alkaliphilic Nitrobacter species, N. alkalicus sp. nov

BACKGROUND: The American College of Rheumatology (ACR) established criteria to discriminate among patients with seven types of vasculitis. Although designated as "classification criteria" for research, these criteria are often used for diagnosis. OBJECTIVE: To examine the operating characteristics of the 1990 ACR classification criteria in the diagnosis of Wegener granulomatosis, giant-cell arteritis, polyarteritis nodosa, and hypersensitivity vasculitis. DESIGN: Prospective cohort study. SETTING: University medical center and Veterans Affairs medical center. PATIENTS: 198 consecutive patients referred to rheumatologists for evaluation of possible vasculitis. Measurements: Blinded chart audits were done to classify patients according to the 1990 ACR classification criteria for Wegener granulomatosis, polyarteritis nodosa, giant-cell arteritis, and hypersensitivity vasculitis on the basis of the patients' initial presentation. Chart audits done 2 to 8 months after baseline provided the patients' final diagnoses, which were considered the gold standard, as in the development of the ACR criteria. Test operating characteristics of the ACR classification criteria were calculated according to 2 x 2 tables for the entire cohort and for only the patients with a final diagnosis of vasculitis. RESULTS: Vasculitis was diagnosed in 51 (26%) patients. Thirty-eight (75%) of 51 patients with vasculitis and 31 (21%) of 147 patients without vasculitis met ACR criteria for one or more types of vasculitis. The positive predictive values for the four vasculitides according to ACR criteria were 17% to 29% for the entire cohort and 29% to 75% for only the patients with a final diagnosis of vasculitis. CONCLUSION: The 1990 ACR classification criteria function poorly in the diagnosis of specific vasculitides.     

Stetteria hydrogenophila, gen. nov. and sp. nov., a novel mixotrophic sulfur-dependent crenarchaeote isolated from Milos, Greece

To test the therapeutic efficacy of levamisole, 5-week-old DBA/2 mice were inoculated intraperitoneally with 10 plaque-forming units of encephalo-myocarditis virus. Levamisole (2.5 mg/kg/per day) was administered intraperitoneally daily, starting simultaneously with the virus inoculation, in experiment I for 14 days, and daily on days 14 to 28 in experiment II in mice that survived to 14 days after virus inoculation. In experiment I, survival was higher, the severity of myocarditis was less, and myocardial virus titers were lower in treated than in untreated animals. In experiment II, levamisole was not effective. No significant changes in serum neutralizing antibody titers occurred in either experiment. Furthermore, levamisole prevented associated lymphoid organ atrophy induced by the virus infection. An additional in vitro study revealed the absence of anti-viral activity of the drug. Thus, levamisole may have favorable effects upon encephalomyocarditis virus myocarditis by preventing the virus-induced lymphoid organ atrophy and reducing myocardial virus replication in the acute stage.     

Amaricoccus gen. nov., a gram-negative coccus occurring in regular packages or tetrads, isolated from activated sludge biomass, and descriptions of Amaricoccus veronensis sp. nov., Amaricoccus tamworthensis sp. nov., Amaricoccus macauensis sp. nov., and Amaricoccus kaplicensis sp. nov

Three isolates of gram-negative bacteria, strains Ben 102T, Ben 103T, and Ben 104T, were obtained in pure culture by micromanipulation from activated sludge biomass from wastewater treatment plants in Italy, Australia, and Macau, respectively. These isolates all had a distinctive morphology; the cells were cocci that usually were arranged in tetrads. Based on this criterion, they resembled other bacteria from activated sludge previously called "G" bacteria. On the basis of phenotypic characteristics and the results of 16S ribosomal DNA sequence analyses, the three isolates were very similar to each other, but were sufficiently different from their closest phylogenetic relatives (namely, the genera Rhodobacter, Rhodovulum, and Paracoccus in the alpha subdivision of the Proteobacteria) to be placed in a new genus, Amaricoccus gen. nov. Each of the three isolates represents a new species of the genus Amaricoccus; strains Ben 102T, Ben 103T, and Ben 104T are named Amaricoccus veronensis, Amaricoccus tamworthensis, and Amaricoccus macauensis, respectively. An isolate designated Ben 101T, which was isolated independently by Cech and Hartman in Kaplice, Czech Republic, was also characterized and belongs to the same genus. We propose that the isolate of Cech and Hartman should be placed in another new species, Amaricoccus kaplicensis.     

Vibrio trachuri sp. nov., a new species isolated from diseased Japanese horse mackerel

A new species, Vibrio trachuri sp. nov., was isolated from the cultured Japanese horse mackerel (Trachurus japonicus). These Vibrio were Gram negative, motile rods and formed yellow colonies on BTB teepol and TCBS plate, turned TSI medium to yellow and was sensitive to 150 microM O/129 (2,4-diamino-6,7-diisopropyl pteridine phosphate) like Listonella anguillarum which has been described as Vibrio anguillarum. However, the results of VP test and decarboxylation of lysine or dihydrolation of arginine suggested that these Vibrio are rather closely related to V. parahaemolyticus. DNA similarity determined by the microplate hybridization technique revealed that these Vibrio are genetically quite distant from Listonella anguillarum or V. parahaemolyticus and rather close to V. harveyi, although there was no Vibrio species which had more than 70% similarity value. From these results we propose to nominate Vibrio trachuri sp. nov. for this new Vibrio species.     

Bogoriella caseilytica gen. nov., sp. nov., a new alkaliphilic actinomycete from a soda lake in Africa

A new gram-positive, alkaliphilic, nonsporulating, rod-shaped bacterium is described. The organism was isolated from soda soil (Lake Bogoria, Kenya) and has the following characteristics. It is nonmotile, not acid fast, halotolerant, and microaerophilic, and optimal growth occurs at pH values between 9 and 10. The peptidoglycan type is of type A4 alpha, with lysine as the characteristic diamino acid and glutamic acid as a component of the interpeptide bridge. The major menaquinone is MK-8(H4). The polar lipids are phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, and an unknown phospholipid. 12-Methyltetradecanoic acid is the predominant fatty acid. The G + C content of the DNA is 70 mol%. The results of 16S ribosomal DNA sequence comparisons revealed that strain HKI 0088T represents a new lineage in the order Actinomycetales. Therefore, we concluded that strain HKI 0088T should be assigned to a new genus and species, for which we propose the name Bogoriella caseilytica gen. nov., sp. nov. The type strain and only strain of this genus and species is HKI 0088 (= DSM 11294).     

Alterococcus agarolyticus, gen.nov., sp.nov., a halophilic thermophilic bacterium capable of agar degradation

Five strains of facultatively anaerobic moderately thermophilic bacteria were isolated from two hot springs in the intertidal zone of Lutao, Taiwan. They produced extracellular agarase on agar medium, yielding reducing sugars and organic acids as the end products under either aerobic or anaerobic conditions. The growth temperature range was approximately 38-58 degrees C with an optimal temperature of about 48 degrees C. The five strains tolerated a relatively narrow pH range from 7.0 to 8.5. They were Gram-negative halophiles growing optimally at 2.0-2.5% NaCl (ca. 0.34-0.43 M). They were capable of anaerobic growth by fermenting glucose and producing various organic acids such as butyrate, propionate, formate, lactate, and acetate. Cells grown in liquid medium were motile monotrichous cocci, normally 0.8-0.9 micron in diameter. They possessed saturated anteiso-15-carbon acid (anteiso-C15:0) as the most abundant cellular fatty acid (46.0-51.3 mo1%) and had G + C contents ranging from 65.5 to 67.0 mo1%. They are the first thermophiles found to degrade agar and also the first halophilic thermophilic bacteria known to be capable of both aerobic and anaerobic fermentative growth. These bacteria are considered to represent a new genus that we named Alterococcus, and Alterococcus agarolyticus is the type species.     

Corynebacterium riegelii sp. nov., an unusual species isolated from female patients with urinary tract infections

Four strains of an unknown coryneform bacterium were isolated in pure culture from females with urinary tract infections. Strong urease activity and the ability to slowly ferment maltose but not glucose were the most significant phenotypic features of this catalase-positive, nonmotile, nonlipophilic, rod-shaped bacterium which served to distinguish it from all other presently defined coryneform bacteria. Chemotaxonomic investigations demonstrated that the unknown bacterium belonged to the genus Corynebacterium. Comparative 16S rRNA gene sequence analysis revealed that the isolates were genealogically identical and represented a new subline within the genus Corynebacterium, for which the designation Corynebacterium riegelii sp. nov. is proposed. The type strain of Corynebacterium riegelii is CCUG 38180 (DSM 44326, CIP 105310).     

Massilia timonae gen. nov., sp. nov., isolated from blood of an immunocompromised patient with cerebellar lesions

A fastidious, slowly growing, strictly aerobic, gram-negative bacterium was isolated from a culture of blood from a 25-year-old man with common variable immunodeficiency. The man had been admitted to hospital with febrile progressive cerebellar ataxia. The use of standard phenotypic schemes did not lead to identification, but sequence analysis demonstrated that the 16S rRNA gene of the isolate was most similar to those of the environmental bacteria Duganella zoogloeoides (formerly Zoogloea ramigera 115) and Telluria mixta. Further characterization of the bacterium by biochemical analysis, electron microscopy, G+C content estimation, and fatty acid analysis demonstrated significant differences between the bacterium and D. zoogloeoides and Telluria species; thus, we propose it as a new taxon with the name Massilia timonae gen. nov., sp. nov.     

Luteococcus japonicus gen. nov., sp. nov., a new gram-positive coccus with LL-diaminopimelic acid in the cell wall

A new gram-positive, nonmotile coccus is described. Strains IFO 12422T (T = type strain) and IFO 15385 in the Institute for Fermentation, Osaka, culture collection, which were isolated from soil and water, respectively, have the following chemotaxonomic characteristics: menaquinone MK-9(H4); G + C content of DNA of 67 mol%; and LL-diaminopimelic acid, alanine, glycine, and glutamic acid in a molar ratio of ca. 1:2:1:1 (type A3 gamma). Mycolic acids are not present. The taxonomic characteristics of these organisms are different from those of previously described gram-positive, high-G + C-content cocci. The partial 16S rRNA sequence indicated that IFO 12422T represents a distinct line of descent among gram-positive bacteria with a high G + C content. The name Luteococcus japonicus gen. nov., sp. nov. is proposed. The type strain is strain IFO 12422.     

Thermotoga hypogea sp. nov., a xylanolytic, thermophilic bacterium from an oil-producing well

A new thermophilic, xylanolytic, strictly anaerobic, rod-shaped bacterium, strain SEBR 7054T, was isolated from an African oil-producing well. Based on the presence of an outer sheath (toga) and 16S rRNA sequence analysis data, this organism was identified as a member of the genus Thermotoga. Strain SEBR 7054T possessed lateral flagella, had a G + C content of 50 mol%, produced traces of ethanol from glucose but no lactate, and grew optimally in the presence of 0 to 0.2% NaCl at 70 degrees C. Its phenotypic and phylogenetic characteristics clearly differed from those reported for the five previously validly described Thermotoga species. Therefore, we propose that strain SEBR 7054T is a member of a new species of the genus Thermotoga, Thermotoga hypogea sp. nov. The type strain of T. hypogea is SEBR 7054 (= DSM 11164).     

Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall

Two strains of a new gram-positive coryneform bacterium isolated from soil and from a sandstone surface are described. Strain 2002-39/1T (T = type strain) is a coccoid, nonmotile, non-acid-fast, microaerophilic organism. The menaquinones of this strain are MK-12 and MK-11, and the main components of the whole-cell sugars are glucose and rhamnose. No mycolic acids are present. The G+C content of the DNA is 74 mol%. Comparative 16S ribosomal DNA studies and a cell wall analysis revealed that this strain represents a new genus belonging to the group of actinomycetes that have diaminobutyric acid in their peptidoglycans. The second strain, strain ST54, which was isolated from a sandstone surface, had the same characteristic features as strain 2002-39/1T. The name Agrococcus jenensis gen. nov., sp. nov., is proposed for these organisms. The type strain is strain 2002-39/1, which has been deposited in the German Collection of Microorganisms and Cell Cultures as strain DSM 9580.     

Isolation of Arthrobacter spp. from clinical specimens and description of Arthrobacter cumminsii sp. nov. and Arthrobacter woluwensis sp. nov

Arthrobacter spp. are very widely distributed in the environment (e.g., soil) but have not been described as causing disease in humans. Over a 6-year period, two reference laboratories isolated or received 11 strains which were eventually identified as belonging to the genus Arthrobacter. These strains had been initially identified as Centers for Disease Control and Prevention coryneform group B-1 and B-3 bacteria (whitishgrayish colonies of 2 mm or greater in diameter after 24 h of incubation, respiratory metabolism, absent or weak acid production from sugars, and hydrolysis of gelatin). However, chemotaxonomic investigations revealed lysine as the diamino acid of the cell wall and the presence of branched cellular fatty acids (with anteiso-pentadecanoic acid predominating) which was compatible with an assignment of the 11 isolates to the genus Arthrobacter only. Peptidoglycan and 16S rRNA gene sequence analyses demonstrated that three of the strains studied were representatives of a new Arthrobacter species for which the name Arthrobacter cumminsii sp. nov. is proposed and that one other strain represented a second new Arthrobacter species for which the name Arthrobacter woluwensis sp. nov. is proposed. This report is the first on the isolation of Arthrobacter spp. from clinical specimens.     

Meiothermus cerbereus sp. nov., a new slightly thermophilic species with high levels of 3-hydroxy fatty acids

Strains of Meiothermus cerbereus sp. nov. were isolated from the hot springs within the Geysir geothermal area of Iceland. The strains of Meiothermus cerbereus produce red-orange-pigmented colonies, have an optimum growth temperature of about 55 degrees C, and have higher levels of 3-OH fatty acids than the strains of the other species of the genus Meiothermus. These strains, unlike all other strains of the species of the genus Meiothermus examined previously, required cysteine, thiosulfate, or thioglycolate for growth in liquid Thermus medium, but not in the corresponding medium solidified with agar. Several strains belonging to Meiothermus silvanus, isolated from Geysir, also required reduced sulfur compounds for growth in liquid medium, leading to the hypothesis that this requirement is not a taxonomic characteristic of the new species. The new species represented by strains GY-1T and GY-5 can be distinguished from the other species of the genus Meiothermus by biochemical characteristics, fatty acid composition, DNA-DNA reassociation values, and 16S ribosomal DNA sequence. The type strain for Meiothermus cerbereus is GY-1 (= DSM 11376).     

Characterization of Eubacterium coprostanoligenes sp. nov., a cholesterol-reducing anaerobe

A small, anaerobic, gram-positive coccobacillus that reduces cholesterol to coprostanol was isolated from a hog sewage lagoon. This isolate, strain HLT (T = type strain) does not require cholesterol for growth, but it requires lecithin and has phospholipase activity. Much acid is produced by the fermentation of amygdalin, lactose, and salicin. Arabinose, cellobiose, fructose, glucose, mannose, and melibiose are fermented weakly. Acetic, formic, and succinic acids are produced, as is hydrogen. The isolate does not reduce nitrate, produce indole, or hydrolyze starch and gelatin. Esculin is hydrolyzed. The properties of strain HLT are most similar to those of members of the genus Eubacterium. Because strain HL (= ATCC 51222) has unique morphological and physiological properties, we propose that it should be the type strain of a new species in the genus Eubacterium, Eubacterium coprostanoligenes.     

Desulfovibrio aminophilus sp. nov., a novel amino acid degrading and sulfate reducing bacterium from an anaerobic dairy wastewater lagoon

A mesophilic strain of sulfate-reducing bacterium, designated ALA-3T (T = type strain), was isolated from an anaerobic lagoon of a dairy wastewater treatment plant. The curved, Gram-negative, non-sporeforming cells (0.2 x 3.0-4.0 microns) existed singly or in chains, and were motile by single polar flagella. Optimum growth occurred at 35 degrees C and pH 7.5 on a medium containing lactate and sulfate. Thiosulfate or sulfite but not elemental sulfur, nitrate, or fumarate could also replace sulfate as an electron acceptor. Formate, alanine, aspartate, leucine, isoleucine, valine, and methionine, H2/CO2 and ethanol also served as electron donors with sulfate as an electron acceptor. Pyruvate, casamino acids, peptone, serine, glycine, cysteine and threonine were fermented. Sulfite and thiosulfate were disproportionated to sulfate and sulfide. The G + C content of the DNA was 66 mol % G + C. Phylogenetic analysis revealed that Desulfovibrio africanus was the nearest relative (similarity of 89%). Strain ALA-3T is physiologically and phylogenetically different from other Desulfovibrio species, and is designated Desulfovibrio aminophilus sp. nov. (DSM 12254).     

Methanogenium frigidum sp. nov., a psychrophilic, H2-using methanogen from Ace Lake, Antarctica

Methanogenium frigidum sp. nov. was isolated from the perennially cold, anoxic hypolimnion of Ace Lake in the Vesfold Hills of Antarctica. The cells were psychrophilic, exhibiting most rapid growth at 15 degrees C and no growth at temperatures above 18 to 20 degrees C. The cells were irregular, nonmotile coccoids (diameter, 1.2 to 2.5 microns) that occurred singly and grew by CO2 reduction by using H2 as a reductant. Formate could replace H2, but growth was slower. Acetate, methanol, and trimethylamine were not catabolized. Cells grew with acetate as the only organic compounds in the culture medium, but growth was much faster in medium also supplemented with peptones and yeast extract. The cells were slightly halophilic; good growth occurred in medium supplemented with 350 to 600 mM Na+, but no growth occurred with 100 or 850 mM Na+. The pH range for growth was 6.5 to 7.9; no growth occurred at pH 6.0 or 8.5. Growth was slow (maximum specific growth rate, 0.24 day-1; doubling time, 2.9 days). This is the first report of a psychrophilic methanogen growing by CO2 reduction.     

Pathogenicity of Spiroplasma sp. strain SMCA in Syrian hamsters: clinical, microbiological, and histological aspects

The intracerebral inoculation of newborn Syrian hamsters with pure cultures of Spiroplasma sp. strain SMCA caused severe, prolonged disease involving the central nervous system, culminating in death. The disease was characterized by spasms, muscular tremors, disturbances in motor control, inability to feed, dramatic loss of weight, and runting. The effect ws dose related, with the largest numbers of viable spiroplasmas producing the highest incidence of disease and death in the shortest period of time. Severe hemorrhaging developed throughout the brain, liver, and spleen, and spiroplasmas were readily recovered from these organs, indicating that the agent disseminated from the initial site of infection to distant host tissues. Newborn animals were susceptible, but adults were resistant; these findings are similar to those reported for newborn mice and rats. Unlike mice and rats, hamsters did not develop cataracts visible to the unaided eye. The histopathological features of eye disease in hamsters were different from those in rats and were characterized by microophthalmia (especially in runted hamsters) and abnormal proliferation, disorientation, and disorganization of corneal, lens, and retinal tissues. The significance of these findings is discussed.     

Spiroplasma platyhelix sp. nov., a new mollicute with unusual morphology and genome size from the dragonfly Pachydiplax longipennis

Spiroplasma strain PALS-1T from the gut of the dragonfly Pachydiplax longipennis was shown to be distinct from other species, groups, and subgroups of the genus Spiroplasma as determined by reciprocal serological metabolism inhibition and deformation tests. However, this strain cross-reacted extensively with representatives of other groups when it was used as an antigen. Electron microscopy of cells of strain PALS-1T revealed cells surrounded by a single cytoplasmic membrane. Light microscopy revealed helical cells that exhibited twisting motility rather than rotatory or flexing motility. Variations in the tightness of coiling were transmitted from one end of the helix to the other. The strain was resistant to penicillin, which confirmed that no cell wall was present. The organism grew well in M1D and SP-4 liquid media under either aerobic or anaerobic conditions. Growth also occurred in 1% serum fraction medium and in conventional horse serum medium. The optimum temperature for growth was 30 degrees C, at which the doubling time was 6.4 h. Multiplication occurred at temperatures from 10 to 32 degrees C. Strain PALS-1T catabolized glucose and hydrolyzed arginine but not urea. The guanine-plus-cytosine content of the DNA was 29 +/- 1 mol%. The genome size was 780 kbp, the smallest genome size in the genus Spiroplasma. Strain PALS-1 (= ATCC 51748) is designated the type strain of a new species, Spiroplasma platyhelix.     

Xanthobacter tagetidis sp. nov., an organism associated with Tagetes species and able to grow on substituted thiophenes

Members of the marigold genus of flowering plants (the genus Tagetes), which synthesize and accumulate thiophene compounds in their roots, were investigated as potential sources of bacteria able to degrade substituted thiophenes. Batch and continuous enrichment cultures inoculated with compost from root balls of Tagetes patula and Tagetes erecta reproducibly produced the same predominant type of bacterium when they were supplied with thiophene-2-carboxylate (T2C) or thiophene-2-acetate (T2A) as a carbon and energy substrate. This organism was a yellow-pigmented, neutrophilic, mesophilic, gram-negative, pleomorphic, rodshaped bacterium, which we classify as a new species of the genus Xanthobacter, Xanthobacter tagetidis; strain TagT2C (= DSM 11105) is the type strain. Strain TagT2CT (T = type strain) grew on simple thiophenes, such as T2C, thiophene-3-carboxylate, and T2A, on analogs of these compounds (pyrrole-2-carboxylate and furan-2-carboxylate), and on the condensed thiophene dibenzothiophene. X. tagetidis was facultatively autotrophic, fixing carbon dioxide by means of ribulose bisphosphate carboxylase, and was able to grow on hydrogen, thiosulfate, or sulfide as an energy substrate. It also grew on a wide range of other heterotrophic, chemolithotrophic, and methylotrophic substrates. Its growth on T2C was optimal at 28 to 31 degrees C and pH 7.6 to 7.8, and the maximum growth rate in batch culture was 0.22 h-1. The DNA base composition of X.tagetidis is 68 mol% G + C. A 16S ribosomal DNA sequence analysis of strain TagT2CT showed that this organism represents a distinct lineage within the Aquabacter-Azorhizobium-Xanthobacter cluster of the alpha-2 subclass of the Pro-teobacteria. Discrimination of X. tagetidis from the other genera in this group and from other Xanthobacter species is discussed.     

Description of Gemella sanguinis sp. nov., isolated from human clinical specimens

Six strains of a hitherto undescribed gram-positive, catalase-negative, facultatively anaerobic coccus isolated from human sources were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains were genealogically identical and constitute a new subline within the genus Gemella. The unknown bacterium was readily distinguished from Gemella haemolysans, Gemella bergeriae, and Gemella morbillorum by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Gemella sanguinis sp. nov. The type strain is CCUG 37820(T).