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).     

Thermothrix azorensis sp. nov., an obligately chemolithoautotrophic, sulfur-oxidizing, thermophilic bacterium

A new aerobic, obligately chemolithoautotrophic, thermophilic, sulfur-oxidizing bacterium, Thermothrix azorensis, was isolated from a hot spring on Sao Miguel Island in the Azores. The cells of this organism are gram negative, nonsporulating, and rod shaped. Filament formation appears to occur as a response to nonoptimal growth conditions. Growth occurs at 63 to 86 degrees C, and the optimum temperature is 76 to 78 degrees C. The optimum pH range for growth is 7.0 to 7.5. The G+C content of the DNA of our isolate is 39.7 mol%. This isolate uses thiosulfate, tetrathionate, hydrogen sulfide, and elemental sulfur as energy sources. Of particular interest are the absence of Calvin cycle enzymes and the initial appearance of sulfide during the lag phase of growth of aerobic cultures grown on elemental sulfur. The subsequent formation of thiosulfate is followed by oxidation of the thiosulfate to sulfate. T. azorensis differs from the only other Thermothrix species that has been described, Thermothrix thiopara, by having higher optimum and maximum growth temperatures, by being an obligate chemolithoautotroph, and by its close but separate position on a 16S rRNA sequence-based phylogenetic tree. Our T. azorensis isolate has been deposited in the American Type Culture Collection as strain ATCC 51754T (T = type strain).     

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.     

Riemerella anatipestifer gen. nov., comb. nov., the causative agent of septicemia anserum exsudativa, and its phylogenetic affiliation within the Flavobacterium-Cytophaga rRNA homology group

The phylogenetic position of the causative agent of septicemia anserum exsudativa, now most often referred to as [Moraxella] anatipestifer (brackets indicate a generically misnamed taxon) or "[Pasteurella] anatipestifer," was established by performing rRNA cistron similarity studies. [Moraxella] anatipestifer belongs to rRNA superfamily V, together with the genera Flavobacterium, Cytophaga, Flexibacter, Weeksella, Capnocytophaga, and Sphingobacterium. The detailed structure of rRNA superfamily V, which now contains five major rRNA homology groups, is described. An analysis of various phenotypic parameters, including new data (cellular proteins and fatty acids) and previously published data (respiratory quinones, enzyme activities, and classical phenotypic features), revealed that [Moraxella] anatipestifer differs in many aspects from its closest relatives, Flavobacterium indologenes, Flavobacterium gleum, Flavobacterium indoltheticum, Flavobacterium balustinum, Flavobacterium meningosepticum, and Weeksella zoohelcum. The combined genotypic and phenotypic data indicate that this organism should be placed in a separate genus; the name Riemerella anatipestifer gen. nov., comb. nov. is proposed for this bacterium. The specific epithet anatipestifer is kept in order to avoid nomenclatural confusion. However, it should be emphasized that the illness caused by this organism is a septicemic disease which is not restricted to ducks.     

Mycobacterium novocastrense sp. nov., a rapidly growing photochromogenic mycobacterium

A strain isolated from a biopsy sample taken from a slowly spreading skin granulation on a child's hand was found to have properties consistent with its classification in the genus Mycobacterium. An almost complete gene sequence of the 16S rRNA of the strain was determined following the cloning and sequencing of the amplified gene. The sequence was aligned with those available for mycobacteria, and phylogenetic trees were inferred with four tree-making algorithms. The organism, which formed a distinct phyletic line within the evolutionary radiation occupied by rapidly growing mycobacteria, was readily distinguished from members of validly described species of rapidly growing mycobacteria on the basis of its mycolic acid pattern and a number of other phenotypic features, notably its ability to form yellow pigmented colonies when incubated in the light. The name proposed for this new species is Mycobacterium novocastrense. The type strain is DSM 44203.     

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.     

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).     

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.     

Haloanaerobium lacusroseus sp. nov., an extremely halophilic fermentative bacterium from the sediments of a hypersaline lake

A new extremely halophilic chemoorganotrophic bacterium (strain H200T [T = type strain]) was isolated from the hypersaline sediments of Retba Lake in Senegal. This organism was a sluggishly motile, rod-shaped, non-spore-forming, gram-negative, obligate anaerobe that grew optimally at 40 degrees C in the presence of 180 to 200 g of NaCl per liter. The DNA base composition was 32 mol% guanine plus cytosine. The fermentation products from glucose were ethanol, acetate, H2, and CO2. Yeast extract was required for growth. The fermentable substrates included D-fructose, galactose, D-xylose, cellobiose, lactose, maltose, sucrose, starch, D-mannitol, glycerol, and Casamino Acids. On the basis of the results of a 16S rRNA sequence analysis, strain H200T was found to be related to Haloanaerobium species. The 16S rRNA sequence of strain H200T differed from the sequences of the three previously described Haloanaerobium species, and strain H200T also differed from these organisms in its NaCl range for growth (60 to 340 g/liter); strain H200T grew in the presence of the highest NaCl concentration recorded for any halophilic anaerobic organism, including the three previously described Haloanaerobium species. We propose that strain H200T (= DSM 10165) belongs to a new Haloanaerobium species, Haloanaerobium lacusroseus.     

Amycolatopsis alba sp. nov., isolated from soil

A new Amycolatopsis species isolated from soil produces a new glycopeptide antibiotic related to vancomycin. Traditional taxonomic methods and contemporary fatty acid analysis techniques were used to establish the position of this species. The hyphae fragment extensively when the organism is cultured in liquid media. The organism is characterized by white aerial hyphae that bear long chains of cylindrical conidia. The reverse side is yellowish brown; a faint light brown soluble pigment is occasionally produced. The organism has a type IV cell wall (meso-diaminopimelic acid), a type A whole-cell sugar pattern, and a type PII phospholipid pattern. Mycolic acids are not present in whole-cell hydrolysates. The major menaquinone is MK-9(H4); there is also a minor amount of MK-8(H4). The name proposed for this new species is Amycolatopsis alba. The type strain is strain A83850 (= NRRL 18532).     

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).     

Phenotypic and phylogenetic characterization of some Gemella-like organisms from human infections: description of Dolosigranulum pigrum gen. nov., sp. nov

A phylogenetic analysis was performed on two previously uncharacterized Gram-positive, catalase-negative bacteria from clinical sources. 16S rRNA sequencing studies revealed the isolates represent a new line of descent within the lactic acid group of bacteria. On the basis of the phylogenetic findings and phenotypic distinctiveness of the organisms, it is proposed that they be classified in a new genus Dolosigranulum, as Dolosigranulum pigrum sp. nov. The type strain of Dolosigranulum pigrum is NCFB 2975.     

Spiroplasma lineolae sp. nov., from the horsefly Tabanus lineola (Diptera: Tabanidae)

Spiroplasma strain TALS-2T from the viscera of the striped horsefly, Tabanus lineola, collected in Georgia was serologically distinct from other Spiroplasma species, groups, putative groups, and subgroups. Light and electron microscopy of cells of strain TALS-2T revealed helical motile cells surrounded only by a single cytoplasmic membrane. The organism grew in M1D and SP-4 liquid media. Growth also occurred in 1% serum fraction medium and in conventional horse serum medium. Growth in liquid media was serum dependent. The strain passed through 220-nm filter pores, but was retained in filters with 100-nm pores. The optimum temperature for growth was 30 degrees C. Multiplication occurred at temperatures from 20 to 37 degrees C, with a doubling time at the optimum temperature of 5.6 h in M1D broth. Strain TALS-2T catabolized glucose but hydrolyzed neither arginine nor urea. The guanine-plus-cytosine content of the DNA was 25 +/- 1 mol%. The genome size was 1,390 kbp. Six isolates serologically similar to strain TALS-2T were obtained from the same host in coastal Georgia. Three strains closely related to strain TALS-2T were isolated from the horsefly Poeciloderas quadripunctatus in Costa Rica. Strain TALS-2T (= ATCC 51749), a representative of group XXVII, is designated the type strain of a new species, Spiroplasma lineolae (Mollicutes: Entomoplasmatales).     

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.     

Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antartica soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent

Aseptically collected sandstone and soil samples from the antarctic Dry Valleys were inoculated into oligotrophic media and incubated under low light intensities. A total of 41 Gram-negative isolates were obtained with reddish colonies spreading on agar. A sandstone isolate and four soil strains were characterized further. They were nearly identical in morphological, physiological, biochemical and chemotaxonomic properties. They produced large amounts of extracellular polymer and utilized for growth: glucose, saccharose, mannitol, sorbitol, L-aspartate, malate and acetate, but not D-ribose, adonitol, DL-alanine, glutamate, glycolate, lactate or succinate. All strains hydrolyzed gelatin, starch, casein, xylan, Tweens 80 or 60 and dead or living yeast cells, but not cellulose or pectin. Nitrate was not reduced, ethanol was not oxidized and acid was not produced from maltose, mannitol or dulcitol. Ammonia was not produced from peptone. They were strictly aerobic. Major fatty acids were n 16:1 d 9, n 16:1 d 11, n 17:1 d 11, and i 15:0. The strains contained the quinone MK-7 and phosphatidylethanolamine as the main phospholipid. The base ratio ranged from 55 to 61 mol% G+C. A 16S rRNA sequence analysis of strains AA-688 and AA-718 showed these to be identical and to represent a special phylogenetic group within the Cytophaga/Flavobacterium/Bacteroides major line of descent. Three soil strains labeled "Taxeobacter" Txc1, Txg1, and Txo1 (Reichenbach, 1992) belonged to the same group but had lower sequence similarities (<95%). Some of their characteristics were different from those of the antarctic strains: the utilization of C-compounds, hydrolysis of polymers, temperature tolerances, major fatty acids and base ratios. Txc1 and Txg1 may later have to be considered as members of this group, possibly on the species level, while Txo1 could represent a different related genus. It is concluded that the five antarctic strains represent a new genus and species for which the name of Hymenobacter roseosalivarius is proposed. The type strain is AA-718T (DSM 11622T).     

The flagellin gene of Borrelia miyamotoi sp. nov. and its phylogenetic relationship among Borrelia species

We have cloned and sequenced the flagellin gene from Borrelia miyamotoi strain HT31 and compared it with previously published flagellin sequences. Sequence similarity analysis demonstrated that strain HT31 is phylogenetically distant from the three species of Lyme disease borreliae is deeply branched into the relapsing fever borrelia cluster. The result was in full agreement with the classification of Borrelia strains using 16S tRNA sequences. This finding indicates that a phylogenetic analysis using flagellin gene sequences might be useful for classification of Borrelia strains.     

Exophiala mesophila spec. nov

Serum samples from 2000 cows, 3311 sheep and 638 goats from Iran were examined for antibodies to Toxoplasma gondii by use of the latex agglutination (LAT) and indirect hemagglutination tests (IHAT). Antibodies to T. gondii were found in 24.50% sheep and 19.25% of goats. Antibodies to T. gondii were not detected in cow sera by LAT and IHAT in 1:8 and 1:64 dilutions of bovine sera, respectively. Toxoplasma gondii was not found in tissues of 300 aborted fetuses from cows by direct microscopy and bioassay in mice.     

Facklamia ignava sp. nov., isolated from human clinical specimens

Two strains of a hitherto-undescribed gram-positive, catalase-negative coccus isolated from human sources were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains are genealogically identical and constitute a new line close to, but distinct from, Facklamia hominis. The unknown bacterium was readily distinguished from F. hominis by biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Facklamia ignava sp. nov. The type strain of Facklamia ignava is CCUG 37419.     

Characterization of Borrelia lusitaniae sp. nov. by 16S ribosomal DNA sequence analysis

We determined the complete sequence of the rrs gene from five strains of genomic species PotiB2. Both distance and parsimony methods were used to infer the evolutionary relationships of the rrs gene sequence of this genomic species in comparison with the rrs gene sequence of Borrelia valaisiana and the rrs gene sequences of Borrelia burgdorferi sensu lato species obtained from sequence databases. The phylogenetic analysis revealed that the genomic species PotiB2 strains clustered in a separate lineage, which was consistent with data from previous DNA-DNA hybridization experiments (D. Postic, M. V. Assous, P. A. D. Grimont, and G. Baranton, Int. J. Syst. Bacteriol. 44:743-752, 1994). A PCR-restriction fragment length polymorphism analysis was used to identify genomic species PotiB2 and to differentiate it from B. burgdorferi sensu lato species. Moreover, signature nucleotide positions were identified for each B. burgdorferi sensu lato species. In accordance with DNA relatedness values, our findings suggest that genomic species PotiB2 can be more clearly defined and identified, and we propose that it should be referred to as a new species, Borrelia lusitaniae. The type strain is PotiB2.     

Oxidation of thiosulfate by a new bacterium, Bosea thiooxidans (strain BI-42) gen. nov., sp. nov.: analysis of phylogeny based on chemotaxonomy and 16S ribosomal DNA sequencing

A gram-negative bacterium which was capable of oxidizing reduced inorganic sulfur compounds was isolated from agricultural soil and designated BI-42. This new isolate grew on a wide range of organic substrates but was not able to grow autotrophically and lacked ribulose 1,5-bisphosphate carboxylase, a key enzyme of carbon dioxide fixation. These results suggested that strain BI-42 was a chemolithoheterotroph. Ammonia and nitrate were not used as sole nitrogen sources for growth, and strain BI-42 lacked glutamate synthase activity, which resulted in glutamate auxotrophy. The glutamate dehydrogenase activity of this organism was apparently insufficient for ammonia assimilation. On the basis of the results of additional biochemical tests, the G + C content of the DNA, the results of a respiratory ubiquinone analysis, the results of a 16S ribosomal DNA sequence analysis, the fatty acid composition, and the results of a membrane lipid analysis, strain BI-42 was identified as a phylogenetically and physiologically distinct taxon belonging to the alpha subclass of the Proteobacteria. Bosea thiooxidans gen. nov., sp. nov. is the name proposed for this taxon.