- Volume 52, Issue 5, 2002

A strain of a gram-positive, coccoid, yellow-pigmented bacterium was isolated from human blood. The bacterium was aerobic, non-encapsulated and non-motile. Phenotypically, the bacterium closely resembled Kytococcus sedentarius, but could be distinguished from this species by physiological tests and chemotaxonomic investigations. The peptidoglycan type is L-Lys-Glu2, variation A4alpha. The predominant menaquinones are MK-8 and MK-7. The major cellular fatty acids are iso-C17:1, iso-C17:0, iso-C15:0 and anteiso-C17:0. The strain contains catalase and does not produce acid from carbohydrates. The ability to hydrolyse Tween 80 and the lack of alpha-glucosidase activity are the most characteristic features. The results of comparative 16S rDNA analysis revealed that the strain represents a novel species within the genus Kytococcus, for which the name Kytococcus schroeteri sp. nov. is proposed. The type strain is strain Muenster 2000T (= DSM 13884T = CCM 4918T).

Five strains of butyrate-producing, anaerobic, gram-positive bacteria were isolated from human faecal material. These strains were slightly curved rods that showed motility by means of multiple subterminal flagella. The DNA G + C content of the strains was 29-31 mol%. A detailed investigation of the phenotypic and phylogenetic characteristics of the strains revealed that they represent a novel species of anaerobic, low-G+C-content, butyrate-producing bacterium that shows net acetate utilization during growth on media containing carbohydrates and short-chain fatty acids. The 16S rRNA gene sequences of the five isolates were determined and they confirmed that these strains were closely related to each other. Phylogenetic analysis indicated that the most closely related species are Eubacterium rectale, Eubacterium oxidoreducens and Roseburia cecicola, members of cluster XIVa of the Clostridium subphylum of gram-positive bacteria, although they share less than 95% sequence identity with the novel strains. It is proposed that a novel species, Roseburia intestinalis sp. nov., be created, with strain L1-82T (= DSM 14610T = NCIMB 13810T) as the type strain.

A novel thermophilic, anaerobic, strictly chemoorganoheterotrophic bacterium, designated as AM1114T, was isolated from a deep-sea hydrothermal vent sample from the East-Pacific Rise (EPR 13 degrees N). The cells were long (3-10 microm) rods, motile with peritrichous flagella, and exhibited a gram-negative cell wall ultrastructure. In the late stationary phase of growth, cells formed an ovoid, refractile, terminal endospore. They grew at 45-65 degrees C inclusive (optimum 55-60 degrees C; doubling time approx. 45 min), at pH 4.5-8.0 inclusive (optimum pH 7.5-8.0) and at sea salt concentrations of 20-60 g l(-1) inclusive (optimum 25-30 g l(-1)). Strain AM1114T was an obligately heterotrophic bacterium able to ferment a mixture of 20 amino acids, complex proteinaceous substrates (such as yeast extract, brain-heart infusion or peptone), and carbohydrates such as glucose, galactose or maltose. The main fermentation products on glucose/yeast extract/peptone/sulfur medium were hydrogen, carbon dioxide, butyrate, ethanol, acetate, formate and L-alanine. The G+C content of the genomic DNA (determined by thermal denaturation) was 24.2+/-1 mol%. Phylogenetic analyses of the 16S rRNA gene located the strain within cluster XI of the lineage encompassing the genus Clostridium and related genera (sensu Collins et al., 1994), in the bacterial domain. On the basis of 16S rDNA sequence comparisons and physiological and biochemical characteristics, it is proposed that the isolate should be described as a novel genus, namely Caminicella gen. nov., of which Caminicella sporogenes sp. nov. is the type species. The type strain is AM1114T (= DSM 14501T = CIP 107141T).

A distinct actinomycete strain was isolated from rhizosphere soil of Tsuga chinensis. The isolate, designated A25T, was assigned to the genus Streptomyces on the basis of morphological and chemotaxonomic criteria and was examined by using a polyphasic approach. An almost complete 16S rDNA sequence of the isolate was determined and compared with sequences of representative streptomycetes. The 16S rDNA data not only supported classification of the strain in the genus Streptomyces, but also showed that it formed a separate phyletic line. DNA-DNA hybridization between strain A25T and closely related reference strains confirmed that strain A25T is a novel taxon of Streptomyces. It is proposed, therefore, the strain A25T (= AS 4.1331T = LMG 20251T) is classified in the genus Streptomyces as Streptomyces scopiformis sp. nov.

Five strains received as Gluconobacter cerinus and Gluconobacter asaii were examined for DNA base composition, DNA-DNA similarity, 16S rRNA gene sequences and phenotypic characteristics, including acid production from ethanol, growth on L-arabitol and meso-ribitol and requirement for nicotinic acid. The five strains showed DNA base compositions ranging from 54 to 56 mol% G+C. G. cerinus IFO 3267T and IAM 1832 and G. asaii IFO 3276T and IFO 3275 showed high levels of DNA-DNA similarity (70-100%) between each other and low values of DNA-DNA similarity (16-35%) to Gluconobacter frateurii IFO 3264T and Gluconobacter oxydans IFO 14819T. G. cerinus IFO 3267T and G. asaii IFO 3276T were located at an identical position in a phylogenetic tree deduced from 16S rRNA gene sequences. Two G. cerinus strains and two G. asaii strains did not require nicotinic acid for growth and did not grow on L-arabitol or meso-ribitol. G. cerinus IAM 1832 did not produce acid and required nicotinic acid and/or other growth factors. G. asaii IFO 3265 showed a high degree of DNA-DNA similarity (97%) to G. frateurii IFO 3264T and low similarity values (each 32%) to G. cerinus IFO 3267T and G. asaii IFO 3276T. This strain did not require nicotinic acid and grew well on L-arabitol and meso-ribitol. Therefore, G. asaii IFO 3265 was reclassified as G. frateurii. The results obtained revealed a synonymous relationship between G. cerinus and G. asaii. G. asaii is a junior subjective synonym of G. cerinus because G. cerinus has priority over G. asaii.

From two samples of microbial biofilms, damaging the mural paintings at the Saint-Catherine chapel of Castle Herberstein (Austria), four and nine coryneform bacteria were isolated, respectively. A polyphasic taxonomic study of these isolates, including morphological, biochemical and chemotaxonomic characterization, REP-PCR fingerprinting, 16S rDNA sequence analysis, DNA base ratio and DNA-DNA hybridizations, allocated them to the genus Brachybacterium. The isolates of the two samples both represent new species, for which the names Brachybacterium fresconis sp. nov. and Brachybacterium sacelli sp. nov. are proposed. The respective type strains are LMG 20336T (= DSM 14564T) and LMG 20345T (= DSM 14566T).

Two novel filamentous bacterial isolates, strains WR-30T and WR-220, with an optimum growth temperature of approximately 55-60 degrees C were isolated from Wu-rai hot springs in the northern part of Taiwan. These isolates were aerobic, thermophilic, non-sporulating, red-pigmented and heterotrophic and formed extremely long, filamentous trichomes from cells of different lengths. Phylogenetic analysis of 16S rDNA, DNA-DNA hybridization, morphological and biochemical features and fatty acid composition revealed that the isolates represent a novel species of the genus Meiothermus. The name Meiothermus taiwanensis sp. nov. is proposed for this novel species. The type strain of M. taiwanensis is strain WR-30T (= ATCC BAA-399T = CCRC 17170T = DSM 14542T); strain WR-220 (= ATCC BAA400 = CCRC 17171 = DSM 14543) is a reference strain.

Two facultatively oligotrophic, intensely yellow-pigmented bacterial strains, RE35F/1T and RE10F/45, have been previously isolated from the western Mediterranean Sea (Bay of Calvi, Corsica, France) by 0.2 microm membrane filtration. The organisms were gram-negative, catalase- and oxidase-positive, strictly aerobic, rod-shaped and non-motile. Their respiratory lipoquinone profiles consisted exclusively of ubiquinone-10 (Q-10) and the G+C contents of their DNAs were 62.0 and 62.4 mol%, respectively. Among the cellular fatty acids, octadecenoic acid (18:1omega7c) was the major component. Both isolates also contained hydroxy fatty acids (14:0 2-OH, 18:1 2-OH and 16:0 iso 3-OH) and branched fatty acids (15:0 anteiso, 16:0 anteiso and 17:0 anteiso). Polar lipid fingerprints were characterized by the presence of a sphingoglycolipid. Comparative analyses of their 16S rRNA gene sequences indicated that both isolates were phylogenetically closely related (sequence similarity of 99.9%) and formed a coherent cluster with aerobic bacteriochlorophyll a-containing species of the Erythrobacter/Porphyrobacter/Erythromicrobium cluster within the family Sphingomonadaceae. The closest relative was Erythrobacter litoralis DSM 8509T (97.4 and 97.5% 16S rRNA gene sequence similarity between this strain and RE35F/1T and RE10F/45, respectively). DNA-DNA reassociation studies confirmed that strains RE35F/1T and RE10F/45 represent a single species (79.6% DNA homology), but also demonstrated that they do not belong to the species Erythrobacter litoralis (25.2 and 34.2% DNA homology, respectively). Notably, both RE35F/1T and RE10F/45 lacked bacteriochlorophyll a. Based upon phenotypic and molecular evidence, a novel species of the genus Erythrobacter, Erythrobacter citreus sp. nov., is proposed. Strain RE35F/1T (= CIP 107092T = DSM 14432T) is the type strain.

A freshwater isolate from Campus Lake, Baton Rouge, LA, USA, strain ATCC 35122 (= ICPB 4362 = Schmidt CLPM White = Tekniepe BT2 white), which had been proposed as a putative reference strain for 'Planctomyces staleyi' (later reclassified as Pirellula staleyi), has been re-examined to establish its relationship to the type strain of Pirellula staleyi, ATCC 27377T. 165 rRNA sequencing confirms its very close relationship to ATCC 27377T and its membership of the order Planctomycetales. Ultrastructural characteristics are also consistent with its membership of the planctomycetes and of the genus Pirellula. These characteristics include polar crateriform structures and the occurrence of the unique internal, single-membrane-bounded compartment enclosing the nucleoid and ribosome-like particles, the pirellulosome, and a polar cap region. Cells of strain ATCC 35122 often displayed pointed, hump-like protrusions opposite each other on the cell, constituting prosthecae, and these were also found to be present on cells of strain ATCC 27377T. The original identification of ATCC 35122 as a strain of Pirellula staleyi is confirmed on both molecular and phenotypic grounds.

A novel bacterial strain, DS-1T, was isolated that degrades heteropolysaccharide produced by the cyanobacterium Nostoc commune. The isolate was identified by a combination of phenotypic characterization, cellular fatty acid analysis, DNA base composition, DNA-DNA hybridization and 165 rRNA gene sequence analysis. Phylogenetic analysis placed strain DS-1T within the Paenibacillus cluster on a phylogenetic tree and the phenotypic characteristics of this strain appear to be similar to those of Paenibacillus curdlanolyticus IFO 15724T and Paenibacillus kobensis IFO 15729T. The strain was distinguished from P. curdlanolyticus IFO 15724T and P. kobensis IFO 15729T by its ability to degrade the polysaccharide of Nostoc commune, by assimilation of rhamnose, inositol and L-fucose and by its wide range of optimal growth temperature (28-37 degrees C). Like other Paenibacillus species, this strain contains anteiso-C15:0 as a major cellular fatty acid, and it has a DNA G+C content of 50.5 mol %. Based on these results, it is concluded that this isolate should be placed within a novel species of Paenibacillus, Paenibacillus glycanilyticus sp. nov., with the type strain DS-1T (= IFO 16618T = JCM 11221T = NRRL B-23455T).

A novel thermophilic, strictly anaerobic, thiosulfate-reducing bacterium, designated strain ToBE(T), was isolated from a geothermal aquifer at a depth of 550 m in the Toyoha Mines (Hokkaido, Japan). The cells of this bacterium were rod-shaped (0.6 x 2.6 microm), non-motile and sporulating. Strain ToBE(T) was able to grow on formate, lactate, pyruvate or various sugars in the presence of thiosulfate as an electron acceptor. The strain could grow at 55-73 degrees C and pH 5.5-8.5. The optimum temperature and pH for the growth were 70 degrees C and pH 6.5. The G+C content of the DNA was 49.6 mol %. The major quinone and cellular fatty acids were respectively menaquinone-7 and iso-C15:0 and iso-C17:0. Analysis of the 16S rDNA revealed that the isolate was a member of the gram-positive bacteria and was related to the genus Thermoanaerobacter. However, the phylogenetic tree showed that the strain was distant from any other known bacteria, with sequence similarities of less than 90%. On the basis of phenotypic features and phylogenetic analysis, the name Thermanaeromonas toyohensis gen. nov., sp. nov., is proposed for the isolate, with strain ToBE(T) (= DSM 14490T = JCM 11376T) as the type strain.

A novel thermo-acidophilic bacterium was isolated from an acidic beverage that had the odour of guaiacol. The cells are aerobic, gram-positive, spore-forming rods. The organism, strain TA-67T, grows at temperatures from 20 to 55 degrees C (optimum, 50 degrees C) and at pH values from 2.5 to 5.5 (optimum, pH 3.0). It possesses omega-cyclohexane fatty acid as a major cellular fatty acid. The G+C content of the DNA is 54.1 mol%. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain TA-67T constituted a distinct lineage in the Alicyclobacillus cluster, with Alicyclobacillus acidoterrestris as the closest neighbour (96.6% homology). Phenotypically, it is similar to, but can be distinguished from, omega-cyclohexane fatty acid-possessing alicyclobacilIi (A. acidoterrestris, Alicyclobacillus acidocaldarius, Alicyclobacillus hesperidum and 'Alicyclobacillus mali') by the morphology of spores and sporangia, by the growth response to different temperatures, and by the profiles for acid production from carbon sources. It is the alicyclobacillus that produces guaiacol, a causative substance for an 'off' flavour of orange juice. On the basis of the phenotypic and phylogenetic evidence, it is concluded that strain TA-67T represents a new species of the genus Alicyclobacillus, for which the name Alicyclobacillus acidiphilus is proposed. The type strain is TA-67T (= DSM 14558T = IAM 14935T = NRIC 6496T).

Sinorhizobium morelense sp. nov. is described to designate a group of bacteria isolated from root nodules of Leucaena leucocephala. S. morelense shows 98% 16S rRNA gene sequence similarity to some Sinorhizobium species and to Ensifer adhaerens. This novel species is distinguished from other Sinorhizobium species and from E. adhaerens by DNA-DNA hybridization, 165 rRNA gene restriction fragments and sequence and some distinctive phenotypic features. Strains of this species are highly resistant to some antibiotics, such as carbenicillin (1 mg ml(-1)), kanamycin (500 microg ml(-1)) and erythromycin (300 microg ml(-1)). They do not form nodules, but a nodulating strain, Lc57, is closely related to the novel species. Strain Lc04T (= LMG 21331T = CFN E1007T) is designated as the type strain of this novel species.

A psychrotolerant actinomycete, strain YIM6T, was isolated from a soil sample collected from Beijiang in Xinjiang Province, China. Both vegetative and aerial hyphae grew well on various media after 4 weeks. Long spore chains, borne on the aerial mycelium, were straight to flexuous or occasionally Retinaculiaperti and non-motile. The novel isolate grew well at between 8 and 20 degrees C; the lower and upper temperature limits for growth were 0 and 32 degrees C. The cell wall of strain YIM6T contained LL-diaminopimelic acid (A2pm) and traces of meso-A2pm. Whole-cell hydrolysates contained mainly glucose and small amounts of xylose, galactose and arabinose. The predominant menaquinones were MK-9(H6) and MK-9(H8) and phosphatidylethanolamine was the diagnostic phospholipid. The predominant cellular fatty acids were 15:0 anteiso, 16:0 iso and 17:0 cyclo. Phylogenetic analysis indicated that strain YIM6T belongs to the genus Streptomyces. In its morphology, physiological and biochemical characteristics and 16S rDNA sequence, strain YIM6T differed from other members of Streptomyces. Thus, strain YIM6T (= CCTCC 99005T = AS 4.1718T = DSM 41794T) is proposed as the type strain of a novel species, Streptomyces beijiangensis sp. nov.

Recently, the genus Salmonella has been studied by multilocus enzyme electrophoresis (MLEE) and three collections of strains defined by this method, SARA, SARB and SARC, have been assembled to represent the genetic diversity of Salmonella choleraesuis (commonly known as Salmonella enterica) subspecies I and of the genus as a whole. The novel technique fluorescent amplified-fragment length polymorphism (FAFLP) analysis was applied to these collections to determine the genetic diversity of Salmonella. FAFLP broadly confirmed the MLEE findings but added precision to them, successfully distinguishing between the subspecies of S. enterica. It revealed the clonal nature of some serotypes of S. enterica subspecies I and the diversity of others. The enteric Salmonella Paratyphi B strains clustered separately from those associated with gastroenteritis. FAFLP is a powerful, highly flexible, whole-genome method that can be used to provide an unweighted view of genetic variation within Salmonella.

Strictly anaerobic, thermophilic bacteria (strains SL24T, SL25T, SL27, SL29 and SL32) were isolated from a deep, continental oil reservoir in Western Siberia (Russia). These motile, rod-shaped organisms were surrounded by a sheath-like structure, a feature characteristic of the Thermotogales. On the basis of partial 16S rDNA sequences (500 nucleotides), strains SL25T, SL27, SL29 and SL32 were identical. Therefore, only strains SL24T and SL25T were studied in detail. The optimum temperature for growth of both strains was 55 degrees C. Their optimum pH for growth was 7.5 and their optimum NaCl concentration was between 20 and 30 g l(-1). The novel isolates reduced elemental sulfur and cystine, but not thiosulfate or sulfate, to hydrogen sulfide. The G+C contents of the genomic DNA of strains SL24T and SL25T were respectively 35 and 33 mol%. Phylogenetically, both strains are most closely related to Petrotoga miotherma, there being 98.9-99.4% similarity between their 16S rDNA sequences. Phenotypic properties and DNA-DNA hybridization experiments indicate that the strains belong to two novel species, for which the names Petrotoga olearia (type strain SL24T = DSM 13574T = JCM 11234T) and Petrotoga sibirica (type strain SL25T= DSM 13575T = JCM 11235T) are proposed.

The taxonomic position was examined of three isolates, MTCC 3249T, SH and SLH, from the midgut of female Culex quinquefasciatus and Aedes aegyptii mosquitoes. Numbers of cells of these isolates increased 2000-fold after a blood meal of the mosquitoes. 16S rRNA gene sequence analysis of the novel strains showed that they were highly homologous to strains of Aeromonas. DNA-DNA hybridization studies showed that DNA of strain MTCC 3249T was 96 and 88% similar to that of strains SH and SLH, respectively, and showed 54% relatedness to Aeromonas jandaei and 61% relatedness to Aeromonas sobria, which is below the cut-off value for species differentiation. The biochemical profiles of all three novel strains were identical. On the basis of a polyphasic approach using phenotypic analysis, 16S rRNA gene sequencing and DNA-DNA hybridization studies, a novel species is proposed for these isolates, Aeromonas culicicola sp. nov., with the type strain MTCC 3249T (= NCIM 5147T). Isolation of A. culicicola from the midgut of mosquitoes might help to explain the origin of Aeromonas infections caused without exposure to contaminated water, soil or food.

An anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium, strain SI(T), isolated previously from granular sludge in a thermophilic upflow anaerobic sludge blanket (UASB) reactor, was characterized. The strain could grow fermentatively on pyruvate and fumarate in pure culture. The strain grew on propionate, ethanol, lactate, 1-butanol, 1-pentanol, 1,3-propanediol, 1-propanol and ethylene glycol in co-culture with the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus strain deltaH(T). The optimum temperature for growth was 55 degrees C and the pH optimum was 7.0. The G+C content of the DNA was 52.8 mol %. Strain SI(T) contained MK-7 and MK-7(H4) as the major quinones and contained iso-C15:0 as the major fatty acid. Based on 16S rDNA sequence analysis, strain SI(T) formed a novel lineage within the gram-positive, spore-forming, sulphate-reducing bacterial group Desulfotomaculum. However, the strain lacked the ability to conduct dissimilatory sulphate reduction. Instead, it could reduce fumarate to succinate with concomitant growth on several organic substances as electron donor. These phenotypic and genetic properties support the formation of a novel species of a new genus, for which the name Pelotomaculum thermopropionicum gen. nov., sp. nov. is proposed. The type strain is strain SI(T) (= DSM 13744T = JCM 10971T).

A thermophilic, anaerobic, spore-forming bacterium (strain Z-9801T) was isolated from a terrestrial hydrothermal source in the Uzon caldera on the Kamchatka peninsula. Cells of strain Z-9801T were straight, sometimes branched rods, 0.5-0.6 microm in diameter and 1.5-7.0 microm in length, with peritrichous flagella. The temperature range for growth was 45-76 degrees C, with an optimum at 63-65 degrees C. The pH range for growth was 4.8-8.2, with an optimum at 6.7-6.9. The substrates utilized by strain Z-9801T included peptone, yeast extract, beef extract, Casamino acids, starch, pyruvate, melibiose, sucrose, fructose, maltose, xylose and ribose. The fermentation products from melibiose were ethanol, acetate, H2 and CO2. Strain Z-9801T used H2 in the presence of Fe(III) and an organic electron donor. Strain Z-9801T reduced Fe(III), Mn(IV), nitrate, fumarate, sulfite, thiosulfate, elemental sulfur and 9,10-anthraquinone 2,6-disulfonate. The G+C content of strain Z-9801T DNA was 36 mol%. 16S rDNA sequence analysis revealed that the isolated organism forms a separate branch within the Bacillus/Clostridium group. On the basis of physiological properties and phylogenetic analysis, it is proposed that strain Z-9801T (= DSM 14006T = UNIQEM 210T) should be assigned to a novel species of a new genus, Thermovenabulum ferriorganovorum gen. nov., sp. nov.