- Volume 56, Issue 9, 2006

Forty-five mycobacterial strains isolated from 23 Colombian HIV-positive patients were identified as members of the Mycobacterium avium complex (MAC) and were characterized using different molecular approaches. Seven of the isolates showed characteristic features that allowed them to be differentiated from other members of the complex. The isolates had a novel 16S–23S rRNA internal transcribed spacer (ITS 1) gene sequence which is described as a new sequevar, MAC-X. All of the seven novel isolates gave a positive result with the MAC-specific AccuProbe (Gen-Probe), but tested negative for Mycobacterium avium and Mycobacterium intracellulare species-specific probes (64 and 100 % of the isolates, respectively). The novel isolates could be differentiated phenotypically from other members of the MAC on the basis of the production of urease and by a consistent mycolic acid pattern. The novel isolates shared some characteristics with M. avium, such as the avium variant I (av-I) pattern of the hsp65 gene as determined by PCR restriction analysis and a positive PCR result for the mig (macrophage-induced) gene. However, the novel isolates showed a unique 16S rRNA gene sequence. DNA–DNA relatedness values, from 24 to 44 %, confirmed the distinction of the novel isolates from other members of the MAC at the genetic level and their status as members of a separate species. The novel isolates are proposed as representatives of a novel species, Mycobacterium colombiense sp. nov., that is closely related to M. avium within the MAC. The type strain is 10BT (=CIP 108962T=CECT 3035T).

Three novel bacterial strains were isolated from a soil sample collected in Japan by culture on a GPM agar plate supplemented with superoxide dismutase and catalase. The strains were Gram-positive, catalase-positive, non-motile bacteria with l-ornithine as a diagnostic diamino acid of the peptidoglycan. The acyl type of the peptidoglycan was N-glycolyl. The major menaquinones were MK-12, 13 and 14. Mycolic acids were not detected. G+C contents of the DNA were in the range 69–71 mol%. Comparative 16S rRNA gene sequence analysis revealed that the isolates belonged to the genus Microbacterium and were closely related to Microbacterium terregens, Microbacterium aurum, Microbacterium koreense, Microbacterium schleiferi and Microbacterium lacticum. However, M. aurum, M. koreense and M. lacticum clearly differed from the isolated strains based on the presence of l-lysine as the cell-wall diamino acid and various other chemotaxonomic characteristics. Levels of DNA–DNA relatedness showed that the isolated strains represented three separate genomic species. Based on both phenotypic and genotypic data, the following novel species of the genus Microbacterium are proposed: Microbacterium deminutum sp. nov. (type strain KV-483T=NRRL B-24453T=NBRC 101278T), Microbacterium pumilum sp. nov. (type strain KV-488T=NRRL B-24452T=NBRC 101279T) and Microbacterium aoyamense sp. nov. (type strain KV-492T=NRRL B-24451T=NBRC 101280T).

The taxonomic status of ‘Actinoplanes liguriae’ A/6353 and ‘Actinoplanes teichomyceticus’ AB8327 was established by using a polyphasic approach. Strains A/6353 and AB8327 form distinct phylogenetic lineages in the 16S rRNA gene tree of members of the genus Actinoplanes and are related moderately and closely to Actinoplanes rectilineatus and Actinoplanes cyaneus, respectively. Morphological, cultural and physiological properties indicated that strains A/6353 and AB8327 represent separate, novel species of the genus Actinoplanes, Actinoplanes liguriensis sp. nov. (type strain A/6353T=FH 2244T=DSM 43865T=ATCC 31048T=BCRC 12121T=CBS 355.75T=IMSNU 22127T=JCM 3250T=KCTC 9536T=KCC A-0250T=NBRC 13997T=NCIMB 12636T=NRRL B-16723T=SANK 62178T) and Actinoplanes teichomyceticus sp. nov. (type strain AB8327T=FH 2149T=DSM 43866T=ATCC 31121T=BCRC 12106T=FERM P-3462T=IMSNU 20043T=IMET 9254T=JCM 3252T=KCC A-0252T=KCTC 9543T=NBRC 13999T=NCIMB 12640T=NRRL B-16726T=SANK 60479T).

A high-G+C-content, Gram-positive bacterium, strain D10T, was isolated from the root of Oroxylum indicum, a Chinese medicinal plant. Based on 16S rRNA gene sequence analysis, strain D10T was a member of the genus Pseudonocardia and was most closely related, albeit loosely, to Pseudonocardia halophobica. Morphological and chemotaxonomic characteristics support the affiliation of strain D10T to the genus Pseudonocardia. Results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain D10T from related Pseudonocardia species. Strain D10T (=CGMCC 4.3143T=DSM 44984T) therefore represents a novel species, for which the name Pseudonocardia oroxyli sp. nov. is proposed.

A novel actinomycete, strain WS-26T, was isolated from beach sand on the coast of Jeju Island, Republic of Korea, and subjected to a polyphasic taxonomic characterization. The organism produced reddish orange-coloured substrate mycelium and white aerial mycelium, both of which fragmented into rod-shaped elements. A neighbour-joining tree, based on 16S rRNA gene sequence studies, revealed that the isolate formed a distinct branch at the base of a cluster that included Nocardia carnea, N. flavorosea, N. pigrifrangens, N. sienata and N. testacea. This branching pattern was also found in a tree constructed using the maximum-likelihood method, but was not supported by the maximum-parsimony method. Levels of 16S rRNA gene sequence similarity between the isolate and its phylogenetic neighbours ranged from 96.5 to 97.8 %. Chemotaxonomic properties, such as the principal amino acid of peptidoglycan, predominant menaquinone and polar lipids, supported its assignment to the genus Nocardia. On the basis of phenotypic and phylogenetic data, the organism was different from Nocardia species with validly published names. The name Nocardia harenae sp. nov. is proposed, with WS-26T (=KCCM 42317T=NRRL B-24459T) as the type strain.

A Gram-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated TR6-04T, was isolated from compost and characterized taxonomically by using a polyphasic approach. The organism grew optimally at 30 °C and at pH 6.5–7.0. The isolate was positive for catalase and oxidase tests but negative for gelatinase, indole and H2S production. Comparative 16S rRNA gene sequence analysis showed that strain TR6-04T fell within the radiation of the cluster comprising Sphingobacterium species and clustered with Sphingobacterium mizutaii ATCC 33299T (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-C15 : 0, iso-C17 : 0 3-OH and summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c). These chemotaxonomic data supported the affiliation of strain TR6-04T to the genus Sphingobacterium. However, on the basis of its phenotypic properties and phylogenetic distinctiveness, strain TR6-04T (=KCTC 12579T=LMG 23402T=CCUG 52468T) should be classified as the type strain of a novel species, for which the name Sphingobacterium daejeonense sp. nov. is proposed.

A heterotrophic, aerobic, Gram-negative, pigmented and gliding bacterium, strain KMM 6258T, was isolated from the sea urchin Strongylocentrotus intermedius and investigated using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis revealed that the closest relatives of the novel strain are Aquimarina muelleri, Stanierella latercula and Gaetbulimicrobium brevivitae, members of the family Flavobacteriaceae, with sequence similarities of 96.3, 96.4 and 96.2 %, respectively. Phylogenetic evidence, supported by chemotaxonomic and phenotypic data, assigned strain KMM 6258T to the genus Aquimarina as Aquimarina intermedia sp. nov. (type strain KMM 6258T=DSM 17527T=JCM 13506T=LMG 23204T). The reclassification of Stanierella latercula as Aquimarina latercula comb. nov. and Gaetbulimicrobium brevivitae as Aquimarina brevivitae comb. nov. is proposed.

Two airborne bacterial isolates, NS/2 and NS/50T, were examined in order to determine their taxonomic position. Their almost complete 16S rRNA gene sequences shared 95.9 % similarity. Sequence comparisons demonstrated that their next relatives are species of the genus Hymenobacter (93.6–95.7 % similarity) and the strains ‘Taxeobacter chitinovorans’ Txc1T, ‘Taxeobacter gelupurpurascens’ Txg1T and ‘Taxeobacter ocellatus’ Myx 2105T (90.5–96.4 %). Phylogenetic calculations indicated that these five strains together with the three recognized Hymenobacter species form a separate line of descent within the family ‘Flexibacteraceae’. Isolates NS/2 and NS/50T, as well as ‘Taxeobacter chitinovorans’ Txc1T, ‘Taxeobacter gelupurpurascens’ Txg1T and ‘Taxeobacter ocellatus’ Myx 2105T, possessed the characteristics of the genus Hymenobacter, the quinone system menaquinone MK-7 and a polyamine pattern with the major polyamine being sym-homospermidine. Each of the five strains had complex, unique polar lipid profiles, with phosphatidylethanolamine and several unknown aminophospho-, amino-, phospho-, glyco- and polar lipids of which several compounds were also found in established Hymenobacter species. All the strains studied possessed fatty acids characteristic of Hymenobacter species, including major acids iso-C15 : 0, anteiso-C15 : 0, C16 : 1 ω5c, summed feature 3 (C16 : 1 ω7c/iso-C15 : 0 2-OH) and summed feature 4 (iso-C17 : 1 I/anteiso-C17 : 1 B). The five strains could be distinguished from each other and from the three established species of the genus Hymenobacter based on relatively low 16S rRNA gene sequence similarities (<97 %), unique polar lipids and differing fatty acid profiles and physiological characteristics. In conclusion, the description of four novel species of the genus Hymenobacter appears to be justified, for which the names Hymenobacter norwichensis sp. nov. (type strain NS/50T=LMG 21876T=DSM 15439T), Hymenobacter chitinivorans sp. nov. (type strain Txc1T=LMG 21951T=DSM 11115T), Hymenobacter gelipurpurascens sp. nov. (type strain Txg1T=LMG 21873T=DSM 11116T) and Hymenobacter ocellatus sp. nov. (type strain Myx 2105T=Txo1T=LMG 21873T=DSM 11117T) are proposed. For strain NS/2, a description only is provided without proposal of a name because its status as a novel species was not demonstrated unambiguously.

The taxonomic positions of five bacterial strains isolated from the Yaeyama Islands of Japan and ‘Microscilla arenaria’ NBRC 15982 were determined using a polyphasic taxonomic approach. 16S rRNA gene sequence analyses placed all of the strains close to the genus Flammeovirga. DNA–DNA hybridization studies, biochemical and physiological characterizations and chemotaxonomic analyses suggested that ‘M. arenaria’ NBRC 15982 and the five novel isolates represented two separate species of the genus Flammeovirga. Emendation of the genus Flammeovirga Nakagawa et al. 1997 and the species Flammeovirga aprica (Reichenbach 1989) Nakagawa et al. 1997 is proposed. In addition, ‘Microscilla arenaria’ Lewin 1969 is proposed as Flammeovirga arenaria nom. rev., comb. nov. (with the type strain NBRC 15982T=CIP 109101T) and the novel isolates are proposed as Flammeovirga yaeyamensis sp. nov. (type strain IR25-3T=NBRC 100898T=CIP 109099T).

A non-motile, rod-shaped and pinkish-red-pigmented bacterium, designated strain WPCB131T, was isolated from freshwater of Woopo wetland, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that this isolate represents a novel member of the genus Hymenobacter with sequence similarities of 93.2–95.5 % to known Hymenobacter species. No other taxa in the phylum Bacteroidetes showed more than 90 % sequence similarity to the isolate. Cells were Gram-negative, oxidase-negative and catalase-positive. Optimum growth was observed at pH 6 and 30 °C. The major fatty acids were iso-C15 : 0 (34.8 %), C16 : 1 ω5c (15.0 %), anteiso-C17 : 1 B/iso-C17 : 1 I (14.4 %) and C16 : 1 ω7c/iso-C15 : 0 2-OH (13.8 %). The DNA G+C content of strain WPCB131T was 65 mol%. The isolate could be readily distinguished from other Hymenobacter species using a combination of phenotypic characters. On the basis of the polyphasic evidence presented in this study, it is proposed that strain WPCB131T (=IMSNU 14116T=KCTC 12533T=NBRC 101118T) represents a novel species, Hymenobacter rigui sp. nov.

A strictly anaerobic, xylanolytic bacterium, strain KB3T, isolated from rice-plant residue in flooded anoxic rice-field soil in Japan, was characterized phenotypically and phylogenetically. Cells were Gram-negative, non-motile, non-spore-forming, short to filamentous rods. Growth of the strain was remarkably stimulated by the addition of haemin to the medium. The novel strain utilized various sugars including xylan, xylose, pectin and carboxymethylcellulose and produced acetate, propionate and succinate with a small amount of malate. Propionate production was stimulated by the addition of a B-vitamin mixture or cobalamin to the medium. The novel strain was slightly acidophilic with an optimum pH 5.7–6.2 and the optimum growth temperature was 30 °C. Oxidase, catalase and nitrate-reducing activities were negative. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C15 : 0 and iso-3-OH C17 : 0. The major respiratory quinones were menaquinones MK-12(H2) and MK-13(H2). The genomic DNA G+C content was 43.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence placed the strain in the phylum Bacteroidetes. The closest related species was Prevotella bivia with a 16S rRNA gene sequence similarity of 89.5 %. Prevotella albensis and Prevotella oulorum were the next closest recognized species with sequence similarities of 89.1 %. Based on a comprehensive examination of the differences in phylogenetic, ecological, physiological and chemotaxonomic characteristics of strain KB3T and those of related species, a novel genus and species, Xylanibacter oryzae gen. nov., sp. nov., is proposed to accommodate strain KB3T. The type strain of the novel species is KB3T (=JCM 13648T=DSM 17970T).

Analysis of the 16S rRNA gene sequences of species currently assigned to the genus Flexibacter has shown extensive intrageneric phylogenetic heterogeneity. It has been shown in previous studies that the species [Flexibacter] sancti, [Flexibacter] filiformis and [Flexibacter] japonensis were most closely related to Chitinophaga pinensis. In addition, [Cytophaga] arvensicola and species of the genus Terrimonas also clustered into this phylogenetic group. Although the similarities of 16S rRNA gene sequences were low (88.5–96.4 %), there is no evidence for clear phenotypic differences between these organisms that justify assignment to different genera. A proposal is made to transfer these species to the genus Chitinophaga as Chitinophaga sancti comb. nov., Chitinophaga filiformis comb. nov., Chitinophaga japonenis comb. nov. and Chitinophaga arvensicola comb. nov. on the basis of phylogenetic and phenotypic data. Furthermore, a novel species is described within this genus, Chitinophaga skermanii sp. nov., with strain CC-SG1BT (=CCUG 52510T=CIP 109140T) as the type strain.

A marine bacterium, strain Pol012T, was isolated from the Mediterranean sponge Axinella polypoides and subsequently characterized as belonging to subphylum 1 of the phylum ‘Verrucomicrobia’. Strain Pol012T was non-motile, Gram-negative, coccoid or rod-shaped and red in colour. The menaquinones MK-8 and MK-9 were detected. The G+C content of the genomic DNA was 50.9 mol%. Growth was possible at temperatures between 8 and 30 °C and at pH values between 6.8 and 8.2. The closest cultured relative of strain Pol012T was Akkermansia muciniphila (83 % sequence similarity), while the closest environmental 16S rRNA gene sequence was the marine clone Arctic96BD-2 (95 % sequence similarity). Strain Pol012T is the first marine pure-culture representative of ‘Verrucomicrobia’ subphylum 1 and represents a novel genus and species, for which the name Rubritalea marina gen. nov., sp. nov. is proposed. The type strain is Pol012T (=DSM 177716T=CIP 108984T).

A novel moderately halophilic, sulfate-reducing bacterium, strain EtOH3T, was isolated from anoxic hypersaline (270 g NaCl l−1) sediment of the northern arm of the Great Salt Lake, Utah, USA. Cells of strain EtOH3T were oval to rod-shaped, non-motile, non-sporulating and stained Gram-negative. The strain required sodium and magnesium ions for growth and grew at salinities of up to 240 g NaCl l−1 and 121 g MgCl2.6H2O l−1. The optimum NaCl concentration was 80–100 g l−1. Strain EtOH3T grew at temperatures ranging from 15 to 44 °C (optimum 37 °C). The pH range for growth was 6.5–8.3 (optimum around pH 6.8). Only sulfate and thiosulfate served as electron acceptors for a broad range of electron donors including various short-chain fatty acids and primary (C1–5) alcohols, amino acids, H2/acetate and H2/yeast extract. The G+C content of the genomic DNA was 51.4 mol%. Phylogenetic analysis of dsrAB [genes encoding the major subunits of dissimilatory (bi)sulfite reductase] and 16S rRNA gene sequence data placed strain EtOH3T within the deltaproteobacterial family Desulfohalobiaceae. Strain EtOH3T shared 76 and 91 % dsrAB and 16S rRNA gene sequence similarity, respectively, with the type strain of the phylogenetically most closely related species with a validly published name, Desulfohalobium retbaense DSM 5692T. High 16S rRNA gene sequence similarity (~97 %) was shared with the recently described strain ‘Desulfovermiculus halophilus’ VKM B-2364. Strain EtOH3T, however, clearly differed from this strain in both genomic G+C content and in several of its phenotypic properties. On the basis of phenotypic and genotypic characteristics, the novel species Desulfohalobium utahense sp. nov. is proposed, with strain EtOH3T (=VKM B-2384T=DSM 17720T) as the type strain.

A novel strain, R2A16-10T, was isolated from greenhouse soil in Yeoju, Korea. The taxonomy of strain R2A16-10T was studied by using polyphasic methods. On the basis of 16S rRNA gene sequence analyses, strain R2A16-10T was found to be phylogenetically related to type strains of Dyella species (96.7–96.9 %), Frateuria aurantia DSM 6220T (96.5 %), Fulvimonas soli LMG 19981T (96.3 %) and Rhodanobacter species (94.9–95.7 %). Strain R2A16-10T, which produced yellow-coloured colonies, was Gram-negative, rod-shaped (0.3–0.4×1.5–3.5 μm) and motile. The predominant fatty acids were 17 : 1 iso ω9c (25.5 %), 15 : 0 iso (18.7 %) and 17 : 0 iso (14.6 %), and the major hydroxy fatty acids were 11 : 0 iso 3-OH (5.0 %), 13 : 0 iso 3-OH (3.4 %) and 17 : 0 iso 3-OH (1.0 %). The major isoprenoid quinone was Q-8. The G+C content of the DNA of the type strain was 63.0 mol%. On the basis of the data from this study, strain R2A16-10T represents a novel species of the genus Dyella, for which the name Dyella yeojuensis sp. nov. is proposed. The type strain is R2A16-10T (=KACC 11405T=DSM 17673T).

A Gram-negative, aerobic, heterotrophic, non-pigmented, dimorphic prosthecate bacterium was isolated from tundra wetland soil and designated strain Z-0023T. Cells of this strain had a dimorphic life cycle and developed a non-adhesive stalk at a site not coincident with the centre of the cell pole, a characteristic typical of representatives of the genus Asticcacaulis. A highly distinctive feature of cells of strain Z-0023T was the presence of a conical, bell-shaped sheath when grown at low temperature. This prosthecate bacterium was a psychrotolerant, moderately acidophilic organism capable of growth between 4 and 28 °C (optimum 15–20 °C) and between pH 4.5 and 8.0 (optimum 5.6–6.0). The major phospholipid fatty acid was 18 : 1ω7c and the major phospholipids were phosphatidylglycerols. The G+C content of the DNA was 60.4 mol%. On the basis of 16S rRNA gene sequence similarity, strain Z-0023T was most closely related to Asticcacaulis biprosthecium (98 % similarity), Asticcacaulis taihuensis (98 %) and Asticcacaulis excentricus (95 %). However, low levels of DNA–DNA relatedness to these organisms and a number of distinctive features of the tundra wetland isolate indicated that it represented a novel species of the genus Asticcacaulis, for which the name Asticcacaulis benevestitus sp. nov. is proposed. The type strain is Z-0023T (=DSM 16100T=ATCC BAA-896T).

Ten strains previously assigned to Acetobacter hansenii (=Gluconacetobacter hansenii), Acetobacter pasteurianus LMG 1584 and eight reference strains of the genus Gluconacetobacter were reclassified by 16S rRNA gene sequencing, DNA–DNA similarity, DNA base composition and phenotypic characteristics. The A. hansenii strains and A. pasteurianus LMG 1584 were included in the cluster of acetic acid bacteria (family Acetobacteraceae) by 16S rRNA gene sequences. Further, they were separated into seven distinct groups by DNA–DNA similarity. DNA–DNA similarity group I was identified as G. hansenii. DNA–DNA similarity group II was retained as Gluconacetobacter sp., because DNA–DNA similarity between the strain and Gluconacetobacter entanii LTH 4560T could not be determined. This was due to a lack of availability of the type strain from any source. DNA–DNA similarity group III was regarded as a novel species, for which the name Gluconacetobacter saccharivorans sp. nov. (type strain, LMG 1582T=NRIC 0614T) is proposed. DNA–DNA similarity group IV included the type strains of Gluconacetobacter oboediens and Gluconacetobacter intermedius, and three A. hansenii strains. This group was identified as G. oboediens because high values of DNA–DNA similarity were obtained between the type strains and G. oboediens has priority over G. intermedius. DNA–DNA similarity group V was identified as Gluconacetobacter europaeus. DNA–DNA similarity group VI was regarded as a novel species, for which the name Gluconacetobacter nataicola sp. nov. (type strain, LMG 1536T=NRIC 0616T) is proposed. DNA–DNA similarity group VII was reclassified as Gluconacetobacter xylinus. The description of G. hansenii is emended.