- Volume 56, Issue 5, 2006

The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.

This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.

The taxonomic position of an actinomycete, strain K07-23T, isolated from a cold desert of the Himalayas, India, was established by a polyphasic approach. The strain exhibited phenotypic characters that were typical of the genus Rhodococcus. 16S rRNA gene sequence (1467 bases) comparisons confirmed that strain K07-23T belongs to the genus Rhodococcus. 16S rRNA sequence similarity studies showed that the isolate is very closely related to Nocardia corynebacterioides DSM 20151T (98.6 %), which has been recently reclassified as Rhodococcus corynebacterioides. It showed 94.4–96.6 % sequence similarity with other species of the genus Rhodococcus. However, genomic relatedness between strain K07-23T and R. corynebacterioides as revealed by DNA–DNA hybridization was low (62 %). Based on polyphasic analysis, strain K07-23T could be clearly distinguished from other species. It is proposed that strain K07-23T (=MTCC 6634T=DSM 44908T=JCM 13011T) represents a novel species of Rhodococcus, Rhodococcus kroppenstedtii sp. nov.

A novel actinomycete, strain N3-7T, was isolated from a natural cave in Jeju, Republic of Korea, using a dilution method and was subjected to characterization using polyphasic taxonomy. A 16S rRNA gene sequence analysis revealed that the organism belonged to the phylogenetic cluster of the genus Actinocorallia and was most closely related to Actinocorallia glomerata and Actinocorallia longicatena (97.6 and 97.5 % similarity, respectively). The main chemotaxonomic properties of strain N3-7T, such as the principal amino acid of the peptidoglycan, the predominant menaquinone and the polar lipid profile, supported classification in the genus Actinocorallia. The organism was readily differentiated from Actinocorallia species with validly published names on the basis of a broad range of phenotypic properties. Thus the isolate represents a novel species of the genus Actinocorallia, for which the name Actinocorallia cavernae sp. nov. is proposed. The type strain is strain N3-7T (=JCM 13278T=NRRL B-24429T).

Five novel Nocardiopsis strains isolated from hypersaline soils in China were subjected to a polyphasic analysis to determine their taxonomic position. All of the novel isolates could grow on agar plates at NaCl concentrations of up to 18 % (w/v), with optimum growth at 5–8 %. The DNA G+C contents of the novel strains ranged from 67.9 to 73.2 mol%. The morphological and chemotaxonomic characteristics of the isolates matched those described for members of the genus Nocardiopsis. Based on their 16S rRNA gene sequence analysis, DNA–DNA hybridization values and phenotypic characteristics, including the composition of cell-wall amino acids and sugars, menaquinones, polar lipids and cellular fatty acids, the isolates are proposed as representing five novel species of the genus Nocardiopsis. The novel species are proposed as Nocardiopsis gilva sp. nov. [type strain YIM 90087T (=KCTC 19006T=CCTCC AA 2040012T=DSM 44841T)], Nocardiopsis rosea sp. nov. [type strain YIM 90094T (=KCTC 19007T=CCTCC AA 2040013T=DSM 44842T), Nocardiopsis rhodophaea sp. nov. [type strain YIM 90096T (=KCTC 19049T=CCTCC AA 2040014T=DSM 44843T), Nocardiopsis chromatogenes sp. nov. [type strain YIM 90109T (=KCTC 19008T=CCTCC AA 2040015T=DSM 44844T) and Nocardiopsis baichengensis sp. nov. [type strain YIM 90130T (=KCTC 19009T=CCTCC AA 2040016T=DSM 44845T). On the basis of the chemotaxonomic data, the description of the recently described species Nocardiopsis salina Li et al. 2004 is emended.

Two novel nocardioform actinomycetes, strains Q41T and HMC25T, were isolated from soil samples collected in the Western Cape province, South Africa. Rapid genus identification revealed that the isolates belonged to the genus Kribbella (based on single-digestion restriction analysis of the 16S rRNA gene sequences with MboI, VspI, SphI, SnaBI, SalI and AgeI). Both isolates had ll-diaminopimelic acid and glycine in their cell-wall peptidoglycan, and contained mannose and ribose as whole-cell sugars. Strain HMC25T is able to grow at 45 °C and in the presence of NaCl (3 %), cephaloridine (10 μg ml−1) and gentamicin sulphate (10 μg ml−1). Strain Q41T grows in the presence of NaCl (2 %). Neither strain was able to grow under anaerobic conditions, whereas Kribbella flavida KACC 20248T, Kribbella jejuensis HD9T, Kribbella koreensis KACC 20250T and Kribbella sandramycini KACC 20249T exhibited weak but distinct growth under anaerobic conditions. Physiological test results and 16S rRNA gene sequence analysis allowed Q41T and HMC25T to be distinguished from other members of the genus with validly published names. Strains HMC25T (=NRRL B-24426T=DSM 17345T) and Q41T (=NRRL B-24425T=DSM 17344T) therefore represent the type strains of novel species, for which the names Kribbella swartbergensis sp. nov. and Kribbella karoonensis sp. nov., respectively, are proposed.

The taxonomic status of six neutrotolerant acidophilic streptomycetes isolated from acidic soils in Yunnan Province, China, was established using a polyphasic approach. The morphological and chemotaxonomic characteristics revealed that the isolates belong to the genus Streptomyces. Almost complete 16S rRNA gene sequences of the isolates were determined and aligned with available corresponding sequences of representatives of the family Streptomycetaceae; phylogenetic trees were inferred using four tree-making algorithms. The isolates formed a distinct, albeit heterogeneous, subclade in the Streptomyces 16S rRNA gene tree together with the type strain of Streptomyces yeochonensis, but were readily distinguishable from the latter using DNA–DNA hybridization and phenotypic data. It was evident from the genotypic and phenotypic data that the isolates belonged to four novel Streptomyces species, for which the following names are proposed: Streptomyces guanduensis sp. nov. (type strain 701T=CGMCC 4.2022T=JCM 13274T), Streptomyces paucisporeus sp. nov. (type strain 1413T=CGMCC 4.2025T=JCM 13276T), Streptomyces rubidus sp. nov. (type strain 13c15T=CGMCC 4.2026T=JCM 13277T) and Streptomyces yanglinensis sp. nov. (type strain 1307T=CGMCC 4.2023T=JCM 13275T); isolates 317 and 913 belong to this latter species.

The taxonomic status of an actinomycete isolated from sediment collected from the Mariana Trench was established using a combination of genotypic and phenotypic data. Isolate MT8T had chemotaxonomic and morphological properties consistent with its classification in the genus Williamsia, and formed a distinct phyletic line in the 16S rRNA gene tree together with the type strain of Williamsia muralis. The isolate was readily distinguished from the latter, and from representatives of other Williamsia species, using DNA–DNA relatedness and phenotypic criteria. Predominant cellular fatty acids were oleic, palmitic and tuberculostearic acids and a hexadecenoic acid. The DNA G+C content was 65.2 mol%. It is apparent that the isolate belongs to a novel species of Williamsia. Strain MT8T (=DSM 44944T=NCIMB 14085T) was thus considered to be the type strain of a novel species in the genus Williamsia, for which the name Williamsia marianensis sp. nov. is proposed.

Consortia containing a novel coccus-shaped, anaerobic heterotroph together with Pyrobaculum rods were cultivated from geothermal environments in New Zealand. Pure cultures of the cocci were only obtained from one such consortium, despite extensive attempts. Cells of this strain (AQ1.S1T) were regular to irregular cocci in morphology and occasionally formed large aggregates, especially when utilizing polysaccharides such as konjac glucomannan as a carbon source. Strain AQ1.S1T is a hyperthermophile, with an optimal temperature for growth between 92 and 95 °C (range 85–98 °C), and a moderate acidophile, with optimal growth occurring at pH 6.4 (range 5.4–7.0). Growth was inhibited by the addition of sulphur and NaCl (optimal growth occurred without addition of NaCl) and an electron acceptor was not required. Strain AQ1.S1T utilized starch, trypticase peptone, lactose, glucose, konjac glucomannan, mannose, galactose, maltose, glycogen and β-cyclodextrin as carbon sources. The G+C content was 52.9 mol%. Based on 16S rRNA gene sequence analysis and physiological features it is proposed that isolate AQ1.S1T (=DSM 17230T=JCM 13409T) represents the type strain of a novel species of a new genus within the Crenarchaeota, Ignisphaera aggregans gen. nov., sp. nov.

Two strains, 199T and 176, of Gram-negative, anaerobic, rod-shaped, non-spore-forming bacteria were isolated during studies of microbiota in human faeces using polyamine-deficient medium. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolated strains belonged to the genus Bacteroides. The G+C content (42.4–43.0 mol%) and major fatty acid composition (anteiso-C15 : 0, 31.8–36.2 %) supported the affiliation of the two strains to the genus Bacteroides. 16S rRNA gene sequence similarities with their closest neighbours, Bacteroides thetaiotaomicron and Bacteroides ovatus, ranged from 94.6 to 96.5 %. DNA–DNA hybridization and phenotypic analysis showed that the two strains belonged to the same species (DNA–DNA relatedness of 89 %) and were distinct from their close relatives, B. thetaiotaomicron and B. ovatus (<23 % DNA–DNA relatedness). On the basis of these data, a novel species of the genus Bacteroides, Bacteroides finegoldii sp. nov., is proposed, comprising the designated type strain 199T (=JCM 13345T=DSM 17565T) and strain 176 (=JCM 13346).

The taxonomic position of three novel marine, heterotrophic, pigmented and agarolytic bacteria with gliding motility, isolated from the sea urchin Strongylocentrotus intermedius, was investigated. 16S rRNA gene sequence analysis revealed that strains KMM 6166, KMM 6172T and KMM 6173 are members of the phylum Bacteroidetes; their nearest neighbours were Belliella baltica and Hongiella marincola (similarities of 94.5 and 93.6 %, respectively). The DNA G+C content of the strains was 44–45 mol%. The predominant fatty acids were C15 : 0 iso, C16 : 1 ω5c, C17 : 1 iso ω9c, C17 : 0 iso 3-OH and summed feature 3 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH). The major respiratory quinone was MK-7. Results of molecular experiments supported by phenotypic and chemotaxonomic data enabled the isolates to be classified as representatives of a novel species in a new genus, for which the name Echinicola pacifica gen. nov., sp. nov. is proposed. Echinicola pacifica is the type species of the genus Echinicola, and its type strain is KMM 6172T (=KCTC 12368T=LMG 23350T).

Four Gram-negative, orange-coloured, aerobic, heterotrophic bacteria were isolated from sediment samples collected on the Pacific coast of Japan near the cities of Toyohashi and Katsuura. 16S rRNA gene sequence analysis indicated that these strains form a distinct lineage within the family Flavobacteriaceae. The four isolates shared 99.9–100 % 16S rRNA gene sequence similarity with each other and showed 88–90.9 % similarity with their neighbours in the family Flavobacteriaceae. The four strains also shared high DNA–DNA reassociation values of 67–99 % with each other. All the strains grew at 37 °C but not at 4 °C, and degraded gelatin, starch and DNA. The major fatty acids were i-C15 : 0, a-C15 : 0, i-C16 : 0 and i-C17 : 0 3-OH. However, two common fatty acids of members of the Flavobacteriaceae, i-C15 : 1 and a-C15 : 1, were absent in these strains. The DNA G+C contents of the four strains were in the range 35–37 mol%. On the basis of the polyphasic evidence, it was concluded that these strains should be classified as a novel genus and a novel species in the family Flavobacteriaceae, for which the name Sandarakinotalea sediminis gen. nov., sp. nov. is proposed. The type strain of Sandarakinotalea sediminis is CKA-5T (=NBRC 100970T=LMG 23247T).

An aquatic bacterium, strain GPTSA100-15T, was isolated on nutritionally poor medium TSBA100 (tryptic soy broth diluted 100 times and solidified with 1.5 % agarose) and characterized using a polyphasic approach. The isolate was unable to grow on commonly used nutritionally rich media such as tryptic soy agar, nutrient agar and Luria–Bertani agar. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was affiliated with the family ‘Flexibacteraceae’ in the phylum Bacteroidetes. Phylogenetically, it showed closest similarity (94.0 %) with an uncultured bacterial clone, HP1A92, detected in a sludge microbial community. Among the culturable bacteria, the isolate had highest 16S rRNA gene sequence similarity with Leadbetterella byssophila 4M15T (87.8 %). Sequence similarities with other members of the phylum Bacteroidetes were less than 85 %. The fatty acid profile of the isolate grown on TSBA100 indicated that the major fatty acid was iso-C15 : 0, which is also present in many members of the family ‘Flexibacteraceae’. Cells of strain GPTSA100-15T are Gram-negative, strictly aerobic rods. The DNA G+C content of the isolate is 36.9 mol%. Results of phenotypic, chemotaxonomic and phylogenetic analyses clearly indicate that strain GPTSA100-15T represents a new genus within the family ‘Flexibacteraceae’; the name Emticicia gen. nov. is proposed for the genus, with Emticicia oligotrophica sp. nov. as the type species. The type strain of Emticicia oligotrophica is GPTSA100-15T (=MTCC 6937T=DSM 17448T).

A Gram-negative, rod-shaped Flavobacterium-like bacterial strain, DS-6T, was isolated from soil from the island of Dokdo, Korea, and subjected to a polyphasic taxonomic study. Strain DS-6T grew optimally at pH 7.0 and 25 °C in the presence of 0–0.5 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 36.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DS-6T belonged to the genus Flavobacterium. Levels of 16S rRNA gene sequence similarity between strain DS-6T and the type strains of Flavobacterium species were below 95.4 %. Strain DS-6T differed from some phylogenetically related Flavobacterium species in several phenotypic characteristics. On the basis of phenotypic and phylogenetic distinctiveness, DS-6T (=KCTC 12542T=CIP 108840T) was classified in the genus Flavobacterium as the type strain of a novel species, for which the name Flavobacterium soli sp. nov. is proposed.

A number of marine bacteria isolated from young biofilms were characterized as belonging to the family Flavobacteriaceae. The taxonomic characterization of strain KOPRI 13649T, which was isolated from an acrylic surface at the seashore at Gangneung, Korea, is reported here. The nearly complete 16S rRNA gene sequence of strain KOPRI 13649T was determined and was found to have a high level of similarity with that of Psychroserpens burtonensis (95.0–95.6 %). In addition, phylogenetic analysis and comparison with closely related strains confirmed that the strain represented a novel member of the genus Psychroserpens. The major respiratory quinone of strain KOPRI 13649T was MK-6 and the DNA G+C content was 29.8 mol%. The dominant fatty acid methyl esters were i-15 : 0, a-15 : 0, i-16 : 0, i-15 : 1ω10, 16 : 1ω7 and 15 : 0. Growth was observed at 10–34 °C (optimum 30 °C), at pH 6–9 (optimum 6.5–8.0) and with 0.5–4 % NaCl (optimum 1 %). On the basis of the polyphasic taxonomic evidence presented, strain KOPRI 13649T (=KCCM 42261T=JCM 13413T) should be classified as the type strain of a novel species in the genus Psychroserpens, for which the name Psychroserpens mesophilus sp. nov. is proposed.

Bacterial strains UST030701-097T and UST030701-084T were isolated from a marine sponge in the Bahamas. Both strains were pink-pigmented, Gram-negative, strictly aerobic and chemo-organotrophic. Cells of strain UST030701-097T were short, curved rods with fast-gliding motility, whereas those of strain UST030701-084T were straight rods with a less rapid gliding motion. The two strains had MK-7 as the major respiratory quinone and did not produce flexirubin-type pigments. The DNA G+C contents of strains UST030701-097T and UST030701-084T were 42.5 and 43.7 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains belonged to the family ‘Flexibacteraceae’ of the phylum Bacteroidetes. 16S rRNA gene sequence similarity between strains UST030701-097T and UST030701-084T was 95.0 %; their closest relative was [Marinicola] seohaensis, with 93.3 % and 96.0 % sequence similarity, respectively. Phylogenetic tree topology indicated that the two strains belonged to the same lineage, but were on separate branches. Whilst strain UST030701-084T and [Marinicola] seohaensis were found on one branch, strain UST030701-097T was in another branch that had no species with validly published names. Based on the polyphasic taxonomic data obtained in the present study, we propose that strain UST030701-097T represents a novel genus and that strain UST030701-084T represents a novel species in the phylum Bacteroidetes. The genus Fabibacter gen. nov. is proposed, with strain UST030701-097T (=NRRL B-41220T=JCM 13334T) as the type strain of the type species, Fabibacter halotolerans sp. nov. Strain UST030701-084T (=NRRL B-41219T=JCM 13337T) is proposed as the type strain of Roseivirga spongicola sp. nov. In an earlier study, it was suggested that the genus Marinicola is a later heterotypic synonym of the genus Roseivirga. However, a formal proposal to reclassify [Marinicola] seohaensis, the only member of the genus Marinicola, has not yet been made. The results of phylogenetic analyses in this study support the reclassification of [Marinicola] seohaensis as Roseivirga seohaensis comb. nov.

Strain DYT, which was isolated from garden soil in Japan, was subjected to a polyphasic taxonomic study. Sequence analysis of the 16S rRNA gene and the GyrB protein revealed that the closest relative of strain DYT was [Flavobacterium] ferrugineum Sickles and Shaw 1934, with 94.8 and 90.1 % similarity, respectively. The two strains had similar chemotaxonomic characteristics, with menaquinone 7 as the major quinone system, 47.2–48.9 mol% DNA G+C content and 15 : 0 iso, 15 : 1 iso, 17 : 0 iso 3-OH and summed feature 3 as the major fatty acids. Based on genotypic and phenotypic characteristics, [Flavobacterium] ferrugineum IAM 15098T could be clearly differentiated from other members of the genus Flavobacterium. Strain DYT and [Flavobacterium] ferrugineum IAM 15098T could be easily distinguished from neighbouring taxa by morphological features (non-motile, non-gliding and non-filamentous single cells). Therefore, it is proposed that [Flavobacterium] ferrugineum IAM 15098T and strain DYT represent two separate species of a new genus, Terrimonas gen. nov., with the names Terrimonas ferruginea comb. nov. (type species; type strain IAM 15098T=ATCC 13524T) and Terrimonas lutea sp. nov. (type strain DYT=IAM 15284T=CCTCC AB205006T), respectively.

A reassessment was undertaken of published characteristics of the five species of anaerobic intestinal spirochaetes in the genus Brachyspira (Brachyspira aalborgi, Brachyspira alvinipulli, Brachyspira hyodysenteriae, Brachyspira innocens and Brachyspira pilosicoli) and the two species in the genus Serpulina (Serpulina intermedia and Serpulina murdochii). Comparisons were made of published descriptions, including phenotypic properties, grouping by multilocus enzyme electrophoresis, DNA base composition, DNA–DNA relative reassociation values and 16S rRNA gene sequence similarity. On the basis of extensive similarities between all the species, it is proposed to reclassify Serpulina intermedia Stanton et al. 1997 and Serpulina murdochii Stanton et al. 1997 in the genus Brachyspira, as Brachyspira intermedia comb. nov. (type strain ATCC 51140T) and Brachyspira murdochii comb. nov. (type strain ATCC 51284T).

Two bacterial strains were isolated from greenhouse soils of Daejeon and Yangpyeong regions in Korea. The strains, designated GH1-9T and GH19-3T, were Gram-negative and aerobic, with rod-shaped cells. Their DNA G+C contents were 61.7 and 67.3 mol%, respectively. The major fatty acids of strain GH1-9T were iso-C16 : 0, iso-C15 : 0, iso-C14 : 0, iso-C17 : 1 ω9c and iso-C11 : 0 3-OH and the major components of strain GH19-3T were iso-C16 : 0, iso-C15 : 0, C16 : 1 ω7c alcohol, iso-C17 : 1 ω9c and iso-C11 : 0 3-OH. None of the species of the genus Lysobacter with validly published names showed 16S rRNA gene sequence similarity values of more than 97 % with respect to the novel isolates. The closest sequence similarity of strain GH1-9T was with Lysobacter concretionis DSM 16239T (96.4 %), whereas strain GH19-3T showed the highest sequence similarity with Lysobacter enzymogenes DSM 2043T (96.6 %). Polyphasic taxonomic studies indicated that the two strains should be classified as representing novel members of the genus Lysobacter. The names Lysobacter daejeonensis sp. nov. and Lysobacter yangpyeongensis sp. nov. are proposed, with strains GH1-9T (=KACC 11406T=DSM 17634T) and GH19-3T (=KACC 11407T=DSM 17635T), respectively, as the type strains.

Taxonomic studies were performed on ten hydrogen-oxidizing, facultatively chemolithotrophic bacteria that were isolated from volcanic mudflow deposits derived from the eruption of Mt. Pinatubo in the Philippines in 1991. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these isolates belonged to the genus Cupriavidus of the Betaproteobacteria; sequence similarity values with their nearest phylogenetic neighbour, Cupriavidus basilensis, were 97.1–98.3 %. In addition to phylogenetic analysis, results of whole-cell protein profiles and biochemical tests revealed that these strains were members of two distinct species. DNA–DNA hybridizations and whole-cell protein profiles enabled these isolates to be differentiated from related Cupriavidus species with validly published names. The isolates were aerobic, Gram-negative, non-sporulating, peritrichously flagellated rods. Their G+C contents ranged from 65.2 to 65.9 mol% and their major isoprenoid quinone was ubiquinone Q-8. On the basis of these results, two novel species are proposed, Cupriavidus pinatubonensis sp. nov. [nine strains, with 1245T (=CIP 108725T=PNCM 10346T) as the type strain] and Cupriavidus laharis sp. nov. [one strain, the type strain 1263aT (=CIP 108726T=PNCM 10347T)]. It is also suggested that Ralstonia sp. LMG 1197 (=JMP 134) should be included in the species C. pinatubonensis.