- Volume 58, Issue 1, 2008

A Gram-positive, yellow-pigmented bacterium, strain KOPRI 21702T, was isolated from sea sand on King George Island, Antarctica. Cells were irregular rods with peritrichous flagella; their optimum growth temperature was 23–26 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the Antarctic isolate formed a distinct phyletic line in a clade of the genus Sanguibacter and showed highest sequence similarity (97.7 %) to the type strain of Sanguibacter keddieii. The major isoprenoid quinone, predominant cellular fatty acids and DNA G+C content were consistent with placement of the Antarctic isolate in the genus Sanguibacter. Phylogenetic analysis and differences in physiological and biochemical characteristics between strain KOPRI 21702T and the four recognized Sanguibacter species indicate that the isolate represents a novel species of this genus. The name Sanguibacter antarcticus sp. nov. (type strain KOPRI 21702T =KCTC 13143T =JCM 14623T =DSM 18966T) is proposed for this isolate.

Two novel bacterial strains were isolated from a paddy soil sample collected in Japan using GPM agar plates supplemented with superoxide dismutase and/or catalase. The strains were Gram-positive, catalase-positive and motile, with lysine as the peptidoglycan diagnostic diamino acid and acetyl as the peptidoglycan acyl type. The major menaquinone was MK-9(H2). Mycolic acids were not detected. The G+C content of the DNA was 66–68 mol%. On the basis of phenotypic analysis, 16S rRNA gene sequence comparisons and DNA–DNA hybridization data, it is proposed that these strains represent two novel species, Arthrobacter oryzae sp. nov. (type strain is KV-651T=NRRL B-24478T=NBRC 102055T) and Arthrobacter humicola sp. nov. (type strain is KV-653T=NRRL B-24479T=NBRC 102056T), respectively.

Two bacterial strains, designated BBH5 and BBH7T, were isolated from a deep-sea sediment sample collected from the Chagos Trench of the Indian Ocean (1 ° 06′ S 7 ° 31′ E). Based on their 16S rRNA gene sequence similarity (99.9 %), level of DNA–DNA relatedness (93 %) and a number of similar phenotypic characteristics, the two strains are identified as representing the same species. Their phylogenetically nearest neighbours, based on 16S rRNA gene sequence similarity values (97.9–98.4 %), were identified as Brevibacterium iodinum, Brevibacterium epidermidis, Brevibacterium linens and Brevibacterium permense. However, strains BBH5 and BBH7T could be distinguished from the above four species by a number of phenotypic characteristics, and levels of DNA–DNA relatedness between the two new isolates and these Brevibacterium species were 35–42 %. Therefore, strains BBH5 and BBH7T are considered to represent a novel species of the genus Brevibacterium, for which the name Brevibacterium oceani sp. nov. is proposed. The type strain is BBH7T (=LMG 23457T =IAM 15353T).

An actinomycete isolated from an immunocompetent patient suffering from confluent and reticulated papillomatosis was characterized using a polyphasic taxonomic approach. The organism had chemotaxonomic and morphological properties that were consistent with its assignment to the genus Dietzia and it formed a distinct phyletic line within the Dietzia 16S rRNA gene tree. It shared a 16S rRNA gene sequence similarity of 98.3 % with its nearest neighbour, the type strain of Dietzia cinnamea, and could be distinguished from the type strains of all Dietzia species using a combination of phenotypic properties. It is apparent from genotypic and phenotypic data that the organism represents a novel species in the genus Dietzia. The name proposed for this taxon is Dietzia papillomatosis; the type strain is N 1280T (=DSM 44961T=NCIMB 14145T).

A Gram-positive, rod-shaped or coccoid, yellow-pigmented bacterial strain, D287T, was isolated from the water flea Daphnia cucullata (Crustacea: Cladocera) collected from Lake Balaton in Hungary. Phylogenetic analysis on the basis of 16S rRNA gene sequence comparisons revealed that the strain represented a distinct lineage within the cluster of the genera Nocardioides and Marmoricola. The following characteristics were consistent with the affiliation of strain D287T to the genus Nocardioides: peptidoglycan based on ll-2,6-diaminopimelic acid, MK-8(H4) as the major menaquinone, iso-C16 : 0 as the predominant cellular fatty acid, the presence of phosphatidylglycerol and diphosphatidylglycerol and a DNA G+C content of 69.9 mol%. Owing to characteristic differences in physiological traits and levels of 16S rRNA gene sequence similarity to its phylogenetically closest neighbours that were below 97 %, strain D287T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides daphniae sp. nov. is proposed. The type strain is D287T (=DSM 18664T=CCM 7403T).

A cream-white-coloured, aerobic, Gram-positive, ovoid to spherical-shaped bacterial strain, designated L-143T, was isolated from soil in Taiwan. The highest 16S rRNA gene sequence similarities of strain L-143T (98.3–95.8 %) were with members of the genus Rothia. Chemotaxonomic and phenotypic properties of this organism were consistent with its classification in the genus Rothia. The novel isolate was distinguished from all Rothia species by several phenotypic characteristics. The peptidoglycan type was A3α, containing lysine, glutamic acid and alanine. The isolate contained MK-7 as the major component of the quinone system. The predominant polar lipid consisted of phosphatidylglycerol and diphosphatidylglycerol, with some unknown phospho- and glycolipids as minor components. The major fatty acids were anteiso-15 : 0 (57.3 %), anteiso-17 : 0 (17.0 %) and 16 : 0 (9.3 %). The G+C content of the genomic DNA was 56.1 mol%. Hence, genotypic, chemotaxonomic and phenotypic data demonstrate that strain L-143T should be classified as a novel species in the genus Rothia, for which the name Rothia terrae sp. nov. is proposed. The type strain is L-143T (=BCRC 17588T=LMG 23708T).

The bacterial strain LW6T was isolated from activated sludge of a wastewater treatment bioreactor. Cells of strain LW6T are Gram-positive, irregular, short rods and cocci, 0.5–0.8×1.0–1.6 μm. Colonies are light-yellow, smooth, circular and 0.2–1.0 mm in diameter after 3 days incubation. Strain LW6T is aerobic and heterotrophic. It grows at a temperature range of 26–38 °C and pH range of 6–9, with optimal growth at 33–37 °C and pH 7.8–8.2. The predominant cellular fatty acids of strain LW6T are iso-C15 : 0 (38.9 %) and iso-C17 : 1 ω9c (18.8 %). Strain LW6T has the major respiratory menaquinones MK-8(H4) and MK-8(H2) and polar lipids phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol and unknown glycolipid/phospholipids. The cell wall peptidoglycan of strain LW6T contained the amino acids ornithine, lysine, glutamic acid, alanine, glycine and aspartic acid. Its molar DNA G+C content is 69 mol% (T m). Analysis of 16S rRNA gene sequences indicated that strain LW6T was related phylogenetically to members of the genus Ornithinimicrobium, with similarities ranging from 98.3 to 98.7 %. The DNA–DNA relatedness of strain LW6T to Ornithinimicrobium humiphilum DSM 12362T and Ornithinimicrobium kibberense K22-20T was respectively 31.5 and 15.2 %. Based on these results, it is concluded that strain LW6T represents a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium pekingense sp. nov. is proposed. The type strain is strain LW6T (=CGMCC 1.5362T =JCM 14001T).

Three novel micro-organisms, designated strains OMB115T, OMB118 and OMB120, were isolated from dental plaque from golden hamsters fed with a high-carbohydrate diet. The three strains were Gram-positive, facultatively anaerobic rods that lacked catalase activity. Analysis of their partial 16S rRNA gene sequences indicated that these isolates belonged to the genus Bifidobacterium. They grew under aerobic conditions and each had a DNA G+C content of 53 mol%. On the basis of phylogenetic analyses involving phenotypic characterization and partial 16S rRNA gene sequencing, strain OMB115T represents a novel species of the genus Bifidobacterium, for which the name Bifidobacterium tsurumiense sp. nov. is proposed. The type strain is OMB115T (=JCM 13495T =DSM 17777T).

An actinomycete, strain HBUM 20038T, was isolated from soil from Ganjiahu Natural Reserve in Xinjiang Province, in north-western China, and then characterized using a polyphasic approach. 16S rRNA gene sequence analysis confirmed that strain HBUM 20038T was a member of the genus Nocardiopsis, and the morphological and chemotaxonomic characteristics of the strain were also consistent with those of species of Nocardiopsis. DNA–DNA hybridization between the strain and related type strains gave relatedness values far below 70 %. These results, together with physiological characteristics, showed that strain HBUM 20038T represents a novel species within the genus Nocardiopsis, for which the name Nocardiopsis ganjiahuensis sp. nov. is proposed. The type strain is HBUM 20038T (=DSM 45031T =CGMCC 4.3500T).

Two novel actinomycete strains, designated HFW-18 and HFW-21T, were isolated from a water sample around Hwasun Beach on the coast of Jeju Island, Republic of Korea. The cells of the organisms were aerobic, Gram-positive, non-motile rods. The temperature and initial pH ranges for growth were 4–37 °C and pH 5.1–9.1, respectively. They had ll-diaminopimelic acid in their cell-wall peptidoglycan, MK-8(H4) as the major menaquinone and DNA G+C contents of 71.1–72.2 mol%. The cellular fatty acids consisted of straight-chain saturated, branched, monounsaturated and 10-methyl fatty acids, with a major component of iso-C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown phospholipid. The isolates were identical in terms of their 16S rRNA gene sequences and BOX-PCR DNA fingerprints. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates occupied distinct positions within the radiation of the genus Nocardioides. According to 16S rRNA gene sequence similarity, the closest relatives were Nocardioides ganghwensis JC2055T (97.4 %), Nocardioides oleivorans DSM 16090T (97.3 %) and Nocardioides furvisabuli SBS-26T (97.0 %). Levels of 16S rRNA gene sequence similarity between the isolates and other members of the genus Nocardioides were in the range 91.8–95.3 %. On the basis of the phenotypic and molecular genetic data presented here, the isolates represent members of a novel species of the genus Nocardioides. The name Nocardioides hwasunensis sp. nov. is proposed, and the type strain is HFW-21T (=KCTC 19197T=DSM 18584T).

An extremely halophilic archaeon was isolated from a sample of the brine–sediment interface of the Shaban Deep in the northern Red Sea. Phylogenetic analysis of the 16S rRNA gene sequence revealed a close proximity to Halorhabdus utahensis (99.3 %), the sole species of the genus Halorhabdus. Strain SARL4BT formed non-pigmented colonies and showed optimum growth at 45 °C, in 27 % (w/v) NaCl and at pH 6.5–7.0. This organism utilized a few complex substrates, such as yeast extract and starch, for growth. Strain SARL4BT grew under anaerobic and microaerophilic conditions but grew extremely poorly under aerobic conditions. The ether lipids were diphytanyl derivatives. The DNA G+C content of the type strain was 61.7 mol%. On the basis of the phylogenetic data and physiological and biochemical characteristics, strain SARL4BT represents a novel species of the genus Halorhabdus, for which the name Halorhabdus tiamatea is proposed. The type strain is SARL4BT (=DSM 18392T=JCM 14471T). An emended description of the genus Halorhabdus is also proposed.

A novel methane-producing archaeon, strain NOBI-1T was isolated from an anaerobic, propionate-degradation enrichment culture, which was originally obtained from a mesophilic methanogenic sludge digesting municipal sewage sludge. Cells were non-motile, rod-shaped, 0.7–1.0 μm by 2.0 μm, and formed multicellular filaments longer than 8 μm. Growth was observed between 35 and 55 °C (optimum 50 °C) and pH 6.7 and 8.0 (optimum pH 7.0). The G+C content of the genomic DNA was 56.3 mol%. The strain utilized H2 and formate for growth and methane production. Based on comparative sequence analyses of the 16S rRNA gene and mcrA gene (encoding the alpha subunit of methyl-coenzyme M reductase, a key enzyme in the methane-production pathway), strain NOBI-1T was affiliated with the order Methanomicrobiales, but it was significantly distant from any other known species within the order. The most closely related species based on 16S rRNA and mcrA gene sequence similarity were respectively ‘Candidatus Methanoregula boonei’ (93.7 % 16S rRNA gene sequence similarity) and Methanocorpusculum parvum (74.2 % deduced McrA amino acid sequence similarity to the type strain). These phenotypic and genetic properties justified the creation of a novel species of a new genus for the strain, for which we propose the name Methanolinea tarda gen. nov., sp. nov. The type strain of Methanolinea tarda is strain NOBI-1T (=DSM 16494T =JCM 12467T =NBRC 102358T).

Two Gram-negative, rod-shaped, gliding bacterial strains, designated strain LL04 11.1.1T and strain A37.1T, were isolated from a diseased sole (Solea senegalensis) and from seawater from a holding tank for turbot (Psetta maxima), respectively. The strains grew on solid media as bright yellow colonies with uneven edges; the colonies did not adhere to the agar. The bacteria were able to grow at temperatures in the range 14 to 38 °C and from pH 6.0 to pH 8.0. The DNA G+C contents of strains LL04 11.1.1T and A37.1T were 32.1 and 32.7 mol%, respectively. Analysis of the 16S rRNA gene sequences indicated that strains LL04 11.1.1T and A37.1T were members of the genus Tenacibaculum in the family Flavobacteriaceae. The sequence similarities of the two isolates with respect to the type strains of recognized members of the genus ranged from 94.2 to 99.4 %. DNA–DNA hybridization studies revealed that the strains studied represent two distinct novel species of the genus Tenacibaculum, for which the names Tenacibaculum discolor sp. nov. [type strain LL04 11.1.1T (=NCIMB 14278T=DSM 18842T)] and Tenacibaculum gallaicum sp. nov. [type strain A37.1T (=NCIMB 14147T=DSM 18841T)] are proposed.

Four Gram-negative, rod-shaped, non-spore-forming and non-motile bacterial strains were isolated from surfaces and biofilms associated with beer-bottling plants. Based on their 16S rRNA gene sequences these isolates were allocated to the genus Chryseobacterium. The sequence similarities of the isolates to the next most closely related type strains of this genus ranged from 96.4 to 98.3 %. The presence of menaquinone MK-6 and predominant fatty acids 15 : 0 iso, 17 : 1 iso cis9, 15 : 0 iso 2-OH and 17 : 0 iso 3-OH supported the affiliation of these strains to the genus. The results of DNA–DNA hybridization, biochemical tests and chemotaxonomic properties allowed genotypic and phenotypic differentiation of the strains from the next most closely related Chryseobacterium species with validly published names. Therefore, the isolates represent four novel species for which the names Chryseobacterium ureilyticum (type strain F-Fue-04IIIaaaaT=DSM 18017T=CCUG 52546T), Chryseobacterium gambrini (type strain 5-1St1aT=DSM 18014T=CCUG 52549T), Chryseobacterium pallidum (type strain 26-3St2bT=DSM 18015T=CCUG 52548T) and Chryseobacterium molle (type strain DW3T=DSM 18016T=CCUG 52547T) are proposed.

Two Gram-negative, anaerobic, non-spore-forming, rod-shaped organisms were isolated from human amniotic fluid. Based on morphological and biochemical criteria, the strains were tentatively identified as Bacteroidaceae but they did not appear to correspond to any recognized species of this family. Comparative 16S rRNA gene sequencing studies showed the strains were highly related to each other and confirmed their placement in the genus Prevotella, but sequence divergence values of >4 % with reference Prevotella species demonstrated that the organisms from human clinical sources represent a novel species. Phylogenetic analysis revealed the novel organism to be most closely related to Prevotella bivia, an organism frequently associated with pelvic inflammatory diseases. The major long-chain cellular fatty acids of the novel species consist of iso-C14 : 0, anteiso-C15 : 0, iso-C15 : 0, C16 : 0, iso-C16 : 0 and iso-3-OH-C17 : 0. Based on biochemical criteria and phylogenetic considerations, it is proposed that the unknown isolates from human amniotic fluid be assigned to a new species of the genus Prevotella, as Prevotella amnii sp. nov. The type strain of Prevotella amnii is CCUG 53648T (=JCM 14753T).

Numerous novel anaerobic bacteria were isolated from the crevicular spaces of dogs with periodontitis. The phenotypic characteristics of these bacterial isolates indicated that they were similar to members of the genus Porphyromonas. However, comparison of the 16S rRNA gene sequences of the isolates indicated that they were related to members of the Bacteroides splanchnicus subgroup. A representative of the novel isolates, strain B106T, induced alveolar bone loss in a mouse model of experimental periodontal disease. Based on biochemical, morphological, molecular phylogenetic, and pathogenic evidence, it is proposed that the taxonomic subgroup containing these novel isolates and B. splanchnicus should be classified in a new genus, Odoribacter gen. nov., within the family ‘Porphyromonadaceae’. In addition, it is proposed that B. splanchnicus should be reclassified as Odoribacter splanchnicus comb. nov., and that the newly identified isolates should be classified as representing Odoribacter denticanis sp. nov., the type strain of which is B106T (=ATCC PTA-3625T=CNCM I-3225T).