- Volume 64, Issue Pt_7, 2014

Two novel strains, THG-C26T and THG-C31T, were characterized using a polyphasic approach to determine their taxonomic positions. These two isolates were aerobic, Gram-stain-positive, non-motile, non-spore-forming and rod-shaped. 16S rRNA gene sequences and phenotypic features including chemotaxonomic characteristics indicated that the two isolates clearly represented members of the genus Microbacterium . The quinone systems of strains THG-C26T and THG-C31T contained MK-12/MK-13 as major menaquinones. The diamino acid in cell-wall hydrolysates of the two strains was ornithine. The major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The polyamine pattern had spermidine as the predominant component. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and unidentified glycolipids. Phenotypic characteristics supported the affiliation of strains THG-C26T and THG-C31T to the genus Microbacterium . Chemotaxonomic data and DNA–DNA relatedness values allowed differentiation of these strains from other species of the genus Microbacterium with validly published names. Strains THG-C26T and THG-C31T showed highest 16S rRNA gene sequence similarities with Microbacterium resistens DMMZ 1710T (98.5 %) and Microbacterium trichothecenolyticum IFO 15077T (98.8 %), respectively, and the 16S rRNA gene sequence similarity between them was 99.0 %. DNA–DNA hybridization values between the novel isolates and strains of other species of the genus Microbacterium with validly published names were 4–25 %. Therefore, strains THG-C26T and THG-C31T are considered to represent two novel species of the genus Microbacterium , for which the names Microbacterium kyungheense sp. nov. [type strain THG-C26T ( = KACC 17124T = JCM 18735T)] and Microbacterium jejuense sp. nov. [type strain THG-C31T ( = KACC 17123T = JCM 18734T)] are proposed.

A rod-shaped, motile, facultatively anaerobic and moderately halotolerant plant-growth-promoting actinobacterial strain, designated NCCP-11T, was isolated from paddy grains. To delineate its taxonomic position, the strain was subjected to a polyphasic characterization. Cells of strain NCCP-11T grew at 10–37 °C (optimum 28–32 °C), at pH 6–9 (optimum pH 7) and in 0–12 % (w/v) NaCl (optimum 1–2 %) in broth medium. Based on 16S rRNA gene sequence analysis, strain NCCP-11T showed highest similarity to the type strains of Cellulomonas hominis (98.99 %) and Cellulomonas denverensis (98.09 %) and less than 97 % with other closely related taxa. The chemotaxonomic data [major menaquinone: MK-9(H4); cell-wall peptidoglycan: type A4β; major fatty acids: anteiso-C15 : 0, C16 : 0, C14 : 0 and anteiso-C17 : 0; major polar lipids: diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositolmannosides and two unknown polar lipids] also supported the affiliation of strain NCCP-11T to the genus Cellulomonas . The level of DNA–DNA relatedness between strain NCCP-11T and the two type strains mentioned above was less than 42.7 %. On the basis of DNA–DNA relatedness, physiological and biochemical characteristics and phylogenetic position, strain NCCP-11T can be differentiated from species of the genus Cellulomonas with validly published names and thus represents a novel species, for which the name Cellulomonas pakistanensis sp. nov. is proposed. The type strain is NCCP-11T ( = DSM 24792T = JCM 18755T = KCTC 19798T).

A Gram-staining-positive, aerobic, non-spore-forming, irregular rod-shaped actinobacterium, designated YIM C00895T, was isolated from a soil sample collected from Jiuxiang Scenic Region, Yunnan province, south-west China. The strain was able to grow at 10–28 °C, pH 6.0–10.0 and 0–11 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA (95.3 %) gene sequences revealed the highest similarity to Tomitella biformata AHU1821T. The whole-cell hydrolysates of strain YIM C00895T contained meso-diaminopimelic acid, arabinose and galactose, indicating chemotype IV. The muramic acids in the peptidoglycan were glycolated. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and an unidentified glycolipid. MK-9(H2) was the predominant menaquinone. The major fatty acids were C14 : 0, C16 : 0, C16 : 1 and C18 : 1ω9c and tuberculostearic acid (10-methyl C18 : 0) was present in relatively small amounts (4.5 %). TLC analysis of its cellular mycolic acids showed a similar profile to Tomitella biformata DSM 45403T. The DNA G+C content of the strain was 67.5 mol%. The results of physiological and biochemical tests allowed strain YIM C00895T to be differentiated phenotypically from Tomitella biformata DSM 45403T. On the basis of evidence from this polyphasic study, the novel species Tomitella cavernea sp. nov. is proposed. The type strain of Tomitella cavernea is YIM C00895T ( = DSM 45788T = JCM 18542T).

Urolithins are dibenzopyranone metabolites that exert anti-inflammatory activity in vivo and are produced by the gut microbiota from the dietary polyphenols ellagic acid (EA) and ellagitannins. However, the bacteria involved in this process remain unknown. We report here a novel bacterium, strain CEBAS 1/15PT, capable of metabolizing EA to urolithins, that was isolated from healthy human faeces and characterized by determining phenotypic, biochemical and molecular methods. The strain was related to Gordonibacter pamelaeae 7-10-1-bT, the type and only reported strain of the only species of the genus Gordonibacter, with about 97 % 16S rRNA gene sequence similarity; they were both obligately anaerobic, non-spore-forming, Gram-stain-positive, short-rods/coccobacilli and metabolized only small numbers of carbon sources. l-Fucose, d-fructose, turanose, d-galacturonic acid and α-ketobutyric acid were metabolized by strain CEBAS 1/15PT, while G. pamelaeae was negative for metabolism of these compounds. The whole-cell fatty acids consisted predominantly of saturated fatty acids (70 %); strain CEBAS 1/15PT differed significantly from G. pamelaeae in the major fatty acid, which was C18 : 1ω9c, while anteiso-C15 : 0 was the major component for G. pamelaeae . The presence of a number of different fatty acid peaks, especially C19 : 0 cyclo and C18 : 1ω6c, was also indicative of distinct species. Six glycolipids (GL1–6) were recognized, while, in G. pamelaeae, only four glycolipids were described. On the basis of these data, the novel species Gordonibacter urolithinfaciens sp. nov. is described, with strain CEBAS 1/15PT ( = DSM 27213T = CCUG 64261T) as the type strain.

A Gram-staining-positive, aerobic and non-motile strain, 0704P10-1T, was isolated from hydrothermal sediment of the Indian Ocean. Phylogenetic, phenotypic and chemotaxonomic data for the organism supported that it belonged to the genus Janibacter . Strain 0704P10-1T showed 97.2–98.7 % 16S rRNA gene sequence similarities to the type strains of recognized members of the genus Janibacter . It contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall. MK-8(H4) was the only menaquinone detected. The major fatty acids were iso-C16 : 0, C17 : 1ω8c and 10-methyl C17 : 0. Meanwhile, the results of DNA–DNA hybridization studies and other physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain 0704P10-1T from closely related species. Thus, strain 0704P10-1T represents a novel species of the genus Janibacter , for which the name Janibacter indicus sp. nov. is proposed. The type strain is 0704P10-1T ( = LMG 27493T = CGMCC 1.12511T).

A Gram-stain-positive, aerobic, non-flagellated bacterium, designated KIS22-12T, was isolated from a soil sample of Baengnyeong Island in Onjin county, Republic of Korea. Cells were non-spore-forming cocci showing catalase-positive and oxidase-negative reactions. Growth of strain KIS22-12T was observed between 10 and 35 °C (optimum, 28–30 °C), between pH 5.0 and 9.0 (optimum, pH 7.0) and with 0–3 % (w/v) NaCl. Strain KIS22-12T contained MK-8(H4) as the predominant menaquinone, and C17 : 1ω8c, iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. Strain KIS22-12T contained diphosphatidylglycerol, phosphatidylinositol, one unknown aminophospholipid, one unknown aminolipid, two unknown phospholipids and one unknown lipid. The peptidoglycan type was A1γ. The G+C content of the genomic DNA was 75.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KIS22-12T formed a phyletic lineage with Oryzihumus leptocrescens KV-628T. 16S rRNA gene sequence similarity between the two strains was 96.5 %. On the basis of phenotypic, chemotaxonomic and molecular properties, strain KIS22-12T represents a novel species within the genus Oryzihumus , for which the name Oryzihumus terrae sp. nov. is proposed. The type strain is KIS22-12T ( = KACC 16543T = DSM 27161T = NBRC 109596T). An emended description of the genus Oryzihumus is also provided.

A novel actinomycete, strain 30EHST, was isolated from the rhizospheric soil under an elephant ear plant (Caladium bicolor) in Jomthong district, Bangkok, Thailand. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 30EHST fell within the cluster of the genus Streptosporangium . Chemical composition analysis confirmed that the strain represented a member of the genus Streptosporangium even though this strain produced a tightly packed single spore on aerial hyphae. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain 30EHST was most closely related to Streptosporangium fragile NBRC 14311T (98.1 %), Streptosporangium carneum NBRC 15562T (97.8 %) and Streptosporangium violaceochromogenes NBRC 15560T (97.4 %). The DNA–DNA hybridization relatedness values between strain 30EHST and the above three strains were below 70 %. Based on combined data for phylogenetic analysis, DNA–DNA hybridization relatedness and physiological characteristics, it was concluded that strain 30EHST should be classified as representing a novel species of the genus Streptosporangium . We propose the name Streptosporangium jomthongense sp. nov., with the type strain 30EHST ( = BCC 53154T = NBRC 110047T). An emended description of the genus Streptosporangium is also proposed.

Two actinomycete strains, designated TRM 49117T and TRM 49136T, were isolated from a hypersaline habitat in Xinjiang Province, north-west China and were characterized taxonomically by using a polyphasic study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TRM 49117T had 93.93 % similarity with the type strain Glycomyces halotolerans TRM 40137T (GenBank accession no. HQ651156) and TRM 49136T had 94.32 % similarity with G. halotolerans TRM 40137T. The 16S rRNA gene sequence similarity between the two new isolates was 93 %. The isolates contained meso-diaminopimelic acid as the diagnostic diamino acid and anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major cellular fatty acids. The predominant menaquinones of the isolates were MK-9(H4) and MK-9(H6). The whole-cell sugar patterns of these strains contained xylose and ribose, and strain TRM 49136T also contained arabinose. The polar lipid pattern of strain TRM 49117T comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylcholine, phosphatidylinositol and three additional unknown phospholipids. The polar lipid pattern of strain TRM 49136T comprised phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, glycolipids and two phosphoglycolipids of unknown composition. Genotypic and phenotypic data confirmed that strains TRM 49117T and TRM 49136T represent two novel species, clearly different from related species of the genus Glycomyces , for which the names Glycomyces fuscus sp. nov. (type strain TRM 49117T = CCTCC AA 2013003T = NRRL B-59998T = KACC 17682T) and Glycomyces albus sp. nov. (type strain TRM 49136T = CCTCC AA 2013004T = NRRL B-24927T = KACC 17681T) are proposed.

A novel actinomycete, strain FMN03T, was isolated from a soil sample collected from Yuga Zapadnaya South-West Forest Park, Moscow, Russia. The isolate had chemical and morphological properties typical of members of the genus Nonomuraea and formed a distinct 16S rRNA gene subclade with the type strains Nonomuraea roseoviolacea subsp. carminata NBRC 15903T and Nonomuraea roseoviolacea subsp. roseoviolacea NBRC 14098T. The organism formed extensively branched substrate and aerial hyphae, which generated spiral chains of spores with smooth surfaces. The cell wall contained meso-diaminopimelic acid and the whole cell sugars were glucose, galactose and trace amounts of madurose, mannose and xylose. The polar lipids were phosphatidylethanolamine, hydroxyphosphatidylethanolamine, four unidentified phospholipids, four unidentified glycolipids and one unidentified lipid. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C16 : 0 2-OH, C17 : 0 10-methyl, C17 : 1 cis9 and iso-C16 : 0. Analyses of its morphological, physiological and biochemical characteristics, together with DNA–DNA relatedness data, confirmed that strain FMN03T is a representative of a novel species of the genus Nonomuraea , which is distinct from closely related reference strains. Strain FMN03T ( = DSM 45913T = KCTC 29233T) is proposed as the type strain of a novel species, for which the name Nonomuraea muscovyensis sp. nov. is proposed.

A Gram-stain-positive aerobic organism, isolated from the healthy stem of a Zea mays plant was studied for its taxonomic position. Based on 16S rRNA gene sequence analysis strain JM-1068T was most closely related to Nocardioides alkalitolerans (97.2 %). The 16S rRNA gene sequence similarity to all other species of the genus Nocardioides was ≤96.1 %. The quinone system of strain JM-1068T contained the major menaquinone MK-8(H4). The diagnostic diamino acid of the peptidoglycan was ll-diaminopimelic acid. In the polar lipid profile, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unidentified phospholipids were predominant. The polyamine pattern contained predominantly spermidine and spermine. The fatty acid profile was composed of iso-C16 : 0 and C18 : 1ω9c in addition to C16 : 0, C17 : 0 and C17 : 1ω8c and low amounts of C16 : 0 2-OH and C17 : 0 2-OH. This supported the allocation of the strain to the genus Nocardioides . In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain JM-1068T from N. alkalitolerans . It is concluded that JM-1068T represents a novel species of the genus Nocardioides , for which we propose the name Nocardioides zeae sp. nov., with JM-1068T ( = CIP 110696T = LMG 28079T) as the type strain.

Two coccoid, non-motile, obligately anaerobic, Gram-stain-negative bacteria, occurring singly or in pairs, or as short chains, with a mean size of 1.4–2.5 µm were isolated from the faeces of two healthy human volunteers, aged 26 and 56 years, and were designated NMBHI-10T and BLPYG-7, respectively. Both the strains were affiliated to the sub-branch Sporomusa of the class Clostridia as revealed by 16S rRNA gene sequence analysis. The isolates NMBHI-10T and BLPYG-7 showed 99.1 and 99.2 % 16S rRNA gene sequence similarity, respectively, with Megasphaera elsdenii JCM 1772T. DNA–DNA hybridization and phenotypic analysis showed that both the strains were distinct from their closest relative, M. elsdenii JCM 1772T (42 and 53 % DNA–DNA relatedness with NMBHI-10T and BLPYG-7, respectively), but belong to the same species (DNA–DNA relatedness of 80.9 % between the isolates). According to DNA–DNA hybridization results, the coccoid strains belong to the same genospecies, and neither is related to any of the recognized species of the genus Megasphaera . Strains NMBHI-10T and BLPYG-7 grew in PYG broth at temperatures of between 15 and 40 °C (optimum 37 °C), but not at 45 °C. The strains utilized a range of carbohydrates as sources of carbon and energy including glucose, lactose, cellobiose, rhamnose, galactose and sucrose. Glucose fermentation resulted in the formation of volatile fatty acids, mainly caproic acid and organic acids such as succinic acid. Phylogenetic analysis, specific phenotypic characteristics and/or DNA G+C content also differentiated the strains from each other and from their closest relatives. The DNA G+C contents of strains NMBHI-10T and BLPYG-7 are 57.7 and 54.9 mol%, respectively. The major fatty acids were 12 : 0 FAME and 17 : 0 CYC FAME. On the basis of these data, we conclude that strains NMBHI-10T and BLPYG-7 should be classified as representing a novel species of the genus Megasphaera , for which the name Megsphaera indica sp. nov. is proposed. The type strain is NMBHI-10T ( = DSM 25563T = MCC 2481T).

A thermophilic bacterium, strain SueokaT, was isolated from steamed Japanese cedar chips from a lumber mill in Gobo, Japan. The strain was able to grow on carboxymethyl cellulose at 60 °C, was Gram-stain-negative, and grew between 40.0 and 67.5 °C (optimum at 55 °C) and between pH 3.5 and 6.5 (optimum at pH 4.8). Comparative analysis of 16S rRNA gene sequences revealed 91.9 , 90.9 , and 90.8 % similarity to Alicyclobacillus macrosporangiidus T , Alicyclobacillus pomorum T , and Alicyclobacillus acidocaldarius T , respectively. The major quinone was MK-7 and the predominant cellular fatty acids were ω-cyclohexane C19 : 0 and ω-cyclohexane C17 : 0. The DNA G+C content was 60.8 mol%. Based on the results of this study, strain SueokaT is a novel species of the genus Alicyclobacillus , and the namehttp://dx.doi.org/10.1601/nm.5071 Alicyclobacillus cellulosilyticus sp. nov. (type strain SueokaT = JCM 18487T = KCTC 33007T) is proposed.

A Gram-positive-staining, aerobic, endospore-forming bacterium, strain P-207T, was isolated from a rhizosphere soil sample in Auburn, AL, USA. On the basis of 16S rRNA gene sequence comparisons, strain P-207T was grouped in the vicinity of representatives of the genera Virgibacillus , Ornithinibacillus , Cerasibacillus , Lentibacillus and Oceanobacillus , but could not be assigned clearly to any of these genera. The highest similarity was found to the sequence of Virgibacillus carmonensis LMG 20964T (94.4 %); however, the 16S rRNA gene sequence similarity to the type strain of the type species of Virgibacillus , Virgibacillus pantothenticus , was only 92.9 %. The quinone system of strain P-207T consisted predominantly of menaquinone MK-7. The polar lipid profile exhibited the major lipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and moderate to minor amounts of several unidentified phospholipids, glycolipids and phosphoglycolipids, an aminophospholipid and an aminolipid. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid and the polyamine pattern contained predominantly spermidine and spermine. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. The G+C content of the genomic DNA was 34 mol%. Because of the low sequence similarity of strain P-207T to all representatives of Virgibacillus , Ornithinibacillus , Cerasibacillus , Lentibacillus and Oceanobacillus , which was always <95 %, and its unique lipid pattern, we propose that strain P-207T represents a novel species in a new genus, for which the name Pseudogracilibacillus auburnensis gen. nov., sp. nov. is proposed. The type strain of Pseudogracilibacillus auburnensis is P-207T ( = CCM 8509T = LMG 28212T = CIP 110797T).

A novel anaerobic succinate-producing bacterium, strain ZWBT, was isolated from sludge collected from a biogas desulfurization bioreactor (Eerbeek, the Netherlands). Cells were non-spore-forming, motile, slightly curved rods (0.4–0.5 µm in diameter and 2–3 µm in length), and stained Gram-negative. The temperature range for growth was 25–40 °C, with an optimum at 37 °C. The pH range for growth was 7.0–9.0, with an optimum at pH 7.5. Strain ZWBT was able to ferment glycerol and several carbohydrates mainly to H2, succinate and acetate. Sulfur and fumarate could be used as electron acceptors by strain ZWBT. The G+C content of the genomic DNA was 37.6 mol%. The most abundant fatty acids were iso-C14 : 0 and iso-C16 : 0 DMA. On the basis of 16S rRNA gene sequence similarity, strain ZWBT belongs to the family Ruminococcaceae and it is distantly related to Saccharofermentans acetigenes JCM 14006T (92.1 %). Based on the physiological features and phylogenetic analysis, strain ZWBT represents a novel species of a new genus, for which the name Ercella succinigenes gen. nov., sp. nov. is proposed. The type strain of Ercella succinigenes is ZWBT ( = DSM 27333T = JCM 19283T).

A novel type of rock-weathering bacterium was isolated from weathered rock (tuff) surface collected from Dongxiang (Jiangxi, eastern China). Cells of strain G19T were Gram-reaction-positive, rod-shaped, endospore-forming and non-motile. The strain was aerobic, catalase- and oxidase-positive, and grew optimally at 30 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain G19T was shown to belong to the genus Bacillus and the closest phylogenetic relatives were Bacillus aryabhattai B8W22T (97.4 %) and Bacillus megaterium IAM 13418T (97.1 %). The DNA G+C content was 36.7 mol% and the predominant respiratory quinone was MK-7. The major fatty acids were iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0. The polar lipid profile of strain G19T contained phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and an unidentified lipid. Based on the low level of DNA–DNA relatedness (ranging from 49.4 % to 55.0 %) to these type strains of species of the genus Bacillus and unique phenotypic characteristics, strain G19T represents a novel species of the genus Bacillus , for which the name Bacillus qingshengii sp. nov. is proposed. The type strain is G19T ( = CCTCC AB 2013273T = JCM 19454T).