Oceanobacillus aidingensis sp. nov., a moderately halophilic bacterium.
ABSTRACT: Two Gram-positive, rod-shaped moderately halophilic bacterial strains, designated AD7-25(T) and AB-11, were isolated from Aiding and Manasi salt lakes in Xinjiang of China, respectively. The strains were found to be able to grow at NaCl concentrations of 0-21 % (w/v), with optimum growth occurring at 6-8 % (w/v) NaCl. The optimal temperature and pH for growth were determined to be 33-37 °C and pH 7.0-7.5. Cells of the strains are motile by means of polar flagella. Both strains can produce ellipsoidal spores. The major cellular fatty acids were identified as anteiso-C15:0, iso-C15:0, iso-C14:0, anteiso-C17:0 and iso-C16:0. The diamino acid in the peptidoglycan and the major quinone system were determined to be meso-diaminopimelic acid (meso-DAP) and MK-7, respectively. The DNA G+C contents of stains AD7-25(T) and AB-11 were 39.8 and 40.0 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that these two novel strains are closely related to the genus Oceanobacillus showing 90-99.5 % similarity with respect to type strains. These two novel strains were most closely related to Oceanobacillus oncorhynchi subsp. incaldanensis DSM 16557(T) (99.1 and 99.5 %), followed by O. oncorhynchi subsp. oncorhynchi JCM 12661(T) (99.1 and 99.4 %), Oceanobacillus neutriphilus CGMCC 1.7693(T) (97.0 and 97.5 %), Oceanobacillus sojae JCM 15792(T) (97.6 and 98.0 %) and Oceanobacillus locisalsi KCTC 13253(T) (96.5 and 96.9 %). The DNA-DNA hybridization data indicated that DNA relatedness between strains AD7-25(T) and AB-11 was 91.0 %, and the genomic homology of representative strain AD7-25(T) with O. oncorhynchi subsp. incaldanensis DSM 16557(T), O. oncorhynchi subsp. oncorhynchi JCM 12661(T), O. neutriphilus CGMCC 1.7693(T), O. sojae JCM 15792(T) and O. locisalsi KCTC 13253(T) were 41, 39, 20, 23 and 17 %, respectively. On the basis of phenotypic and phylogenetic distinctiveness, strains AD7-25(T) and AB-11 should be assigned to the genus Oceanobacillus as a new species, for which the name Oceanobacillus aidingensis sp. nov. was proposed. The type strain is AD7-25(T) (=CGMCC 1.9106 (T) = NBRC 105904(T)).
Project description:Two extremely halophilic archaeal strains, designated SB29T and SB3T, were isolated from the brine-seawater interface of Discovery Deep in the Red Sea. Cells of both strains were pleomorphic (irregular polyhedrals, ovals, and rods) and stained Gram-negative; colonies were pigmented pink. The sequence similarity of the 16S rRNA gene of strain SB29T with that of its most closely related validly described species (Hfx. sulfurifontis DSM 16227T) and that of strain SB3T with its closest validly described relative (Hfx. denitrificans ATCC 35960T) was 98.1% and 98.6%, respectively. The incomplete draft genomes of SB29T and SB3T are 3,871,125 bp and 3,904,985 bp in size, respectively, and their DNA G + C contents are 60.75% and 65.64%, respectively. The highest ANI values between the genomes of SB29T and SB3T and the most closely related genomes in GenBank were determined as 82.6% (Hfx. sulfurifontis ATCC BAA-897T, GenBank accession no. GCA_000337835.1) and 92.6% (Haloferax denitrificans ATCC 35960T, GenBank accession no. GCA_000337795.1), respectively. These data indicate that the two new isolates cannot be classified into any recognized species of the genus Haloferax, and, therefore, two novel species of the genus Haloferax are proposed: Haloferax profundi sp. nov. (type strain SB29T = JCM 19567T = CGMCC 1.14960T) and Haloferax marisrubri sp. nov. (type strain SB3T = JCM 19566T = CGMCC 1.14958T).
Project description:Three Gram-stain-positive, irregular-rod-shaped, non-motile, non-spore-forming bacteria were isolated from nematodes collected from Santa Antao, Cabo Verde (CBX151T, CBX152T) and Kakegawa, Japan (CBX130T). Based on 16S rRNA gene sequence similarity, strains CBX130T, CBX151T and CBX152T were shown to belong to the genus Leucobacter. This affiliation was supported by chemotaxonomic data (2,4-diaminobutyric acid in the cell wall; major respiratory quinones MK-10 and MK-11; major polar lipids phosphatidylglycerol and diphosphatidylglycerol; major fatty acids anteiso-C15?:?0, anteiso-C17?:?0 and iso-C16?:?0). Strains CBX130T and CBX152T were found to share salient characteristics. Based on morphological, physiological, chemotaxonomic and biochemical analysis, strain CBX152T represents a novel species of the genus Leucobacter, for which the name Leucobacter musarum sp. nov. (type strain CBX152T?=?DSM 27160T?=?CIP 110721T) is proposed. Two subspecies of Leucobacter musarum sp. nov. are proposed: Leucobacter musarum sp. nov. subsp. musarum subsp. nov. (type strain CBX152T?=?DSM 27160T?=?CIP 110721T) and Leucobacter musarum sp. nov. subsp. japonicus subsp. nov. (type strain CBX130T?=?DSM 27158T?=?CIP 110719T). The third novel strain, CBX151T, showed genetic similarities with Leucobacter celer NAL101T indicating that these strains belong to the same species. Based on morphological, physiological, chemotaxonomic and biochemical differences it is proposed to split the species Leucobacter celer into two novel subspecies, Leucobacter celer subsp. celer subsp. nov. (type strain NAL101T?=?KACC 14220T?=?JCM 16465T) and Leucobacter celer subsp. astrifaciens subsp. nov. (type strain CBX151T?=?DSM 27159T?=?CIP 110720T), and to emend the description of Leucobacter celerShin et al. 2011.
Project description:Recently, it has been proposed that strains of Propionibacterium acnes from the type III genetic division should be classified as P. acnessubsp. elongatum subsp. nov., with strains from the type I and II divisions collectively classified as P. acnessubsp. acnes subsp. nov. Under such a taxonomic re-appraisal, we believe that types I and II should also have their own separate rank of subspecies. In support of this, we describe a polyphasic taxonomic study based on the analysis of publicly available multilocus and whole-genome sequence datasets, alongside a systematic review of previously published phylogenetic, genomic, phenotypic and clinical data. Strains of types I and II form highly distinct clades on the basis of multilocus sequence analysis (MLSA) and whole-genome phylogenetic reconstructions. In silico or digital DNA-DNA similarity values also fall within the 70-80 % boundary recommended for bacterial subspecies. Furthermore, we see important differences in genome content, including the presence of an active CRISPR/Cas system in type II strains, but not type I, and evidence for increasing linkage equilibrium within the separate divisions. Key biochemical differences include positive test results for β-haemolytic, neuraminidase and sorbitol fermentation activities with type I strains, but not type II. We now propose that type I strains should be classified as P. acnessubsp. acnes subsp. nov., and type II as P. acnessubsp. defendens subsp. nov. The type strain of P. acnessubsp. acnes subsp. nov. is NCTC 737T (=ATCC 6919T=JCM 6425T=DSM 1897T=CCUG 1794T), while the type strain of P. acnessubsp. defendens subsp. nov. is ATCC 11828 (=JCM 6473=CCUG 6369).
Project description:Strains JW1T and JW3, isolated from surface seawater of the Arabian Sea, were subjected to polyphasic taxonomic analysis. Cells of both strains were Gram-stain-negative, aerobic, and rod-shaped. They formed violet pigment and produced violacein. On the basis of 16S rRNA gene sequence analysis, strains JW1T and JW3 showed high 16S rRNA gene sequence similarity with Pseudoalteromonas byunsanensis JCM12483T (98.2%), P. shioyasakiensis SE3T (97.8%), P. arabiensis JCM 17292T (97.3%), and P. gelatinilytica NH153T (97.1%). The 16S rRNA gene sequence similarity between JW1T and JW3 was 100%. Phylogenetic analyses revealed that both strains fell within the cluster of the genus Pseudoalteromonas and represented an independent lineage. The average nucleotide identity and in silico DNA-DNA hybridization values between JW1T and type strains of the closely related Pseudoalteromonas species were 70.9-83.3% and 20.0-26.4%, respectively. The sole respiratory quinone in both strains is ubiquinone 8 (Q-8). The principal fatty acids are summed feature 3 (C16:1?7c and/or iso-C15:0 2OH), C18:1?7c, and C16:0. The major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, one unidentified glycolipid, one unidentified aminolipid, and one unidentified phospholipid. The DNA G+C content was 43.3 mol%. Differential phylogenetic distinctiveness, chemotaxonomic differences, and phenotypic properties indicated that strains JW1T and JW3 could be differentiated from the Pseudoalteromonas species with validly published names. Therefore, it is proposed that strains JW1T and JW3 represent a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas amylolytica sp. nov. (type strain, JW1T = CGMCC 1.15681T = KCTC 52406T = MCCC 1K02162T) is proposed.
Project description:Here, we report the 4.1-Mb draft genome sequence of Bacillus subtilis subsp. natto strain CGMCC 2108, a high producer of poly-?-glutamic acid (?-PGA). This sequence will provide further help for the biosynthesis of ?-PGA and will greatly facilitate research efforts in metabolic engineering of B. subtilis subsp. natto strain CGMCC 2108.
Project description:Properties of Lactobacillus plantarum group strains isolated from two kinds of Japanese post-fermented teas, Ishizuchi-kurocha and Awa-bancha, were compared. Although lactic acid bacteria isolated from the fermented teas were identified as L. plantarum via homology comparison of 16S ribosomal RNA gene sequences, classification of L. plantarum based on ribosomal proteins showed that the strains isolated from Ishizuchi-kurocha and Awa-bancha were different. According to classification by the ribosomal protein typing, Ishizuchi-kurocha-derived strains belong to the same group as L. plantarum subsp. plantarum JCM 1149T. Awa-bancha-derived strains were assigned to a different group. This pattern was also applicable to strains isolated more than 10 years ago. A further analysis based on recA and a dnaK gene showed that Awa-bancha-derived strains were closely related to L. pentosus. The interactions with cultured cells were different between strain JCM 1149T and the Ishizuchi-kurocha-derived strains. The Ishizuchi-kurocha-derived strains showed strong adhesion to Caco-2 cells. In contrast, strain JCM 1149T and the Awa-bancha-derived strains hardly adhered to Caco-2 cells. According to the ribosomal protein typing, sugar utilization, and interaction with Caco-2 cells, although these properties were dependent on the strain strictly speaking, the L. plantarum group strains in this study can be subdivided into two groups: (1) type strain JCM 1149T and Ishizuchi-kurocha-derived strains and (2) Awa-bancha-derived strains. A regionally unique microorganism may persist in each traditional fermented drink.
Project description:Members of the haloarchaeal genera Halosarcina and Halogeometricum (family Halobacteriaceae) are closely related to each other and show 96.6-98?% 16S rRNA gene sequence similarity. This is higher than the accepted threshold value (95?%) to separate two genera, and a taxonomic study using a polyphasic approach of all four members of the two genera was conducted to clarify their relationships. Polar lipid profiles indicated that Halogeometricum rufum RO1-4(T), Halosarcina pallida BZ256(T) and Halosarcina limi RO1-6(T) are related more to each other than to Halogeometricum borinquense CGMCC 1.6168(T). Phylogenetic analyses using the sequences of three different genes (16S rRNA gene, rpoB' and EF-2) strongly supported the monophyly of these four species, showing that they formed a distinct clade, separate from the related genera Halopelagius, Halobellus, Haloquadratum, Haloferax and Halogranum. The results indicate that the four species should be assigned to the same genus, and it is proposed that Halosarcina pallida and Halosarcina limi be transferred to the genus Halogeometricum as Halogeometricum pallidum comb. nov. (type strain, BZ256(T)?=?KCTC 4017(T)?=?JCM 14848(T)) and Halogeometricum limi comb. nov. (type strain, RO1-6(T)?=?CGMCC 1.8711(T)?=?JCM 16054(T)).
Project description:The diversity of fungi associated with the gut of Pantala flavescens larvae was investigated using a culture-dependent method and molecular identification based on an analysis of the internally transcribed spacer sequence. In total, 48 fungal isolates were obtained from P. flavescens larvae. Based on phylogenetic analyses, the fungal isolates were grouped in 5 classes and 12 different genera. Fourteen bacterial 16S rDNA sequences derived from total genomic DNA extractions of fungal mycelia were obtained. The majority of the sequences were associated with Proteobacteria (13/14), and one Bacillaceae (1/14) was included. Leclercia sp., Oceanobacillus oncorhynchi and Methylobacterium extorquens, were reported for the first time as bacterial endosymbionts in fungi. High-performance liquid chromatography (HPLC) analysis indicated that bacterial symbionts produced specific metabolites and also exerted an inhibitory effect on fungal metabolites. The biological activity of the fungal culture extracts against the pathogenic bacteria Staphylococcus aureus (ATCC 6538), Bacillus subtilis (ATCC 6633) and Escherichia coli (ATCC 8739) was investigated, and 20 extracts (42%) exhibited antibacterial activity against at least one of the tested bacterial strains. This study is the first report on the diversity and antibacterial activity of symbiotic fungi residing in the gut of P. flavescens larvae, and the results show that these fungi are highly diverse and could be exploited as a potential source of bioactive compounds.
Project description:The adenovirus type 7 (Ad7) isolates from the 1995 nationwide outbreak in Japan were genetically and seroepidemiologically analyzed in comparison with Japanese Ad7 strains isolated before 1995 to determine their genome type and to speculate on their origin and causative factors of the outbreak. Twenty-six Ad7 isolates from the outbreak were identified by restriction enzyme analysis as the Ad7d2 genome type, while 22 Ad7 strains sporadically isolated in Japan before 1995 were identified as Ad7d. Partial nucleotide sequencing of the E3 region of Ad7d2 revealed a nucleotide substitution of G to A at position 265, resulting in the absence of the BstEII site and making Ad7d2 distinct from Ad7d. In Hiroshima City, Japan, no Ad7 was isolated from 1982 to 1994, but 43 and 50 Ad7 strains were isolated in 1995 and 1996, respectively. A seroepidemiological study of 251 serum samples collected in 1989 in Hiroshima City showed that only 2.8% of the samples were positive for Ad7. These results indicate that the 1995 outbreak of Ad7 in Japan was caused by the Ad7d2 genome type, which might have been introduced from outside Japan. The results also suggest that the low mass immunity in Japan was critical for the outbreak and that the mutation in the E3 region in Ad7d2 may have influenced transmission.