scholarly journals Simiduia litorea sp. nov., isolated from seashore sediments of the Sea of Japan

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2688-2692 ◽  
Author(s):  
Naoto Tanaka ◽  
Lyudmila A. Romanenko ◽  
Vassilii I. Svetashev ◽  
Valery V. Mikhailov
Keyword(s):  
Sea Of Japan ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

An aerobic, Gram-stain-negative, agarolytic rod-shaped bacterium, designated KMM 9504T, was isolated from a sediment sample collected from the seashore of the Sea of Japan. Comparative 16S rRNA gene sequence analysis showed that strain KMM 9504T belonged to the genus Simiduia as it was most closely related to Simiduia areninigrae KCTC 23293T (97.3 % sequence similarity). Strain KMM 9504T was characterized by the major ubiquinone Q-8, and by the predominance of C16 : 1ω7c, C17 : 1ω8c, followed by C16 : 0, C15 : 0, C17 : 0 and C12 : 1 in its fatty acid profile. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminophospholipid, an unknown aminolipid, unknown phospholipids, and unknown lipids. Based on the distinctive phenotypic characteristics, phylogenetic analysis and DNA–DNA hybridization results, it is concluded that strain KMM 9504T represents a novel species of the genus Simiduia , for which the name Simiduia litorea sp. nov. is proposed. The type strain of the species is strain KMM 9504T ( = NRIC 0917T = JCM 19759T).

Luteimonas vadosa sp. nov., isolated from seashore sediment

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1261-1266 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Vassilii I. Svetashev ◽  
Valeriya V. Kurilenko ◽  
Valery V. Mikhailov
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Organic Substrates ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

An aerobic, Gram-stain-negative, yellow-pigmented, non-motile, rod-shaped bacterium designated strain KMM 9005T was isolated from a sediment sample collected from the Sea of Japan seashore. Comparative 16S rRNA gene sequence analysis showed that strain KMM 9005T belonged to the genus Luteimonas and was most closely related to Luteimonas cucumeris KCTC 23627T (96.5 % sequence similarity) and Luteimonas aquatica LMG 24212T (96.1 % sequence similarity). Strain KMM 9005T was characterized by the presence of thin fimbriae, the major ubiquinone Q-8, by the predominance of iso-C17 : 1 followed by iso-C16 : 0, iso-C15 : 0 and iso-C17 : 0 in its fatty acid profile, weak hydrolytic capacity and the inability to assimilate most organic substrates. Based on these distinctive phenotypic characteristics and phylogenetic analysis, strain KMM 9005T represents a novel species of the genus Luteimonas , for which the name Luteimonas vadosa sp. nov. is proposed. The type strain is KMM 9005T ( = NRIC 0881T = JCM 18392T).

scholarly journals Bifidobacterium faecale sp. nov., isolated from human faeces

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3134-3139 ◽  
Author(s):  
Jung-Hye Choi ◽  
Kyung Min Lee ◽  
Myung-Ki Lee ◽  
Chang-Jun Cha ◽  
Geun-Bae Kim
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bifidobacterium Adolescentis ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Gene Sequence Analysis

A novel strain, designated strain CU3-7T, was isolated from faeces of a two-week-old baby. The isolate was Gram-staining-positive, anaerobic and rod-shaped. Results from 16S rRNA gene sequence analysis revealed that strain CU3-7T was phylogenetically affiliated with members of the genus Bifidobacterium . Strain CU3-7T showed the highest level of sequence similarity with Bifidobacterium adolescentis KCTC 3216T (98.4 %), followed by Bifidobacterium ruminantium KCTC 3425T (97.9 %). Analysis of hsp60 sequences showed that strain CU3-7T was closely related to B. adolescentis KCTC 3216T (94.0 %) and B. ruminantium KCTC 3425T (92.5 %). The DNA–DNA hybridization values with the closely related strains were all below the cut-off value for species delineation, 17.0 % with B. ruminantium KCTC 3425T and 14.9 % with B. adolescentis KCTC 3216T. Fructose-6-phosphate phosphoketolase activity was detected. The predominant cellular fatty acids were C16 : 0 (27.7 %), C18 : 1ω9c (27.4 %) and C18 : 1ω9c dimethylacetate (15.5 %). The DNA G+C content was 58.6 mol%. On the basis of polyphasic taxonomy, strain CU3-7T should be classified as the type strain of a novel species within the genus Bifidobacterium , for which the name Bifidobacterium faecale sp. nov. is proposed ( = KACC 17904T = JCM 19861T).

Weissella diestrammenae sp. nov., isolated from the gut of a camel cricket (Diestrammena coreana)

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2951-2956 ◽  
Author(s):  
Sei Joon Oh ◽  
Na-Ri Shin ◽  
Dong-Wook Hyun ◽  
Pil Soo Kim ◽  
Joon Yong Kim ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The 16S Rrna Gene

A novel, Gram-stain-positive, non-motile, facultatively anaerobic, rod- or coccoid-shaped bacterium, designated strain ORY33T, was isolated from the gut of a camel cricket (Diestrammena coreana). The 16S rRNA gene sequence analysis showed that strain ORY33T belonged to the genus Weissella , with highest sequence similarity to Weissella koreensis S-5623T (97.7 %). The strain grew optimally at 30 °C and pH 7 in the presence of 0 % (w/v) NaCl. Catalase and oxidase activities were negative. The genomic DNA G+C content of strain ORY33T was 45.1 mol%. DNA–DNA hybridization values between strain ORY33T and closely related members of the genus Weissella were less than 27 %. The major fatty acids of strain ORY33T were C18 : 1ω9c, C16 : 0 and C14 : 0. Based on these phenotypic, phylogenetic and genotypic analyses, strain ORY33T represents a novel species belonging to the genus Weissella , for which the name Weissella diestrammenae sp. nov. is proposed. The type strain is ORY33T ( = KACC 16890T = JCM 18559T).

scholarly journals Dyella monticola sp. nov. and Dyella psychrodurans sp. nov., isolated from monsoon evergreen broad-leaved forest soil of Dinghu Mountain, China

2019 ◽  
Vol 69 (4) ◽  
pp. 1016-1023 ◽  
Author(s):  
Xiang-yue Zhou ◽  
Zeng-hong Gao ◽  
Mei-hong Chen ◽  
Mei-qi Jian ◽  
Li-hong Qiu
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Broad Leaved Forest ◽  
Gene Sequence Analysis ◽  
Leaved Forest

Cells of bacterial strains 4 G-K06T and 4MSK11T, isolated from soil samples collected from monsoon evergreen broad-leaved forest of the Dinghushan Mountain (112° 31′ E 23° 10′ N), Guangdong Province, PR China, were Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped. Strain 4 G-K06T grew at 10–37 °C, pH 3.5–7.5 and 0–3.5 % (w/v) NaCl; while 4MSK11T grew at 4–42 °C, pH 3.5–7.5 and 0–2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed strain 4 G-K06T formed a clade with Dyella flagellata 4 M-K16T, Dyella acidisoli 4M-Z03T, Dyella humi DHG40T and Dyella nitratireducens DHG59T, while strain 4MSK11T formed a clade with Dyella caseinilytica DHOB09T and Dyella mobilis DHON07T, both within the genus Dyella . The result of the partial atpD, gyrB and lepA gene sequence analysis supported the conclusion based on 16S rRNA gene sequence analysis, which showed that these two strains represent two novel species of Dyella . The average nucleotide identity and digital DNA–DNA hybridization value for the whole genomes were 75.0–79.0 and 20.3–22.6 % between strains 4 G-K06T, 4MSK11T and those described Dyella species with genome sequences; while the DNA–DNA hybridization rates between strains 4 G-K06T, 4MSK11T and closely related Dyella species (without genome sequence) were 29.5–41.8 %. The major cellular fatty acids of these two strains were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1 ω9c, while the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified phospholipids and aminophospholipids. The only ubiquinone of these two strains was ubiquinone-8. The DNA G+C contents of 4 G-K06T and 4MSK11T were 60.4 and 61.3 mol%, respectively. On the basis of the evidence presented here, strains 4 G-K06T and 4MSK11T represent two novel species of the genus Dyella , for which the names Dyella monticola sp. nov. (type strain 4 G-K06T=LMG 30268T=GDMCC 1.1188T) and Dyella psychrodurans sp. nov. (type strain 4MSK11T=KCTC 62280T=GDMCC 1.1185T) are proposed.

scholarly journals Halioglobus maricola sp. nov., isolated from coastal seawater

2020 ◽  
Vol 70 (3) ◽  
pp. 1868-1875 ◽  
Author(s):  
Shan-Hui Li ◽  
Jaeho Song ◽  
Yeonjung Lim ◽  
Yochan Joung ◽  
Ilnam Kang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
The 16S Rrna Gene

A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated IMCC14385T, was isolated from surface seawater of the East Sea, Republic of Korea. The 16S rRNA gene sequence analysis indicated that IMCC14385T represented a member of the genus Halioglobus sharing 94.6–97.8 % similarities with species of the genus. Whole-genome sequencing of IMCC14385T revealed a genome size of 4.3 Mbp and DNA G+C content of 56.7 mol%. The genome of IMCC14385T shared an average nucleotide identity of 76.6 % and digital DNA–DNA hybridization value of 21.6 % with the genome of Halioglobus japonicus KCTC 23429T. The genome encoded the complete poly-β-hydroxybutyrate biosynthesis pathway. The strain contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C17 : 1 ω8c as the predominant cellular fatty acids as well as ubiquinone-8 (Q-8) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, five unidentified phospholipids, an unidentified aminolipid, an unidentified aminophospholipid and four unidentified lipids. On the basis of taxonomic data obtained in this study, it is suggested that IMCC14385T represents a novel species of the genus Halioglobus , for which the name Halioglobus maricola sp. nov. is proposed. The type strain is IMCC14385T (=KCTC 72520T=NBRC 114072T).

Halobacillus fulvus sp. nov., a moderately halophilic bacterium isolated from shrimp paste (Ka-pi) in Thailand

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Auttaporn Booncharoen ◽  
Wonnop Visessanguan ◽  
Nattakorn Kuncharoen ◽  
Supalurk Yiamsombut ◽  
Pannita Santiyanont ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Halophilic Bacterium ◽  
Rrna Gene ◽  
Content Type ◽  
Moderately Halophilic ◽  
Link Type ◽  
Moderately Halophilic Bacterium

An aerobic, Gram-stain-positive, endospore-forming, rod-shaped and moderately halophilic strain SKP4-6T, was isolated from shrimp paste (Ka-pi) collected from Samut Sakhon Province, Thailand. Phylogenetic analysis revealed that strain SKP4-6T belonged to the genus Halobacillus and was most closely related to Halobacillus salinus JCM 11546T (98.6 %), Halobacillus locisalis KCTC 3788T (98.6 %) and Halobacillus yeomjeoni KCTC 3957T (98.6 %) based on 16S rRNA gene sequence similarity. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain SKP4-6T and its related species were 18.2–19.3 % and 69.84–84.51 %, respectively, which were lower than the threshold recommended for species delineation. The strain grew optimally at 30–40 °C, at pH 7.0 and with 10–15 % (w/v) NaCl. It contained l-Orn–d-Asp in the cell wall peptidoglycan. The DNA G+C content was 44.8 mol%. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The predominant isoprenoid quinone was MK-7. Phosphatidylglycerol and diphosphatidylglycerol were present as major polar lipids. Based on this polyphasic approach, digital DNA–DNA relatedness and ANI values, strain SKP4-6T represents a novel species of the genus Halobacillus , for which the name Halobacillus fulvus sp. nov. is proposed. The type strain is SKP4-6T (=JCM 32624T=TISTR 2595T).

Isolation and description of Selenomonas timonae sp. nov., a novel Selenomonas species detected in a gingivitis patient

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Angéline Antezack ◽  
Manon Boxberger ◽  
Mariem Ben Khedher ◽  
Bernard La Scola ◽  
Virginie Monnet-Corti
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
Optimum Ph

A Gram-stain-negative bacterium, designated strain Marseille-Q3039T, was isolated from subgingival dental plaque of a woman with gingivitis in Marseille, France. Strain Marseille-Q3039T was found to be an anaerobic, motile and spore-forming crescent-shaped bacterium that grew at 25–41.5 °C (optimum, 37 °C), pH 5.5–8.5 (optimum, pH 7.5) and salinity of 5.0 g l−1 NaCl. The results of 16S rRNA gene sequence analysis revealed that strain Marseille-Q3039T was closely related to Selenomonas infelix ATCC 43532T (98.42 % similarity), Selenomonas dianae ATCC 43527T (97.25 %) and Centipedia periodontii DSM 2778T (97.19 %). The orthologous average nucleotide identity and digital DNA–DNA hybridization relatedness between strain Q3039T and its closest phylogenetic neighbours were respectively 84.57 and 28.2 % for S. infelix ATCC 43532T and 83.93 and 27.2 % for C. periodontii DSM 2778T. The major fatty acids were identified as C13 : 0 (27.7 %), C15 : 0 (24.4 %) and specific C13 : 0 3-OH (12.3 %). Genome sequencing revealed a genome size of 2 351 779 bp and a G+C content of 57.2 mol%. On the basis of the results from phenotypic, chemotaxonomic, genomic and phylogenetic analyses and data, we concluded that strain Marseille-Q3039T represents a novel species of the genus Selenomonas , for which the name Selenomonas timonae sp. nov. is proposed (=CSUR Q3039=CECT 30128).

Aquimarina amphilecti sp. nov., isolated from the sponge Amphilectus fucorum

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 501-505 ◽  
Author(s):  
Jonathan Kennedy ◽  
Lekha Menon Margassery ◽  
Niall D. O’Leary ◽  
Fergal O’Gara ◽  
John Morrissey ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Phenotypic Differences ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The Family

A Gram-stain-negative, rod-shaped, orange-coloured, catalase- and oxidase-positive, non-motile bacterium, designated strain 92VT, was isolated from the marine sponge Amphilectus fucorum, collected from Lough Hyne, County Cork, Ireland. 16S rRNA gene sequence analysis revealed that strain 92VT clustered with members of the family Flavobacteriaceae , the closest member being Aquimarina latercula NCIMB 1399T, with a gene sequence similarity of 97.5 %. Strain 92VT required seawater for growth with optimal growth occurring at 25 °C, at pH 6–7 and with 3 % (w/v) NaCl. MK-6 was the sole respiratory quinone present and the major fatty acids were iso-C17 : 0 3-OH, iso-C15 : 0, iso-C17 : 1ω9c and iso-C15 : 0 3-OH. The DNA G+C content was 36.1 mol%. Combined phenotypic differences and phylogenetic analysis indicate that strain 92VT represents a novel species of the genus Aquimarina , for which the name Aquimarina amphilecti sp. nov. is proposed. The type strain is 92VT ( = NCIMB 14723T = DSM 25232T).

Rhodomicrobium udaipurense sp. nov., a psychrotolerant, phototrophic alphaproteobacterium isolated from a freshwater stream

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2684-2689 ◽  
Author(s):  
V. Venkata Ramana ◽  
P. Shalem Raj ◽  
L. Tushar ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two strains (JA643T and JA755) of Gram-stain-negative, facultatively anaerobic phototrophic, bacteria capable of growth at low temperatures (10–15 °C) were isolated from freshwater streams from different geographical regions of India. Both strains contain bacteriochlorophyll a and carotenoids of the spirilloxanthin series. Phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid (PL), unidentified amino lipids (AL1–AL6, AL9) and an unidentified lipid (L1) were the polar lipids present in both strains. The major cellular fatty acid was C18 : 1ω7c (76–79 % of the total). Bacteriohopane derivatives (BHD1,2), unidentified hopanoids (UH1–5), diplopterol (DPL) and diploptene (DPE) were the major hopanoids of both strains. The DNA G+C content was 64.2–64.5 mol%. 16S rRNA gene sequence-based phylogenetic analysis showed that both strains are closely related to the genus Rhodomicrobium and clustered with Rhodomicrobium vannielii DSM 162T (99 % sequence similarity). However, both strains exhibited only 46.1 % DNA–DNA hybridization with R. vannielii DSM 162T. Strains JA643T and JA755 shared >99 % 16S rRNA gene sequence similarity and were >85 % related on the basis of DNA–DNA hybridization; they are therefore considered to represent a novel species in the genus Rhodomicrobium , for which the name Rhodomicrobium udaipurense sp. nov. is proposed. The type strain is JA643T ( = KCTC 15219T = NBRC 109057T).

scholarly journals Gemella parahaemolysans sp. nov. and Gemella taiwanensis sp. nov., isolated from human clinical specimens

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2060-2065 ◽  
Author(s):  
Wei-Chun Hung ◽  
Hsiao-Jan Chen ◽  
Jui-Chang Tsai ◽  
Sung-Pin Tseng ◽  
Tai-Fen Lee ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

Four Gram-staining-positive, catalase-negative, coccoid isolates, designated NTUH_1465T, NTUH_2196, NTUH_4957 and NTUH_5572T, were isolated from human specimens. The four isolates displayed more than 99.6 % 16S rRNA gene sequence similarity with Gemella haemolysans ATCC 10379T, and 96.7 to 98.6 % similarity with Gemella sanguinis ATCC 700632T, Gemella morbillorum ATCC 27824T or Gemella cuniculi CCUG 42726T. However, phylogenetic analysis of concatenated sequences of three housekeeping genes, groEL, rpoB and recA, suggested that the four isolates were distinct from G. haemolysans ATCC 10379T and other species. Isolates NTUH_2196, NTUH_4957 and NTUH_5572T clustered together and formed a stable monophyletic clade. DNA–DNA hybridization values among strains NTUH_1465T and NTUH_5572T and their phylogenetically related neighbours were all lower than 49 %. The four isolates could be distinguished from G. haemolysans and other species by phenotypic characteristics. Based on the phylogenetic and phenotypic results, two novel species Gemella parahaemolysans sp. nov. (type strain NTUH_1465T = BCRC 80365T = JCM 18067T) and Gemella taiwanensis sp. nov. (type strain NTUH_5572T = BCRC 80366T = JCM 18066T) are proposed.

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