scholarly journals Pantoea rodasii sp. nov., Pantoea rwandensis sp. nov. and Pantoea wallisii sp. nov., isolated from Eucalyptus

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1457-1464 ◽  
Author(s):  
Carrie L. Brady ◽  
Ilse Cleenwerck ◽  
Lorinda van der Westhuizen ◽  
Stephanus N. Venter ◽  
Teresa A. Coutinho ◽  
...  
Keyword(s):  
South Africa ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
16S Rrna Gene Sequencing ◽  
Culture Collection ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Rrna Gene Sequencing

Several Gram-negative-staining, facultatively anaerobic bacterial isolates were obtained from Eucalyptus seedlings showing symptoms of bacterial blight and dieback in Colombia, Rwanda and South Africa. Partial 16S rRNA gene sequencing, together with partial gyrB sequencing, placed the isolates in the genus Pantoea and indicated that they constituted three novel species. Multilocus sequence analysis (MLSA) based on partial sequences of gyrB, rpoB, infB and atpD revealed Pantoea dispersa , Pantoea eucrina and Pantoea cypripedii as their closest phylogenetic relatives. DNA–DNA hybridization studies confirmed the classification of the new isolates as three novel species and phenotypic tests allowed them to be differentiated from their closest phylogenetic neighbours. The names Pantoea rodasii sp. nov. [type strain LMG 26273T = BD 943T (deposited with the Plant Pathogenic and Plant Protecting Bacteria Collection, South Africa) = BCC 581T (deposited with the Bacterial Culture Collection, Forestry and Agricultural Institute, South Africa)], Pantoea rwandensis sp. nov. (type strain LMG 26275T = BD 944T = BCC 571T) and Pantoea wallisii sp. nov. (type strain LMG 26277T = BD 946T = BCC 682T) are proposed.

scholarly journals Arcanobacterium bovis sp. nov., isolated from the milk of a cow with mastitis

2020 ◽  
Vol 70 (7) ◽  
pp. 4105-4110 ◽  
Author(s):  
Osama Sammra ◽  
Geoffrey Foster ◽  
Abdulwahed Ahmed Hassan ◽  
Mazen Alssahen ◽  
Christoph Lämmler ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
16S Rrna Gene Sequencing ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Wet Lab ◽  
Rrna Gene Sequencing

A polyphasic taxonomic study was performed on an unidentified Arcanobacterium -like Gram-stain-positive bacterium designated strain C605018/01/1T isolated from a milk sample collected from the udder of a cow at post mortem. Comparative 16S rRNA gene sequencing showed that the bacterium belonged to the genus Arcanobacterium and was most closely related to the type strain of Arcanobacterium pluranimalium (99.76 %); sequence similarities to all other Arcanobacterium species were below 97 %. The wet-lab DNA–DNA hybridization values among strain C605018/01/1T and A. pluranimalium DSM 13483ᵀ were low, 16.9 % (reciprocal, 49.8 %). Pertaining to the whole genome sequence with a total length of 2.02 Mb and 1654 protein counts, the novel strain C605018/01/01T displayed a G+C content of 51.6 % mol%. The presence of the major menaquinone MK-9(H4) supported the affiliation of this strain to the genus Arcanobacterium . The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol-mannoside and unidentified glycolipid and aminophospholipids. Based on these results it is proposed that strain C605018/01/1T should be classified as representing a novel species, Arcanbacterium bovis sp. nov. The type strain C605018/01/1T (CCUG 45425T=DSM 107286T=BCCM/LMG 30783T)

scholarly journals Mucilaginibacter gotjawali sp. nov., isolated from soil of a lava forest

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 952-958 ◽  
Author(s):  
Keun Chul Lee ◽  
Kwang Kyu Kim ◽  
Mi Kyung Eom ◽  
Jong-Shik Kim ◽  
Dae-Shin Kim ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Gram Stain ◽  
Content Type ◽  
Link Type ◽  
Rrna Gene Sequencing

A novel bacterial strain, designated SA3-7T, was isolated from soil of a lava forest located in Jeju, Republic of Korea. Cells of strain SA3-7T were Gram-stain-negative, oxidase- and catalase-positive, non-motile rods and produced creamy white colonies on ten-fold-diluted R2A agar. The isolate contained menaquinone-7 (MK-7) as the predominant isoprenoid quinone and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 43.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain SA3-7T was related most closely to Mucilaginibacter frigoritolerans FT22T (96.7 % sequence similarity) and that it formed a separate lineage in the genus Mucilaginibacter . Combined phenotypic, chemotaxonomic and phylogenetic characteristics supported the conclusion that strain SA3-7T represents a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter gotjawali sp. nov. is proposed; the type strain is SA3-7T ( = KCTC 32515T = CECT 8628T = DSM 29289T).

Vibrio caribbeanicus sp. nov., isolated from the marine sponge Scleritoderma cyanea

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1736-1743 ◽  
Author(s):  
Maria Hoffmann ◽  
Steven R. Monday ◽  
Marc W. Allard ◽  
Errol A. Strain ◽  
Paul Whittaker ◽  
...  
Keyword(s):  
Marine Sponge ◽  
Type Species ◽  
Novel Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Rrna Gene Sequencing

A Gram-negative, oxidase-positive, catalase-negative, facultatively anaerobic, motile, curved rod-shaped bacterium, strain N384T, was isolated from a marine sponge (Scleritoderma cyanea; phylum Porifera) collected from a depth of 795 feet (242 m) off the west coast of Curaçao. On the basis of 16S rRNA gene sequencing, strain N384T was shown to belong to the genus Vibrio , most closely related to Vibrio brasiliensis LMG 20546T (98.8 % similarity), Vibrio nigripulchritudo ATCC 27043T (98.5 %), Vibrio tubiashii ATCC 19109T (98.6 %) and V. sinaloensis DSM 21326T (98.2 %). The DNA G+C content of strain N384T was 41.6 mol%. An analysis of concatenated sequences of five genes (gyrB, rpoA, pyrH, mreB and ftsZ; 4068 bp) demonstrated a clear separation between strain N384T and its closest neighbours and clustered strain N384T into the ‘Orientalis’ clade of vibrios. Phenotypically, the novel species belonged to the arginine dihydrolase-positive, lysine decarboxylase- and ornithine decarboxylase-negative (A+/L−/O−) cluster. The novel species was also differentiated on the basis of fatty acid composition, specifically that the proportions of iso-C13 : 0, iso-C15 : 0, C15 : 0, iso-C16 : 0, C16 : 0, iso-C17 : 0, C17 : 1ω8c and C17 : 0 were significantly different from those found in V. brasiliensis and V. sinaloensis . The results of DNA–DNA hybridization, average nucleotide identity and physiological and biochemical tests further allowed differentiation of this strain from other described species of the genus Vibrio . Collectively, these findings confirm that strain N384T represents a novel Vibrio species, for which the name Vibrio caribbeanicus sp. nov. is proposed, with the type strain N384T ( = ATCC BAA-2122T = DSM 23640T).

scholarly journals Lachnoanaerobaculum gen. nov., a new genus in the Lachnospiraceae : characterization of Lachnoanaerobaculum umeaense gen. nov., sp. nov., isolated from the human small intestine, and Lachnoanaerobaculum orale sp. nov., isolated from saliva, and reclassification of Eubacterium saburreum (Prévot 1966) Holdeman and Moore 1970 as Lachnoanaerobaculum saburreum comb. nov.

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2685-2690 ◽  
Author(s):  
Maria E. Hedberg ◽  
Edward R. B. Moore ◽  
Liselott Svensson-Stadler ◽  
Per Hörstedt ◽  
Vladimir Baranov ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
New Genus ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Rrna Gene Sequencing

Two novel obligately anaerobic, Gram-stain-positive, saccharolytic and non-proteolytic spore-forming bacilli (strains CD3 : 22T and N1T) are described. Strain CD3 : 22T was isolated from a biopsy of the small intestine of a child with coeliac disease, and strain N1T from the saliva of a healthy young man. The cells of both strains were observed to be filamentous, approximately 5 to >20 µm long, some of them curving and with swellings. The novel organisms produced H2S, NH3, butyric acid and acetic acid as major metabolic end products. Phylogenetic analyses, based on comparative 16S rRNA gene sequencing, revealed close relationships (98 % sequence similarity) between the two isolates, as well as the type strain of Eubacterium saburreum and four other Lachnospiraceae bacterium-/ E. saburreum -like organisms. This group of bacteria were clearly different from any of the 19 known genera in the family Lachnospiraceae . While Eubacterium species are reported to be non-spore-forming, reanalysis of E. saburreum CCUG 28089T confirmed that the bacterium is indeed able to form spores. Based on 16S rRNA gene sequencing, phenotypic and biochemical properties, strains CD3 : 22T and N1T represent novel species of a new and distinct genus, named Lachnoanaerobaculum gen. nov., in the family Lachnospiraceae [within the order Clostridiales , class Clostridia , phylum Firmicutes ]. Strain CD3 : 22T ( = CCUG 58757T  = DSM 23576T) is the type strain of the type species, Lachnoanaerobaculum umeaense gen. nov., sp. nov., of the proposed new genus. Strain N1T ( = CCUG 60305T = DSM 24553T) is the type strain of Lachnoanaerobaculum orale sp. nov. Moreover, Eubacterium saburreum is reclassified as Lachnoanaerobaculum saburreum comb. nov. (type strain CCUG 28089T  = ATCC 33271T  = CIP 105341T  = DSM 3986T  = JCM 11021T  = VPI 11763T).

Vibrio ulleungensis sp. nov., isolated from Mytilus coruscus

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Yea-Lin Moon ◽  
Jin-Sook Park
Keyword(s):  
Type Species ◽  
Novel Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Mytilus Coruscus ◽  
Link Type ◽  
Light Yellow ◽  
Rrna Gene Sequencing

A Gram-stain-negative, rod-shaped, motile via polar flagellum, facultatively aerobic, light-yellow, bacterium (designated 188UL20-2T) was isolated from a mussel sample of Mytilus coruscus collected on Ulleung Island, Ulleung-gun, Gyeongsangbuk-do, Republic of Korea. On the basis of 16S rRNA gene sequencing results, strain 188UL20-2T clustered with species of the genus Vibrio and appeared closely related to Vibrio marisflavi DSM 23086T (96.59%), Vibrio variabilis DSM 26147T (96.57%), Vibrio penaeicida DSM 14398T (96.37%) and Vibrio litoralis DSM 17657T (95.97%). The average nucleotide identity and digital DNA–DNA hybridization values between strain 188UL20-2T and its closest related strain were 71.3 and 16.4%, indicating that 188UL20-2T represents a novel species of the genus Vibrio . Growth occurred at 18–37 °C on MA medium in the presence of 1–4% NaCl (w/v) and at pH 5.0–10.0. The DNA G+C content of the genomic DNA was 45.4 mol%, and ubiquinone-8 (Q-8) was the major respiratory quinone. The major cellular fatty acids (>5%) were C16:1 ω6c and/or C16:1 ω7c (summed feature 3), C18:1 ω7c and/or C18:1 ω6c (summed feature 8), C16:0, C16:0 iso, C14:0, C14:0 iso and C12:0. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, unidentified aminophospholipid, unidentified glycolipid and seven unidentified lipids. Physiological and biochemical characteristics indicated that strain 188UL20-2T represents a novel species of the genus Vibrio , for which the name Vibrio ulleungensis sp. nov. is proposed. The type strain is 188UL20-2T (=KACC 22258T=LMG 32202T).

scholarly journals Pseudogulbenkiania gefcensis sp. nov., isolated from soil

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 187-191 ◽  
Author(s):  
Dong-Geol Lee ◽  
Dong-Moon Im ◽  
HeeCheol Kang ◽  
Pyeong Yun ◽  
Sun-Ki Park ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Sequencing Studies ◽  
Major Respiratory Quinone ◽  
Rrna Gene Sequencing

A novel strain, yH16, was isolated on nutrient agar from soil samples collected at KyungHee University, Suwon City, Republic of Korea. Cells of strain yH16T were short rods, Gram-negative-staining, motile and non-spore-forming, with a polar flagellum. Biochemical and molecular characterization revealed that this strain was most similar to Pseudogulbenkiania subflava BP-5T. Further 16S rRNA gene sequencing studies revealed that the new strain clustered with Pseudogulbenkiania subflava BP-5T (95.9 % similarity), Paludibacterium yongneupense 5YN8-15T (95.2 % similarity), Gulbenkiania mobilis E4FC31-5T (94.6 % similarity) and Chromobacterium aquaticum CC-SE-YA-1T (93.9 % similarity). The isolate was able to grow at 25–40 °C, 0.3–2 % NaCl and pH 5.5–7. The DNA G+C content was 65.9±1.0 mol%. The predominant fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16:0. Ubiquinone 8 was the major respiratory quinone. It was evident from the data obtained that the strain should be classified as a novel species of the genus Pseudogulbenkiania . The name proposed for this taxon is Pseudogulbenkiania gefcensis sp. nov., and the type strain is yH16T ( = KCCM 90100T = JCM 17850T).

scholarly journals Arthrobacter yangruifuii sp. nov. and Arthrobacter zhaoguopingii sp. nov., two new members of the genus Arthrobacter

2020 ◽  
Vol 70 (10) ◽  
pp. 5287-5295 ◽  
Author(s):  
Yajun Ge ◽  
Yuanmeihui Tao ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Tibet Plateau ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

Four unknown strains belonging to the genus Arthrobacter were isolated from plateau wildlife on the Qinghai–Tibet Plateau of PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four isolates were separated into two clusters. Cluster I (strains 785T and 208) had the greatest 16S rRNA gene sequence similarity to Arthrobacter citreus (98.6 and 98.7 %, respectively), Arthrobacter luteolus (98.0 and 98.1%, respectively), Arthrobacter gandavensis (97.9 and 98.0 %, respectively) and Arthrobacter koreensis (97.6 and 97.7 %, respectively). Likewise, cluster II (strains J391T and J915) had the highest sequence similarity to Arthrobacter ruber (98.6 and 98.3 %, respectively) and Arthrobacter agilis (98.1 and 97.9  %, respectively). Average nucleotide identity and the digital DNA–DNA hybridization values illustrated that the two type strains, 785T and J391T, represented two separate novel species that are distinct from all currently recognized species in the genus Arthrobacter . These strains had DNA G+C contents of 66.0–66.1 mol% (cluster I) and 68.0 mol% (cluster II). The chemotaxonomic properties of strains 785T and J391T were in line with those of the genus Arthrobacter : anteiso-C15:0 (79.3 and 40.8 %, respectively) as the major cellular fatty acid, MK-8(H2) (65.8 %) or MK-9(H2) (75.6 %) as the predominant respiratory quinone, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipids and phospholipid, and A3α or A4α as the cell wall peptidoglycan type. On the basis of our results, two novel species in the genus Arthrobacter are proposed, namely Arthrobacter yangruifuii sp. nov. (type strain, 785T=CGMCC 1.16725T=GDMCC 1.1592T=JCM 33491T) and Arthrobacter zhaoguopingii sp. nov. (type strain, J391T=CGMCC 1.17382T=GDMCC 1.1667T=JCM 33841T).

Mucilaginibacter soyangensis sp. nov., isolated from a lake

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 413-419 ◽  
Author(s):  
Yochan Joung ◽  
Haneul Kim ◽  
Heeyoung Kang ◽  
Beom-Il Lee ◽  
Tae-Seok Ahn ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Yellow Orange

A non-motile, yellow–orange-pigmented bacterial strain, designated HME6664T, was isolated from Lake Soyang, Republic of Korea. The major fatty acids of strain HME6664T were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c; 44.7 %) and iso-C15 : 0 (20.2 %). The DNA G+C content was 40.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME6664T formed a lineage within the genus Mucilaginibacter . Strain HME6664T was closely related to Mucilaginibacter ximonensis (96.7 %), Mucilaginibacter dorajii (96.5 %) and Mucilaginibacter lappiensis (96.3 %). On the basis of the evidence presented in this study, strain HME6664T represents a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter soyangensis sp. nov., is proposed. The type strain is HME6664T ( = KCTC 23261T = CECT 7824T).

Streptococcus orisasini sp. nov. and Streptococcus dentasini sp. nov., isolated from the oral cavity of donkeys

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2782-2786 ◽  
Author(s):  
Kazuko Takada ◽  
Masanori Saito ◽  
Osamu Tsudukibashi ◽  
Takachika Hiroi ◽  
Masatomo Hirasawa
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Sequencing Studies

Four Gram-positive, catalase-negative, coccoid isolates that were obtained from donkey oral cavities formed two distinct clonal groups when characterized by phenotypic and phylogenetic studies. From the results of biochemical tests, the organisms were tentatively identified as a streptococcal species. Comparative 16S rRNA gene sequencing studies confirmed the organisms to be members of the genus Streptococcus . Two of the isolates were related most closely to Streptococcus ursoris with 95.6 % similarity based on the 16S rRNA gene and to Streptococcus ratti with 92.0 % similarity based on the 60 kDa heat-shock protein gene (groEL). The other two isolates, however, were related to Streptococcus criceti with 95.0 and 89.0 % similarities based on the 16S rRNA and groEL genes, respectively. From both phylogenetic and phenotypic evidence, the four isolates formed two distinct clonal groups and are suggested to represent novel species of the genus Streptococcus . The names proposed for these organisms are Streptococcus orisasini sp. nov. (type strain NUM 1801T = JCM 17942T = DSM 25193T) and Streptococcus dentasini sp. nov. (type strain NUM 1808T = JCM 17943T = DSM 25137T).

scholarly journals Reclassification of Ruminococcus obeum as Blautia obeum comb. nov.

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 789-793 ◽  
Author(s):  
Paul A. Lawson ◽  
Sydney M. Finegold
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Culture Collection ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Strain Number ◽  
Sequence Similarities

During our previous studies we reclassified Clostridium coccoides and a number of misclassified ruminococci into a novel genus Blautia within the family Lachnospiraceae . However, the Rules of the Bacteriological Code currently require that the types of all species and subspecies with new names (including new combinations) be deposited in two different collections in two different countries. The type strain of Ruminococcus obeum was, at that period in time, only deposited in the American Type Culture Collection (ATCC) and a second independent deposit, as required by the Code, was not available. Consequently, the transfer of this species to the genus Blautia could not be made, because the resulting species name would not conform to the Rules governing the valid publication of species names and deposit of type material (Rules 27 and 30) and consequently would not be considered to be validly published. This resulted in a nomenclatural and taxonomic anomaly with R. obeum being phylogenetically placed among members of the genus Blautia with 16S rRNA gene sequence similarities of between 91.8 and 96.6 %. In order to rectify this unsatisfactory situation, through our discussions with the ATCC, the deposit of strain R. obeum ATCC 29174T to the DSMZ as strain number DSM 25238T was completed. Hence, the transfer of R. obeum to the genus Blautia as Blautia obeum comb. nov. is now proposed. The type strain is ATCC 29174T ( = DSM 25238T = KCTC 15206T).

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