Lacibacter daechungensis sp. nov., isolated from deep freshwater of a reservoir

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4519-4523 ◽  
Author(s):  
Long Jin ◽  
Sang-Yoon Shin ◽  
Hyung-Gwan Lee ◽  
Chi-Yong Ahn ◽  
Hee-Mock Oh
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Whole Cells ◽  
Link Type ◽  
The 16S Rrna Gene ◽  
Motile By Gliding

A Gram-stain-negative, aerobic, motile by gliding, non-spore-forming, rod-shaped, orange-pigmented bacterium, designated strain H32-4T, was isolated from 32 m deep water of Daechung reservoir in Daejeon, Republic of Korea. Based on the nucleotide sequence of the 16S rRNA gene, the closest neighbouring type strain was Lacibacter cauensis NJ-8T with which strain H32-4T shared 98.9 % sequence similarity. The most abundant fatty acids in whole cells of strain H32-4T were C15 : 0 iso (40.6 %), C17 : 0 iso 3-OH (22.4 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 9.3 %) and C15 : 0 (6.6 %). The predominant menaquinone was MK-7. The G+C content of the genomic DNA of strain H32-4T was 45.7 mol%. Thus, these combined genotypic and phenotypic data supported the conclusion that strain H32-4T represents a novel species of the genus Lacibacter , for which the name Lacibacter daechungensis sp. nov. is proposed. The type strain is H32-4T ( = KCTC 32395T = JCM 19172T).

scholarly journals Chryseobacterium takakiae sp. nov., a member of the phylum Bacteroidetes isolated from Takakia lepidozioides

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 71-76 ◽  
Author(s):  
Ran Zhao ◽  
Xin Yao Chen ◽  
Xue Dong Li ◽  
Zhi Ling Chen ◽  
Yan Hong Li
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Approach ◽  
The 16S Rrna Gene

A Gram-stain-negative, rod-shaped and non-endospore-forming bacterium, designated strain AG1-2T, was isolated from Takakia lepidozioides collected from the Gawalong glacier in Tibet, China and characterized using a polyphasic taxonomic approach. The predominant fatty acids of strain AG1-2T were iso-C15 : 0 (36.0 %), iso-C17 : 0 3-OH (20.2 %), summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl, 16.4 %) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 11.1 %). The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids and two unidentified lipids. Strain AG1-2T contained MK-6 as the dominant menaquinone, and the genomic DNA G+C content was 37.3 mol%. The phylogenetic analysis based on the 16S rRNA gene sequences showed that strain AG1-2T was affiliated to species of the genus Chryseobacterium , and its closest related species were Chryseobacterium taiwanense Soil-3-27T, Chryseobacterium hispalense AG13T, Chryseobacterium camelliae THG C4-1T and Chryseobacterium taeanense PHA3-4T with a sequence similarity of 98.0, 97.8, 97.3 and 97.1 %, respectively. However, the DNA–DNA relatedness values between these strains and strain AG1-2T were 29, 21, 21 and 45 %, respectively. Based on phylogenetic inference and phenotypic data, strain AG1-2T is considered to represent a novel species of the genus Chryseobacterium , for which the name Chryseobacterium takakiae sp. nov. is proposed. The type strain is AG1-2T ( = CGMCC 1.12488T = DSM 26898T).

scholarly journals Spirosoma endophyticum sp. nov., isolated from Zn- and Cd-accumulating Salix caprea

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4586-4590 ◽  
Author(s):  
Julia Fries ◽  
Stefan Pfeiffer ◽  
Melanie Kuffner ◽  
Angela Sessitsch
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Salix Caprea ◽  
Cellular Fatty Acids ◽  
Link Type ◽  
The 16S Rrna Gene

A Gram-reaction-negative, yellow-pigmented strain, designated EX36T, was characterized using a polyphasic approach comprising phylogenetic, morphological and genotypic analyses. The endophytic strain was isolated from Zn/Cd-accumulating Salix caprea in Arnoldstein, Austria. Analysis of the 16S rRNA gene demonstrated that the novel strain is most closely related to members of the genus Spirosoma (95 % sequence similarity with Spirosoma linguale ). The genomic DNA G+C content was 47.2 mol%. The predominant quinone was and the major cellular fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), C16 : 1ω5c, iso-C17 : 0 3-OH and iso-C15 : 0. On the basis of its phenotypic and genotypic properties, strain EX36T should be classified as a novel species of the genus Spirosoma , for which the name Spirosoma endophyticum sp. nov. is proposed. The type strain is EX36T ( = DSM 26130T = LMG 27272T).

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).

scholarly journals Neisseria oralis sp. nov., isolated from healthy gingival plaque and clinical samples

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1323-1328 ◽  
Author(s):  
William J. Wolfgang ◽  
Teresa V. Passaretti ◽  
Reashma Jose ◽  
Jocelyn Cole ◽  
An Coorevits ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
23S Rrna ◽  
Clinical Samples ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type

A polyphasic analysis was undertaken of seven independent isolates of Gram-negative cocci collected from pathological clinical samples from New York, Louisiana, Florida and Illinois and healthy subgingival plaque from a patient in Virginia, USA. The 16S rRNA gene sequence similarity among these isolates was 99.7–100 %, and the closest species with a validly published name was Neisseria lactamica (96.9 % similarity to the type strain). DNA–DNA hybridization confirmed that these isolates are of the same species and are distinct from their nearest phylogenetic neighbour, N. lactamica . Phylogenetic analysis of 16S and 23S rRNA gene sequences indicated that the novel species belongs in the genus Neisseria . The predominant cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C18 : 1ω7c. The cellular fatty acid profile, together with other phenotypic characters, further supports the inclusion of the novel species in the genus Neisseria . The name Neisseria oralis sp. nov. (type strain 6332T  = DSM 25276T  = LMG 26725T) is proposed.

scholarly journals Rhizobium rhizoryzae sp. nov., isolated from rice roots

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1373-1377 ◽  
Author(s):  
Xiao-Xia Zhang ◽  
Xue Tang ◽  
Rizwan Ali Sheirdil ◽  
Lei Sun ◽  
Xiao-Tong Ma
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
The 16S Rrna Gene

Two strains (J3-AN59T and J3-N84) of Gram-stain-negative, aerobic and rod-shaped bacteria were isolated from the roots of fresh rice plants. The 16S rRNA gene sequence similarity results showed that the similarity between strains J3-AN59T and J3-N84 was 100 %. Both strains were phylogenetically related to members of the genus Rhizobium , and they were most closely related to Rhizobium tarimense ACCC 06128T (97.43 %). Similarities in the sequences of housekeeping genes between strains J3-AN59T and J3-N84 and those of recognized species of the genus Rhizobium were less than 90 %. The polar lipid profiles of both strains were predominantly composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unknown aminophospholipid. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The DNA G+C contents of J3-AN59T and J3-N84 were 55.7 and 57.1 mol%, respectively. The DNA–DNA relatedness value between J3-AN59T and J3-N84 was 89 %, and strain J3-AN59T showed 9 % DNA–DNA relatedness to R. tarimense ACCC 06128T, the most closely related strain. Based on this evidence, we found that J3-AN59T and J3-N84 represent a novel species in the genus Rhizobium and we propose the name Rhizobium rhizoryzae sp. nov. The type strain is J3-AN59T ( = ACCC 05916T = KCTC 23652T).

Litoreibacter roseus sp. nov., a novel bacteriochlorophyll a-containing bacterium

2021 ◽  
Author(s):  
Masataka Kanamuro ◽  
Yuki Sato-Takabe ◽  
So Muramatsu ◽  
Setsuko Hirose ◽  
Yuki Muramatsu ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Near Infrared ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A strictly aerobic, bacteriochlorophyll (BChl) a-containing alphaproteobacterium, designated strain K6T, was isolated from seawater around an aquaculture site in the Uwa Sea in Japan. The novel strain grew optimally at 30 °C at pH 7.0–7.5 and in the presence of 2.0 % (w/v) NaCl. The nonmotile and coccoid or rod-shaped cells formed pink-pigmented colonies on agar plates containing organic compounds. Cells showed an in vivo absorption maximum at 870 nm in the near-infrared region, indicating the presence of BChl a in the light-harvesting 1 complex. The new bacterial strain was Gram-stain-negative and oxidase- and catalase-positive. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain K6T was closely related to species in the genus Litoreibacter . The closest phylogenetic relatives of strain K6T were Litoreibacter ponti GJSW-31T (98.56 % sequence similarity), Litoreibacter janthinus KMM 3842T (97.63 %) and Litoreibacter albidus KMM 3851T (96.88 %). The G+C content of the genomic DNA was 58.26 mol%. The average nucleotide identity value of strain K6T with the type strain of L. ponti was 77.16 % (SD 4.79 %). The digital DNA−DNA hybridization value of strain K6T with the type strain of L. ponti was 19.40 %. The respiratory quinone was ubiquinone-10. The major cellular fatty acids were C18 : 1 ω7c, C16 : 0 and 11-methyl C18 : 1 ω7c. The dominant polar lipids were phosphatidylcholine and phosphatidylglycerol. On the basis of the genetic and phenotypic data obtained in the present study, we propose a new species in the genus Litoreibacter : Litoreibacter roseus sp. nov., whose type strain is K6T (=DSM 110109T=NBRC 114114T). Strain K6T represents the first confirmed species that produces BChl a within the genus Litoreibacter .

scholarly journals Listeria floridensis sp. nov., Listeria aquatica sp. nov., Listeria cornellensis sp. nov., Listeria riparia sp. nov. and Listeria grandensis sp. nov., from agricultural and natural environments

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1882-1889 ◽  
Author(s):  
Henk C. den Bakker ◽  
Steven Warchocki ◽  
Emily M. Wright ◽  
Adam F. Allred ◽  
Christina Ahlstrom ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Amino Acid Sequences ◽  
Rrna Gene ◽  
Natural Environments ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
A Genome

Sampling of agricultural and natural environments in two US states (Colorado and Florida) yielded 18 Listeria-like isolates that could not be assigned to previously described species using traditional methods. Using whole-genome sequencing and traditional phenotypic methods, we identified five novel species, each with a genome-wide average blast nucleotide identity (ANIb) of less than 85 % to currently described species. Phylogenetic analysis based on 16S rRNA gene sequences and amino acid sequences of 31 conserved loci showed the existence of four well-supported clades within the genus Listeria ; (i) a clade representing Listeria monocytogenes , L. marthii , L. innocua , L. welshimeri , L. seeligeri and L. ivanovii , which we refer to as Listeria sensu stricto, (ii) a clade consisting of Listeria fleischmannii and two newly described species, Listeria aquatica sp. nov. (type strain FSL S10-1188T = DSM 26686T = LMG 28120T = BEI NR-42633T) and Listeria floridensis sp. nov. (type strain FSL S10-1187T = DSM 26687T = LMG 28121T = BEI NR-42632T), (iii) a clade consisting of Listeria rocourtiae , L. weihenstephanensis and three novel species, Listeria cornellensis sp. nov. (type strain TTU A1-0210T = FSL F6-0969T = DSM 26689T = LMG 28123T = BEI NR-42630T), Listeria grandensis sp. nov. (type strain TTU A1-0212T = FSL F6-0971T = DSM 26688T = LMG 28122T = BEI NR-42631T) and Listeria riparia sp. nov. (type strain FSL S10-1204T = DSM 26685T = LMG 28119T = BEI NR- 42634T) and (iv) a clade containing Listeria grayi . Genomic and phenotypic data suggest that the novel species are non-pathogenic.

scholarly journals Brenneria goodwinii sp. nov., associated with acute oak decline in the UK

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2451-2456 ◽  
Author(s):  
Sandra Denman ◽  
Carrie Brady ◽  
Susan Kirk ◽  
Ilse Cleenwerck ◽  
Stephanus Venter ◽  
...  
Keyword(s):  
Type Strain ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Oak Decline ◽  
Bacterial Strains ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
The Uk

A group of nine Gram-negative staining, facultatively anaerobic bacterial strains isolated from native oak trees displaying symptoms of acute oak decline (AOD) in the UK were investigated using a polyphasic approach. 16S rRNA gene sequencing and phylogenetic analysis revealed that these isolates form a distinct lineage within the genus Brenneria , family Enterobacteriaceae , and are most closely related to Brenneria rubrifaciens (97.6 % sequence similarity to the type strain). Multilocus sequence analysis based on four housekeeping genes (gyrB, rpoB, infB and atpD) confirmed their position within the genus Brenneria , while DNA–DNA hybridization indicated that the isolates belong to a single taxon. The isolates can be differentiated phenotypically from their closest phylogenetic neighbours. The phylogenetic and phenotypic data demonstrate that these isolates from oak with symptoms of AOD represent a novel species in the genus Brenneria , for which the name Brenneria goodwinii sp. nov. (type strain FRB 141T  = R-43656T  = BCC 845T  = LMG 26270T  = NCPPB 4484T) is proposed.

Sphingobium sufflavum sp. nov., isolated from a freshwater lake

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3444-3450 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Yu-Wen Shiau ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Distinct Branch ◽  
The 16S Rrna Gene

A Gram-stain negative, rod-shaped, non-motile, non-spore-forming and aerobic bacterial strain, designated HL-25T, was isolated and characterized in a taxonomic study using a polyphasic approach. Comparative analysis of the 16S rRNA gene sequences showed that the isolate constituted a distinct branch within the genus Sphingobium , showing the highest level of 16S rRNA gene sequence similarity to Sphingobium vulgare HU1-GD12T (96.6 %). The major fatty acids (>10 %) of strain HL-25T were C18 : 1ω7c, C16 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C18 : 0. The major cellular hydroxy fatty acid was C14 : 0 2-OH. The major isoprenoid quinone was Q-10 and the DNA G+C content was 63.8 mol%. The polar lipid profile consisted of a mixture of sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, diphosphatidylglycerol, an uncharacterized glycolipid, an uncharacterized aminophospholipid and four uncharacterized phospholipids. The polyamine pattern of strain HL-25T contained spermidine and putrescine. On the basis of these genotypic, chemotaxonomic and phenotypic data, strain HL-25T represents a novel species in the genus Sphingobium , for which the name Sphingobium sufflavum sp. nov. is proposed. The type strain is HL-25T ( = BCRC 80413T = KCTC 23953T).

scholarly journals Puniceibacterium antarcticum gen. nov., sp. nov., isolated from seawater

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1566-1572 ◽  
Author(s):  
Chang Liu ◽  
Xi-Ying Zhang ◽  
Hai-Nan Su ◽  
Ming-Yang Zhou ◽  
Bo Chen ◽  
...  
Keyword(s):  
Type Strain ◽  
New Genus ◽  
Novel Species ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-reaction-negative, aerobic, non-flagellated, rod-shaped bacterium, designated strain SM1211T, was isolated from Antarctic seawater. The isolate grew at 4–35 °C and with 0–10 % (w/v) NaCl. It could produce bacteriochlorophyll a, but did not reduce nitrate to nitrite or hydrolyse DNA. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain SM1211T constituted a distinct phylogenetic line within the family Rhodobacteraceae and was closely related to species in the genera Litorimicrobium , Leisingera , Seohaeicola and Phaeobacter with 95.1–96.0 % similarities. The predominant cellular fatty acid was C18 : 1ω7c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid and two unidentified phospholipids. The genomic DNA G+C content of strain SM1211T was 60.7 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain SM1211T is considered to represent a novel species in a new genus within the family Rhodobacteraceae , for which the name Puniceibacterium antarcticum gen. nov., sp. nov. is proposed. The type strain of Puniceibacterium antarcticum is SM1211T ( = CCTCC AB 2013147T = KACC 16875T).

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