scholarly journals Chryseobacterium luteum sp. nov., associated with the phyllosphere of grasses

2007 ◽  
Vol 57 (8) ◽  
pp. 1881-1885 ◽  
Author(s):  
Undine Behrendt ◽  
Andreas Ulrich ◽  
Cathrin Spröer ◽  
Peter Schumann
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Single Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Separate Species

Three isolates obtained from grass samples were investigated by means of a polyphasic taxonomic study and were shown to represent a novel species within the genus Chryseobacterium. Comparison of 16S rRNA gene sequences and phenotypic features indicated that the three isolates belonged to a single species. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic neighbours were Chryseobacterium shigense and Chryseobacterium vrystaatense, which formed a stable cluster with the isolates; this phylogeny was supported by a high bootstrap value and was obtained using different treeing methods. A DNA–DNA hybridization study with the closest neighbour, C. shigense DSM 17126T (98.3 % 16S rRNA gene sequence similarity), clearly demonstrated a separate species status for the grass isolate strain P 456/04T. Comparisons involving physiological properties and whole-cell fatty acid profiles confirmed this result at the phenotypic level. On the basis of these results, strain P 456/04T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium luteum sp. nov. is proposed. The type strain is P 456/04T (=DSM 18605T =LMG 23785T).

scholarly journals Bacteroides dorei sp. nov., isolated from human faeces

2006 ◽  
Vol 56 (7) ◽  
pp. 1639-1643 ◽  
Author(s):  
Mohammad Abdul Bakir ◽  
Mitsuo Sakamoto ◽  
Maki Kitahara ◽  
Mitsuharu Matsumoto ◽  
Yoshimi Benno
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Single Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Human Faeces

Two Gram-negative, anaerobic, non-spore-forming rod-shaped organisms were isolated from human faeces. These isolates were tentatively identified as Bacteroides based on morphological and biochemical criteria and appeared closely related to Bacteroides vulgatus ATCC 8482T. The 16S rRNA gene sequence analysis showed that the isolates were highly related to each other (99.5 %) and confirmed their placement in the genus Bacteroides. 16S rRNA gene sequence similarity values with close phylogenetic neighbours Bacteroides vulgatus ATCC 8482T (96 %) and Bacteroides massiliensis CCUG 48901T (93 %) preliminarily demonstrated that the organisms represented a novel species. The results of phenotypic, chemotaxonomic and 16S rRNA gene sequence analyses, and DNA–DNA homology values provided evidence that these two unknown isolates represent a single species and should be assigned to a novel species of the genus Bacteroides, as Bacteroides dorei sp. nov. The type strain is JCM 13471T (=DSM 17855T).

scholarly journals Corynebacterium tapiri sp. nov. and Corynebacterium nasicanis sp. nov., isolated from a tapir and a dog, respectively

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3885-3893 ◽  
Author(s):  
Sandra Baumgardt ◽  
Igor Loncaric ◽  
Peter Kämpfer ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Established Species

Two Gram-stain-positive bacterial isolates, strain 2385/12T and strain 2673/12T were isolated from a tapir and a dog's nose, respectively. The two strains were rod to coccoid-shaped, catalase-positive and oxidase-negative. The highest 16S rRNA gene sequence similarity identified Corynebacterium singulare CCUG 37330T (96.3 % similarity) as the nearest relative of strain 2385/12T and suggested the isolate represented a novel species. Corynebacterium humireducens DSM 45392T (98.7 % 16S rRNA gene sequence similarity) was identified as the nearest relative of strain 2673/12T. Results from DNA–DNA hybridization with the type strain of C. humireducens demonstrated that strain 2673/12T also represented a novel species. Strain 2385/12T showed a quinone system consisting predominantly of menaquinones MK-8(H2) and MK-9(H2) whereas strain 2673/12T contained only MK-8(H2) as predominant quinone. The polar lipid profiles of the two strains showed the major compounds phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. Phosphatidylinositol was identified as another major lipid in 2673/12T whereas it was only found in moderate amounts in strain 2385/12T. Furthermore, moderate to minor amounts of phosphatidylinositol-mannoside, β-gentiobiosyl diacylglycerol and variable counts of several unidentified lipids were detected in the two strains. Both strains contained corynemycolic acids. The polyamine patterns were characterized by the major compound putrescine in strain 2385/12T and spermidine in strain 2673/12T. In the fatty acid profiles, predominantly C18 : 1ω9c and C16 : 0 were detected. The two strains are distinguishable from each other and the nearest related established species of the genus Corynebacterium phylogenetically and phenotypically. In conclusion, two novel species of the genus Corynebacterium are proposed, namely Corynebacterium tapiri sp. nov. (type strain, 2385/12T = CCUG 65456T = LMG 28165T) and Corynebacterium nasicanis sp. nov. (type strain, 2673/12T = CCUG 65455T = LMG 28166T).

scholarly journals Flavisolibacter ginsengiterrae gen. nov., sp. nov. and Flavisolibacter ginsengisoli sp. nov., isolated from ginseng cultivating soil

2007 ◽  
Vol 57 (8) ◽  
pp. 1834-1839 ◽  
Author(s):  
Min-Ho Yoon ◽  
Wan-Taek Im
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Separate Species

Two strains (Gsoil 492T and Gsoil 643T) isolated in Pocheon Province, South Korea, from soil used for ginseng cultivation were characterized using a polyphasic approach. Both isolates comprised Gram-negative, aerobic, non-motile, rod-shaped bacteria. They had similar chemotaxonomic characteristics, e.g. containing MK-7 as the major quinone, having a DNA G+C content in the range 42.5–43.3 mol% and possessing iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. A phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates formed a tight cluster with several uncultured bacterial clones and with the established genera Terrimonas, Niastella and Chitinophaga in the phylum Bacteroidetes but were clearly separate from these genera. The levels of 16S rRNA gene sequence similarity between the isolates and type strains of related genera ranged from 87.5 to 92.4 %. Furthermore, the results of physiological and biochemical tests allowed phenotypic differentiation of the isolates from phylogenetically closely related species with validly published names. The level of 16S rRNA gene sequence similarity between the two strains was 99.5 %, whereas the DNA–DNA relatedness value was 44 %, indicating that they represent separate species. On the basis of the polyphasic evidence, a novel genus, Flavisolibacter gen. nov., and two novel species, Flavisolibacter ginsengiterrae sp. nov. (type strain Gsoil 492T=KCTC 12656T=DSM 18136T) and Flavisolibacter ginsengisoli sp. nov. (type strain Gsoil 643T=KCTC 12657T=DSM 18119T), are proposed. Flavisolibacter ginsengiterrae is the type species of the genus.

scholarly journals Pantoea allii sp. nov., isolated from onion plants and seed

2011 ◽  
Vol 61 (4) ◽  
pp. 932-937 ◽  
Author(s):  
Carrie L. Brady ◽  
Teresa Goszczynska ◽  
Stephanus N. Venter ◽  
Ilse Cleenwerck ◽  
Paul De Vos ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Rrna Gene Sequence

Eight yellow-pigmented, Gram-negative, rod-shaped, oxidase-negative, motile, facultatively anaerobic bacteria were isolated from onion seed in South Africa and from an onion plant exhibiting centre rot symptoms in the USA. The isolates were assigned to the genus Pantoea on the basis of phenotypic and biochemical tests. 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA), based on gyrB, rpoB, infB and atpD sequences, confirmed the allocation of the isolates to the genus Pantoea. MLSA further indicated that the isolates represented a novel species, which was phylogenetically most closely related to Pantoea ananatis and Pantoea stewartii. Amplified fragment length polymorphism analysis also placed the isolates into a cluster separate from P. ananatis and P. stewartii. Compared with type strains of species of the genus Pantoea that showed >97 % 16S rRNA gene sequence similarity with strain BD 390T, the isolates exhibited 11–55 % whole-genome DNA–DNA relatedness, which confirmed the classification of the isolates in a novel species. The most useful phenotypic characteristics for the differentiation of the isolates from their closest phylogenetic neighbours are production of acid from amygdalin and utilization of adonitol and sorbitol. A novel species, Pantoea allii sp. nov., is proposed, with type strain BD 390T ( = LMG 24248T).

scholarly journals Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov.

2005 ◽  
Vol 55 (1) ◽  
pp. 153-157 ◽  
Author(s):  
Valme Jurado ◽  
Ingrid Groth ◽  
Juan M. Gonzalez ◽  
Leonila Laiz ◽  
Cesareo Saiz-Jimenez
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons

A polyphasic study was carried out to clarify the taxonomic position of two Gram-positive bacteria isolated from soil samples of the Grotta dei Cervi (Italy), a relatively unexplored hypogean environment. The strains, 20-5T and 23-23T, showed phenotypic and phylogenetic characteristics that were consistent with their classification in the genus Agromyces. 16S rRNA gene sequence comparisons revealed that the two strains formed distinct phyletic lines within the genus Agromyces. Based on 16S rRNA gene sequence similarity, chemotaxonomic data and the results of DNA–DNA relatedness studies, it is proposed that the two isolates represent two novel species of the genus Agromyces. Pronounced differences in a broad range of phenotypic characteristics and DNA G+C content distinguished the two strains from each other and from previously described species of the genus Agromyces. Two novel species are proposed: Agromyces salentinus sp. nov. (type strain, 20-5T=HKI 0320T=DSM 16198T=NCIMB 13990T) and Agromyces neolithicus sp. nov. (type strain, 23-23T=HKI 0321T=DSM 16197T=NCIMB 13989T).

Weissella fabaria sp. nov., from a Ghanaian cocoa fermentation

2010 ◽  
Vol 60 (9) ◽  
pp. 1999-2005 ◽  
Author(s):  
Katrien De Bruyne ◽  
Nicholas Camu ◽  
Luc De Vuyst ◽  
Peter Vandamme
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Cell Protein ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Two lactic acid bacteria, strains 257T and 252, were isolated from traditional heap fermentations of Ghanaian cocoa beans. 16S rRNA gene sequence analysis of these strains allocated them to the genus Weissella, showing 99.5 % 16S rRNA gene sequence similarity towards Weissella ghanensis LMG 24286T. Whole-cell protein electrophoresis, fluorescent amplified fragment length polymorphism fingerprinting of whole genomes and biochemical tests confirmed their unique taxonomic position. DNA–DNA hybridization experiments towards their nearest phylogenetic neighbour demonstrated that the two strains represent a novel species, for which we propose the name Weissella fabaria sp. nov., with strain 257T (=LMG 24289T =DSM 21416T) as the type strain. Additional sequence analysis using pheS gene sequences proved useful for identification of all Weissella–Leuconostoc–Oenococcus species and for the recognition of the novel species.

scholarly journals Sphingobium quisquiliarum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH-contaminated soil

2010 ◽  
Vol 60 (2) ◽  
pp. 429-433 ◽  
Author(s):  
Kiran Bala ◽  
Pooja Sharma ◽  
Rup Lal
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Physiological Tests ◽  
The 16S Rrna Gene

A yellow-pigmented, hexachlorocyclohexane (HCH)-degrading bacterial strain, P25T, was isolated from an HCH dump site located in the northern part of India. Phylogenetic analysis based on the 16S rRNA gene sequence showed that the strain belongs to the genus Sphingobium, as it showed highest sequence similarity to Sphingobium amiense IAM 15006T (97.7 %). The 16S rRNA gene sequence similarity between strain P25T and members of other species of the genus Sphingobium with validly published names ranged from 94.0 to 97.7 %. The DNA–DNA relatedness between strain P25T and Sphingobium amiense IAM 15006T and other related strains was found be less than 30 %, confirming it to represent a novel species. The DNA G+C content of strain P25T was 65 mol%. The polyamine profile showed the presence of spermidine. The predominant cellular fatty acids were summed feature 8 (18 : 1ω7c and/or 18 : 1ω6c; 48.3 %), 16 : 0 (13.7 %) and 14 : 0 2-OH (8.8 %). The polar lipid profile of strain P25T also corresponded to those reported for sphingomonads (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid), supporting its identification as a member of the family Sphingomonadaceae. The results obtained from DNA–DNA hybridization and biochemical and physiological tests clearly distinguished strain P25T from closely related members of the genus Sphingobium. Thus, a novel species of the genus Sphingobium is proposed, Sphingobium quisquiliarum sp. nov. The type strain is P25T (=MTCC 9472T =CCM 7543T).

Kaistia geumhonensis sp. nov. and Kaistia dalseonensis sp. nov., two members of the class Alphaproteobacteria

2011 ◽  
Vol 61 (11) ◽  
pp. 2577-2581 ◽  
Author(s):  
Long Jin ◽  
Kwang Kyu Kim ◽  
Sang-Hoon Baek ◽  
Sung-Taik Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

Two strains, designated B1-1T and B6-8T, were isolated from the Geumho River and the Dalseo Stream in Korea. Comparative 16S rRNA gene sequence analysis showed a clear affiliation of these two bacteria with the class Alphaproteobacteria, their closest relatives being Kaistia adipata KCTC 12095T, Kaistia granuli KCTC 12575T, Kaistia soli KACC 12605T and Kaistia terrae KACC 12910T with 16S rRNA gene sequence similarities of 95.3 –97.7 % to the two novel strains. Strains B1-1T and B6-8T shared a 16S rRNA gene sequence similarity value of 96.1 %. Cells of the two strains were Gram-reaction-negative, aerobic, non-motile, short rods or cocci. The predominant ubiquinone was Q-10. The major fatty acids were C16 : 0, C18 : 1ω7c, C18 : 0 and C19 : 0ω8c cyclo for strain B1-1T and C16 : 0, C18 : 1ω7c, C18 : 0, C18 : 1 2-OH, and C19 : 0ω8c cyclo for strain B6-8T. The G+C contents of the genomic DNA of the strains B1-1T and B6-8T were 61.6 and 66.5 mol%, respectively. Based on the results of this polyphasic study, strains B1-1T ( = KCTC 12849T  = DSM 18799T) and B6-8T ( = KCTC 12850T  = DSM 18800T) represent two novel species of the genus Kaistia, for which the names Kaistia geumhonensis sp. nov. and Kaistia dalseonensis sp. nov. are proposed, respectively.

scholarly journals Vibrio casei sp. nov., isolated from the surfaces of two French red smear soft cheeses

2010 ◽  
Vol 60 (8) ◽  
pp. 1745-1749 ◽  
Author(s):  
Anne Bleicher ◽  
Klaus Neuhaus ◽  
Siegfried Scherer
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Separate Species

Three Gram-negative, rod-shaped, catalase- and oxidase-positive, facultatively anaerobic and motile bacteria, strains WS 4538, WS 4539T and WS 4540, were isolated from the surfaces of two fully ripened French red smear soft cheeses. Based on 16S rRNA gene sequence similarity, all three strains were shown to belong to the genus Vibrio. They are most closely related to Vibrio rumoiensis S-1T (96.3 % similarity) and Vibrio litoralis MANO22DT (95.9 %). DNA–DNA hybridization confirmed that all three isolates belong to the same species and clearly separated strain WS 4539T from V. rumoiensis DSM 19141T (38–42 % relatedness) and V. litoralis DSM 17657T (28–37 %). In contrast to their nearest relatives, the strains exhibited β-galactosidase and aesculin hydrolase activities. A 14 bp insertion in the 16S rRNA gene sequence forms an elongated structure at helix 10 in the rRNA molecule and provides a tool for PCR-based identification of the novel species. Partial sequences of the housekeeping genes atpA, recA, rpoA and pyrH supported the conclusion that the three isolates constitute a separate species within the genus Vibrio. The name Vibrio casei sp. nov. is proposed for the novel taxon. Strain WS 4539T (=DSM 22364T =LMG 25240T; DNA G+C content 41.8 mol%) is the type strain and WS 4540 (=DSM 22378 =LMG 25241) is a reference strain.

scholarly journals Actinomyces timonensis sp. nov., isolated from a human clinical osteo-articular sample

2010 ◽  
Vol 60 (7) ◽  
pp. 1516-1521 ◽  
Author(s):  
Aurélie Renvoise ◽  
Didier Raoult ◽  
Véronique Roux
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Acid Production ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Gram-positive, non-spore-forming rods were isolated from a human osteo-articular sample (strain 7400942T). Based on cellular morphology and the results of biochemical analysis, this strain was tentatively identified as a novel species of the genus Actinomyces. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the bacterium was closely related to the type strain of Actinomyces denticolens (96.9 % 16S rRNA gene sequence similarity). A comparison of biochemical traits showed that strain 7400942T was distinct from A. denticolens in a number of characteristics, i.e. in contrast with A. denticolens, strain 7400942T was negative for nitrate reduction and for β-galactosidase, α-glucosidase and alanine arylamidase activities, it was positive for acid production from N-acetylglucosamine, melezitose and glycogen, and it was negative for acid production from turanose. Matrix-assisted laser-desorption/ionization time-of-flight MS protein analysis confirmed that strain 7400942T represents a novel species, as scores obtained for its spectra were significant (>2.2) only with strain 7400942T. On the basis of phenotypic data and phylogenetic inference, it is proposed that this strain should be designated Actinomyces timonensis sp. nov.; the type strain is strain 7400942T (=CSUR P35T=CCUG 55928T).

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