scholarly journals Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov.

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1340-1350 ◽  
Author(s):  
Isolde M. Francis ◽  
Kenneth N. Jochimsen ◽  
Paul De Vos ◽  
Ariena H. C. van Bruggen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Cell Envelope ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Corky Root ◽  
Rhizomonas Suberifaciens

The genus Rhizorhapis gen. nov. (to replace the illegitimate genus name Rhizomonas ) is proposed for strains of Gram-negative bacteria causing corky root of lettuce, a widespread and important lettuce disease worldwide. Only one species of the genus Rhizomonas was described, Rhizomonas suberifaciens , which was subsequently reclassified as Sphingomonas suberifaciens based on 16S rRNA gene sequences and the presence of sphingoglycolipid in the cell envelope. However, the genus Sphingomonas is so diverse that further reclassification was deemed necessary. Twenty new Rhizorhapis gen. nov.- and Sphingomonas -like isolates were obtained from lettuce or sow thistle roots, or from soil using lettuce seedlings as bait. These and previously reported isolates were characterized in a polyphasic study including 16S rRNA gene sequencing, DNA–DNA hybridization, DNA G+C content, whole-cell fatty acid composition, morphology, substrate oxidation, temperature and pH sensitivity, and pathogenicity to lettuce. The isolates causing lettuce corky root belonged to the genera Rhizorhapis gen. nov., Sphingobium , Sphingopyxis and Rhizorhabdus gen. nov. More specifically, we propose to reclassify Rhizomonas suberifaciens as Rhizorhapis suberifaciens gen. nov., comb. nov. (type strain, CA1T = LMG 17323T = ATCC 49355T), and also propose the novel species Sphingobium xanthum sp. nov., Sphingobium mellinum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. with the type strains NL9T ( = LMG 12560T = ATCC 51296T), WI4T ( = LMG 11032T = ATCC 51292T) and SP1T ( = LMG 12581T = ATCC 51289T), respectively. Several strains isolated from lettuce roots belonged to the genus Sphingomonas , but none of them were pathogenic.

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 Streptococcus loxodontisalivarius sp. nov. and Streptococcus saliviloxodontae sp. nov., isolated from oral cavities of elephants

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3288-3292 ◽  
Author(s):  
Masanori Saito ◽  
Noriko Shinozaki-Kuwahara ◽  
Masatomo Hirasawa ◽  
Kazuko Takada
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-stain-positive, catalase-negative, coccoid-shaped organisms were isolated from elephant oral cavities. The isolates were tentatively identified as streptococcal species based on the results of biochemical tests. Comparative 16S rRNA gene sequencing studies confirmed the organisms to be members of the genus Streptococcus . Two isolates (NUM 6304T and NUM 6312) were related most closely to Streptococcus salivarius with 96.8 % and 93.1 % similarity based on the 16S rRNA gene and the RNA polymerase β subunit encoding gene (rpoB), respectively, and to Streptococcus vestibularis with 83.7 % similarity based on the 60 kDa heat-shock protein gene (groEL). The other two isolates (NUM 6306T and NUM 6318) were related most closely to S. vestibularis with 97.0 % and 82.9 % similarity based on the 16S rRNA and groEL genes, respectively, and to S. salivarius with 93.5 % similarity based on the rpoB gene. Based on phylogenetic and phenotypic evidence, these isolates are suggested to represent novel species of the genus Streptococcus , for which the names Streptococcus loxodontisalivarius sp. nov. (type strain NUM 6304T = JCM 19287T = DSM 27382T) and Streptococcus saliviloxodontae sp. nov. (type strain NUM 6306T = JCM 19288T = DSM 27513T) are proposed.

scholarly journals Arenicella chitinivorans sp. nov., a gammaproteobacterium isolated from the sea urchin Strongylocentrotus intermedius

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4124-4129 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Ilse Cleenwerck ◽  
Natalia V. Zhukova ◽  
Seung Bum Kim ◽  
Paul de Vos
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sea Urchin ◽  
Type Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

A strictly aerobic, Gram-stain-negative, rod-shaped, non-motile and yellow-pigmented bacterial strain, designated KMM 6208T, was isolated from a sea urchin. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that this novel isolate was affiliated to the class Gammaproteobacteria and formed a robust cluster with Arenicella xantha KMM 3895T with 98.2 % 16S rRNA gene sequence similarity. Strain KMM 6208T grew in the presence of 0.5–5 % NaCl and at a temperature range of 4–38 °C. The isolate was oxidase-positive and hydrolysed aesculin, casein, chitin, gelatin, starch and Tweens 40 and 80. The prevalent fatty acids of strain KMM 6208T were C16 : 1ω7c, iso-C16 : 0, iso-C18 : 0, C18 : 1ω7c and C16 : 0. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified aminophospholipid, and the major isoprenoid quinone was Q-8. The DNA G+C content of strain KMM 6208T was 46.3 mol%. The DNA–DNA relatedness value of strain KMM 6208T with Arenicella xantha KMM 3895T was 5 %. Molecular data in a combination with phenotypic findings strongly suggest inclusion of this novel strain in the genus Arenicella as a representative of a novel species for which the name Arenicella chitinivorans sp. nov. is proposed. The type strain is KMM 6208T ( = KCTC 12711T = LMG 26983T).

scholarly journals Dissection of the genus Actinobaculum: Reclassification of Actinobaculum schaalii Lawson et al. 1997 and Actinobaculum urinale Hall et al. 2003 as Actinotignum schaalii gen. nov., comb. nov. and Actinotignum urinale comb. nov., description of Actinotignum sanguinis sp. nov. and emended descriptions of the genus Actinobaculum and Actinobaculum suis; and re-examination of the culture deposited as Actinobaculum massiliense CCUG 47753T ( = DSM 19118T), revealing that it does not represent a strain of this species

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 615-624 ◽  
Author(s):  
A. F. Yassin ◽  
C. Spröer ◽  
R. Pukall ◽  
M. Sylvester ◽  
C. Siering ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Methyl Esters ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Actinobaculum Schaalii

The remarkable host specificity of the species of the genus Actinobaculum led us to recharacterize these species by a polyphasic approach. A comparative chemotaxonomic study including analysis of whole-cell sugars, amino acid composition of the peptidoglycan, fatty acid methyl esters, respiratory quinones and polar lipids revealed significant differences that, in combination with molecular data, support a dissection of the genus Actinobaculum . The proposals of this study include the reclassification of Actinobaculum schaalii and Actinobaculum urinale as Actinotignum schaalii gen. nov., comb. nov. (type strain DSM 15541T = CCUG 27420T) and Actinotignum urinale comb. nov. (type strain DSM 15805T = CCUG 46093T), respectively. Emended descriptions of the genus Actinobaculum and Actinomyces suis are also provided. The results of 16S rRNA gene sequence analysis and DNA–DNA hybridization also indicated that the type strain of Actinobaculum massiliense deposited as CCUG 47753T ( = DSM 19118T) should in fact be considered a member of the species Actinobaculum schaalii . In addition, comparative 16S rRNA gene sequencing and DNA–DNA relatedness studies of four strains recovered from clinical materials demonstrated that three of the isolates belonged to Actinotignum schaalii; the remaining strain represents a novel species, for which the name Actinotignum sanguinis sp. nov. is proposed. The type strain is IMMIB L-2199T ( = DSM 26039T = CCUG 64068T).

Multilocus sequence analysis and 16S rRNA gene sequencing reveal that Yersinia frederiksenii genospecies 2 is Yersinia massiliensis

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3124-3129 ◽  
Author(s):  
Roberto A. Souza ◽  
Priscilla F. M. Imori ◽  
Juliana P. Falcão
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequencing ◽  
The Other ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

Since Yersinia frederiksenii was first described in 1980, it has been recognized genotypically as a heterogeneous species, comprising three phenotypically indistinguishable genospecies. In this study, the sequence of the 16S rRNA gene and the concatenated sequences of six housekeeping genes (glnA, gyrB, hsp60, recA, rpoB and sodA) of all the currently known species of the genus Yersinia were used to determine the phylogenetic position of Y. frederiksenii genospecies 2 in the genus Yersinia . The phylogenetic analyses grouped the Y. frederiksenii genospecies 2 strains in a monophyletic group together with representative strains of Yersinia massiliensis . Moreover, the Y. frederiksenii genospecies 2 strains were also grouped apart from the other species of the genus Yersinia and far from the other two genospecies of Y. frederiksenii . All of the observations made in this study support the conclusion that Y. frederiksenii genospecies 2 should be reclassified as Y. massiliensis .

scholarly journals Arthrobacter siccitolerans sp. nov., a highly desiccation-tolerant, xeroprotectant-producing strain isolated from dry soil

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4174-4180 ◽  
Author(s):  
L. SantaCruz-Calvo ◽  
J. González-López ◽  
M. Manzanera
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Nerium Oleander ◽  
Rrna Gene ◽  
Dna Base Composition ◽  
Content Type ◽  
Link Type

A novel desiccation-tolerant, xeroprotectant-producing bacterium, designated strain 4J27T, was isolated from a Nerium oleander rhizosphere subjected to seasonal drought in Granada, Spain. Phylogenetic analysis based on 16S rRNA gene sequencing placed the isolate within the genus Arthrobacter , its closest relative being Arthrobacter phenanthrenivorans Shep3 DSM 18606T, with which it showed 99.23 % 16S rRNA gene sequence similarity. DNA–DNA hybridization measurements showed less than 25 % relatedness between strain 4J27T and Arthrobacter phenanthrenivorans DSM 18606T. The DNA base composition of strain 4J27T was 65.3 mol%. The main fatty acids were anteiso C15 : 0, anteiso C17 : 0, C16 : 0 and iso C16 : 0 and the major menaquinone was MK-9 (H2). The peptidoglycan type was A3α with an l-Lys–l-Ser–l-Thr–l-Ala interpeptide bridge. The bacterium tested positive for catalase activity and negative for oxidase activity. Phylogenetic, chemotaxonomic and phenotypic analyses indicated that the desiccation-tolerant strain 4J27T represents a novel species within the genus Arthrobacter , for which the name Arthrobacter siccitolerans is proposed. The type strain is 4J27T ( = CECT 8257T = LMG 27359T).

scholarly journals Blautia faecis sp. nov., isolated from human faeces

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 599-603 ◽  
Author(s):  
Seong-Kyu Park ◽  
Min-Soo Kim ◽  
Jin-Woo Bae
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Dimethyl Acetal ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Rrna Gene Sequencing

A strictly anoxic, Gram-stain-positive, non-motile Blautia -like bacterium, designated strain M25T, was isolated from a human faecal sample. Strain M25T was negative for both catalase and oxidase activity, utilized carbohydrates as fermentable substrates, produced lactate and acetate as the major end products of glucose fermentation in PYG medium, and had a DNA G+C content of 41.6 mol%. Comparative 16S rRNA gene sequencing showed that strain M25T was closely related to Ruminococcus obeum ATCC 29174T (96.40 % 16S rRNA gene sequence similarity) and Blautia glucerasea HFTH-1T (96.17 %) within the family Lachnospiraceae . Straight-chain saturated and monounsaturated cellular fatty acids were also detected, the majority being C14 : 0, C16 : 0 and C16 : 0 dimethyl acetal acids. Based on the phenotypic, genotypic and phylogenetic characteristics presented in this study, strain M25T represents a novel species within the genus Blautia for which the name Blautia faecis sp. nov. is proposed. The type strain is M25T ( = KCTC 5980T = JCM 17205T).

Fusicatenibacter saccharivorans gen. nov., sp. nov., isolated from human faeces

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3691-3696 ◽  
Author(s):  
Toshihiko Takada ◽  
Takashi Kurakawa ◽  
Hirokazu Tsuji ◽  
Koji Nomoto
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Content Type ◽  
Human Faeces ◽  
Link Type

Three Gram-stain-positive, obligately anaerobic, non-motile, non-spore-forming, spindle-shaped bacterial strains (HT03-11T, KO-38 and TT-111), isolated from human faeces were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing showed that the strains were highly related to each other genetically (displaying >99 % sequence similarity) and represented a previously unknown subline within the Blautia coccoides rRNA group of organisms (cluster XIVa). The closest phylogenetic neighbours of strain HT03-11T were Clostridium bolteae WAL 16351T (93.7 % 16S rRNA gene sequence similarity) and Clostridium saccharolyticum WM1T (93.7 % similarity). All isolates produced lactic acid, formic acid, acetic acid and succinic acid as fermentation end products from glucose. Their chemotaxonomic properties included lysine as the cell wall diamino acid and C16 : 0, C18 : 1ω7c DMA and C16 : 0 DMA as the major fatty acids. The G+C contents of the genomic DNA were 46.9–47.2 mol% (HPLC). Several phenotypic and chemotaxonomic characteristics could be readily used to differentiate the isolates from phylogenetically related clostridia. Therefore, strains HT03-11T, KO-38 and TT-111 represent a novel species in a new genus of the family Lachnospiraceae , for which the name Fusicatenibacter saccharivorans gen. nov., sp. nov. is proposed. The type strain of the type species is HT03-11T ( = YIT 12554T = JCM 18507T = DSM 26062T).

scholarly journals Corynebacterium godavarianum Jani et al. 2018 and Corynebacterium hadale Wei et al. 2018 are both later heterotypic synonyms of Corynebacterium gottingense Atasayar et al. 2017, proposal of an emended description of Corynebacterium gottingense Atasayar et al. 2017

2020 ◽  
Vol 70 (5) ◽  
pp. 3534-3540 ◽  
Author(s):  
K. A. Bernard ◽  
A. L. Pacheco ◽  
T. Burdz ◽  
D. Wiebe ◽  
Anne-Marie Bernier
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Rrna Gene Sequencing

Seven strains of an unidentifiable Corynebacterium species recovered from blood cultures, urine or cerebrospinal fluid over 26 years, closest to but differentiated from Corynebacterium imitans by 16S rRNA gene and partial rpoB gene sequencing, were studied. In November 2017, Atasayar et al. described a blood culture isolate as Corynebacterium gottingense sp. nov., which had >99 % similarity by 16S rRNA gene sequencing to the Canadian strains. In January 2018, Jani et al. described Corynebacterium godavarianum sp. nov., recovered from the Godavari River, India, which also had >99 % similarity by 16S/rpoB sequencing to the Canadian strains and C. gottingense. In May 2018, Wei et al. described Corynebacterium hadale recovered from hadopelagic water; this too had >99 % similarity by 16S rRNA gene sequencing to C. gottingense , C. godavarianum and the Canadian strains. C. gottingense DSM 103494T and C. godavarianum LMG 29598T were acquired and whole genome sequencing was performed (not previously done). Results were compared with genomes from C. hadale (GenBank accession NQMQ01) and the Canadian isolates. We found that these ten genomes formed a single taxon when compared using digital DNA–DNAhybridization, average nucleotide identity using blastn and average amino acid identity criteria but exhibited some subtle biochemical and chemotaxonomic differences. Heuristically, we propose that C. godavarianum and C. hadale are later heterotypic synonyms of, and the Canadian isolates are identifiable as, C. gottingense . We provide an emended description of Corynebacterium gottingense Atasayar et al. 2017; genomes ranged from 2.48 to 2.69 Mb ( C. gottingense DSM 103494T, 2.62 Mb) with G+C content of 65.1–65.6 mol% (WGS), recovered from clinical and environmental sites.

scholarly journals Faecalicoccus acidiformans gen. nov., sp. nov., isolated from the chicken caecum, and reclassification of Streptococcus pleomorphus (Barnes et al. 1977), Eubacterium biforme (Eggerth 1935) and Eubacterium cylindroides (Cato et al. 1974) as Faecalicoccus pleomorphus comb. nov., Holdemanella biformis gen. nov., comb. nov. and Faecalitalea cylindroides gen. nov., comb. nov., respectively, within the family Erysipelotrichaceae

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3877-3884 ◽  
Author(s):  
Celine De Maesschalck ◽  
Filip Van Immerseel ◽  
Venessa Eeckhaut ◽  
Siegrid De Baere ◽  
Margo Cnockaert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Strains LMG 27428T and LMG 27427 were isolated from the caecal content of a chicken and produced butyric, lactic and formic acids as major metabolic end products. The genomic DNA G+C contents of strains LMG 27428T and LMG 27427 were 40.4 and 38.8 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were most closely related to the generically misclassified Streptococcus pleomorphus ATCC 29734T. Strain LMG 27428T could be distinguished from S. pleomorphus ATCC 29734T based on production of more lactic acid and less formic acid in M2GSC medium, a higher DNA G+C content and the absence of activities of acid phosphatase and leucine, arginine, leucyl glycine, pyroglutamic acid, glycine and histidine arylamidases, while strain LMG 27428 was biochemically indistinguishable from S. pleomorphus ATCC 29734T. The novel genus Faecalicoccus gen. nov. within the family Erysipelotrichaceae is proposed to accommodate strains LMG 27428T and LMG 27427. Strain LMG 27428T ( = DSM 26963T) is the type strain of Faecalicoccus acidiformans sp. nov., and strain LMG 27427 ( = DSM 26962) is a strain of Faecalicoccus pleomorphus comb. nov. (type strain LMG 17756T = ATCC 29734T = DSM 20574T). Furthermore, the nearest phylogenetic neighbours of the genus Faecalicoccus are the generically misclassified Eubacterium cylindroides DSM 3983T (94.4 % 16S rRNA gene sequence similarity to strain LMG 27428T) and Eubacterium biforme DSM 3989T (92.7 % 16S rRNA gene sequence similarity to strain LMG 27428T). We present genotypic and phenotypic data that allow the differentiation of each of these taxa and propose to reclassify these generically misnamed species of the genus Eubacterium formally as Faecalitalea cylindroides gen. nov., comb. nov. and Holdemanella biformis gen. nov., comb. nov., respectively. The type strain of Faecalitalea cylindroides is DSM 3983T = ATCC 27803T = JCM 10261T and that of Holdemanella biformis is DSM 3989T = ATCC 27806T = CCUG 28091T.

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