scholarly journals Helicobacter mesocricetorum sp. nov., a Novel Helicobacter Isolated from the Feces of Syrian Hamsters

2000 ◽  
Vol 38 (5) ◽  
pp. 1811-1817 ◽  
Author(s):  
J. H. Simmons ◽  
L. K. Riley ◽  
C. L. Besch-Williford ◽  
C. L. Franklin
Keyword(s):  
Alkaline Phosphatase ◽  
Sequence Analysis ◽  
Type Strain ◽  
Rrna Gene ◽  
The Novel ◽  
Accession Number ◽  
Syrian Hamsters ◽  
Novel Bacterium ◽  
Microaerobic Conditions ◽  
The 16S Rrna Gene

A spiral-shaped bacterium with bipolar, single, nonsheathed flagella was isolated from the feces of Syrian hamsters. The bacterium grew as a thin spreading film at 37°C under microaerobic conditions, did not hydrolyze urea, was positive for catalase and alkaline phosphatase, reduced nitrate to nitrite, did not hydrolyze hippurate, and was sensitive to nalidixic acid but resistant to cephalothin. Sequence analysis of the 16S rRNA gene and biochemical and phenotypic criteria indicate that the novel bacterium is a helicobacter. The novel bacterium is most closely related to the recently described mouse enteric helicobacter, Helicobacter rodentium. This is the first urease-negative Helicobacter species with nonsheathed flagella isolated from feces of asymptomatic Syrian hamsters. We propose to name this novel helicobacter Helicobacter mesocricetorum. The type strain is MU 97-1514 (GenBank accession number AF072471).

scholarly journals Solimonas soli gen. nov., sp. nov., isolated from soil of a ginseng field

2007 ◽  
Vol 57 (11) ◽  
pp. 2591-2594 ◽  
Author(s):  
Myung Kyum Kim ◽  
Yu-Jin Kim ◽  
Dong-Ha Cho ◽  
Tae-Hoo Yi ◽  
Nak-Kyun Soung ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Phylogenetic Analysis ◽  
Type Strain ◽  
Gene Sequence ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Gram Negative ◽  
The 16S Rrna Gene

A micro-organism, DCY12T, comprising Gram-negative, non-motile, pale-yellow rods was isolated from soil from a ginseng field in South Korea and was investigated to determine its taxonomic status. It grew optimally at 30 °C and at pH 7.0, the G+C content of its DNA was 40.5 mol%, the major components of the fatty acid profile were C16 : 0 and C18 : 1 and the major ubiquinone was Q-8. A phylogenetic analysis based on the 16S rRNA gene sequence revealed that the novel isolate was most closely related to Hydrocarboniphaga effusa AP103T (89.2 %), Nevskia ramosa Soe1 (88.8 %) and Pseudomonas aeruginosa ATCC 10145T (83.2 %). The phenotypic, physiological, metabolic and phylogenetic properties of DCY12T suggest that it represents a novel genus (class Gammaproteobacteria) and species, for which the name Solimonas soli gen. nov., sp. nov. is proposed. The type strain of Solimonas soli is DCY12T (=KCTC 12834T =LMG 24014T).

Amycolatopsis helveola sp. nov. and Amycolatopsis pigmentata sp. nov., isolated from soil

2010 ◽  
Vol 60 (11) ◽  
pp. 2629-2633 ◽  
Author(s):  
Tomohiko Tamura ◽  
Yuumi Ishida ◽  
Misa Otoguro ◽  
Ken-ichiro Suzuki
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Monophyletic Cluster ◽  
The 16S Rrna Gene ◽  
Taxonomical Study

Three short spore chain-forming actinomycete strains were isolated from soil samples collected from subtropical islands in Japan. The cell-wall peptidoglycan of these strains contained meso-diaminopimelic acid (meso-A2pm), glutamic acid and alanine. The major isoprenoid quinone was MK-9(H4), iso-C16 : 0 and 2-OH iso-C16 : 0 were the major cellular fatty acids and phosphatidylethanolamine was a component of the polar lipids. The G+C content of the genomic DNA was 67–69 mol%. Phylogenetic analyses based on the 16S rRNA gene sequences showed that the novel strains consistently formed a monophyletic cluster with Amycolatopsis taiwanensis. On the basis this polyphasic taxonomical study, it is proposed that the two new isolates represent two novel species: Amycolatopsis helveola (type strain TT00-43T=NBRC 103394T=KCTC 19329T) and Amycolatopsis pigmentata (type strain TT99-32T=NBRC 103392T=KCTC 19330T).

scholarly journals Description of Ruminococcus catenae SW178 sp. nov., a new anaerobic species isolated from feral chicken

2019 ◽  
Author(s):  
Supapit Wongkuna ◽  
Sudeep Ghimire ◽  
Surang Chankhamhaengdecha ◽  
Tavan Janvilisri ◽  
Joy Scaria
Keyword(s):  
Sequence Analysis ◽  
South Dakota ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
The 16S Rrna Gene

AbstractA Gram-positive, obligately anaerobic coccobacillus, with the white raised circular colony was isolated from the cecum of feral chickens in Brookings, South Dakota, USA. The 16S rRNA gene sequence analysis suggested that the closest species to strain SW178 was Ruminococcus torques ATCC 27756T (96.94% similarity) that belongs to the family Lachnospiraceae. The genome of strain SW178 is 3.18 Mbp with G+C content of 46.9 mol%. Based on the phylogenetic and phenotypic comparison, we propose that strain SW178 be assigned to the genus Ruminococcus as a novel species, for which the name Ruminococcus catenae is proposed. The type strain is SW178 (= CCOS 1886 T, =DSM 109242T).

scholarly journals Reclassification of Paralactobacillus selangorensis Leisner et al. 2000 as Lactobacillus selangorensis comb. nov.

2011 ◽  
Vol 61 (12) ◽  
pp. 2979-2983 ◽  
Author(s):  
Monique Haakensen ◽  
Vanessa Pittet ◽  
Barry Ziola
Keyword(s):  
Cell Division ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Taxonomic Status ◽  
Multilocus Sequence Analysis ◽  
Rrna Gene ◽  
Phenotypic Information ◽  
The 16S Rrna Gene

The taxonomic status of Paralactobacillus selangorensis is described and, based on evidence presented, transfer of the species to the genus Lactobacillus with the name Lactobacillus selangorensis comb. nov. is proposed. This reclassification is supported by multilocus sequence analysis of the 16S rRNA gene and portions of the cpn60, pheS and rpoA genes. Mode of cell division and existing phenotypic information also show that P. selangorensis cannot be differentiated from the genus Lactobacillus. The type strain of Lactobacillus selangorensis comb. nov. is ATCC BAA-66T ( = LMG 17710T  = CIP 106482T).

scholarly journals Description of Wautersiella falsenii gen. nov., sp. nov., to accommodate clinical isolates phenotypically resembling members of the genera Chryseobacterium and Empedobacter

2006 ◽  
Vol 56 (10) ◽  
pp. 2323-2329 ◽  
Author(s):  
Peter Kämpfer ◽  
Véronique Avesani ◽  
Michèle Janssens ◽  
Jacqueline Charlier ◽  
Thierry De Baere ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Reference Strain ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
The 16S Rrna Gene

A total of 26 isolates of non-fermenting, Gram-negative rods, obtained between 1980 and 2004 by various clinical laboratories in Belgium, with phenotypic characteristics resembling those of members of the genera Chryseobacterium and Empedobacter (indole-positive) and a biochemical profile resembling that of CDC group II-h, but urease-positive, were collected at the Université Catholique de Louvain Microbiology Laboratory, Belgium. The 16S rRNA gene sequences were determined for most of the isolates and showed 94–95 % similarity with the type strain of Empedobacter brevis as the closest relative, indicating that these isolates might belong to a separate genus. Furthermore, the 16S rRNA gene sequences of the isolates were similar, but two clusters (genomovars) could be distinguished. The sequence similarities were 99.5–100 % for the 14 isolates of genomovar 1 and 99.4–100 % for the 12 isolates of genomovar 2. The similarity between the two clusters was 98.3–99.5 %. The presence of two clearly different groups was corroborated by using tRNA intergenic length polymorphism analysis, which also enabled differentiation of the novel species from all other species studied thus far using this technique. DNA–DNA hybridization results excluded a close relatedness to Empedobacter brevis. The DNA G+C contents of the reference strains of genomovars 1 and 2 were 33.8±0.4 and 34.4±0.2 mol%, respectively. The name Wautersiella falsenii gen. nov., sp. nov., is proposed for this group, comprising two closely related genomovars. The type strain of the species and reference strain for genomovar 1 is NF 993T (=CCUG 51536T=CIP 108861T), which was isolated from a surgical wound. The reference strain for genomovar 2 is NF 770 (=CCUG 51537=CIP 108860), which was isolated from blood.

scholarly journals Sporaefaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse

2019 ◽  
Author(s):  
Torben Sølbeck Rasmussen ◽  
Theresa Streidl ◽  
Thomas C.A. Hitch ◽  
Esther Wortmann ◽  
Paulina Deptula ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Obese Mouse ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Accession Number ◽  
Novel Bacterium ◽  
The Family ◽  
The 16S Rrna Gene

AbstractA bacterial strain, designated WCA-9-b2, was isolated from the caecal content of an 18-week-old obese C57BL/6NTac male mouse. According to phenotypic analyses, the isolate is rod-shaped, Gram-positive, strictly anaerobic, spore-forming and non-motile under the conditions tested. Bacterial colonies were irregular and non-pigmented. Analysis of the 16S rRNA gene indicated that the isolate belonged to the family Lachnospiraceae with Clostridium scindens ATTC 35704 (94.9% sequence identity) and Dorea formicigenerans ATCC 27755 (94.8%) being the closest relatives. Whole genome sequencing showed average nucleotide identity (ANI) ranging from 69.80–74.23% and percentage of conserved proteins (POCP) values < 50% against the nine closest relatives. The genome-based G+C content of genomic DNA was 44.4%. The predominant metabolic end products of glucose fermentation were acetate and succinate. Based on these data, we propose that strain WCA-9-b2 represents a novel species within a novel genus, for which the name Sporaefaciens musculi gen. nov., sp. nov. is proposed. The type strain is WCA-9-b2T (=DSM 106039T = CCUG pending IDT).RepositoriesThe GenBank accession number for the 16S rRNA gene sequence of strain WCA-9-b2T is MN756014, and the accession number for the genome assembly is PRJNA592877. Raw sequencing Illumina NextSeq (PRJEB35655) and ONT MinION (PRJEB35656) data can be accessed at EMBL-EBI.

scholarly journals Antrihabitans stalactiti gen. nov., sp. nov., a new member of the family Nocardiaceae isolated from a cave

2020 ◽  
Vol 70 (10) ◽  
pp. 5503-5511 ◽  
Author(s):  
Soon Dong Lee ◽  
In Seop Kim ◽  
Susanne Verbarg ◽  
Yochan Joung
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The 16S Rrna Gene

Two Gram-stain-positive, strictly aerobic, non-spore-forming actinobacterial strains, designated YC2-7T and YC5-17, were isolated from the Yongcheondonggul (larva cave) in Jeju, Republic of Korea and their taxonomic ranks were examined by a polyphasic approach. The 16S rRNA gene tree showed that the novel isolates occupied an independent position separated from recognized genera of the family Nocardiaceae . In the 92 core gene-based phylogenomic analysis, strain YC2-7T was loosely associated with the type strain of Aldersonia kummingensis with 66.2 % average amino acid identity. The 16S rRNA gene sequence simairity between the isolate and members of the family Nocardiaceae was below 96.7 %. The cell-wall peptidoglycan was meso-diaminopimelic acid as a diagnostic diamino acid. Whole-cell sugars consisted of arabinose, galactose and glucose. The predominant menaquinone was MK-8(H4, ω-cycl). The major polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The cellular fatty acids consisted mainly of saturated and unsaturated components with small amounts of tuberculostearic acid. Mycolic acids of 52–58 carbon atoms were present. The DNA G+C content of the genome was 63.8 mol%. On the basis of combination of morphological and chemotaxonomic differences, in addition to phylogenetic distinctness, the novel isolates are considered to constitute members of a novel species of a new genus in the family Nocardiaceae , for which the name Antrihabitans stalactiti gen. nov., sp. nov. is proposed. The type strain is YC2-7T (=KACC 19965T=DSM 108733T).

scholarly journals Nocardioides oleivorans sp. nov., a novel crude-oil-degrading bacterium

2005 ◽  
Vol 55 (4) ◽  
pp. 1501-1504 ◽  
Author(s):  
Axel Schippers ◽  
Peter Schumann ◽  
Cathrin Spröer
Keyword(s):  
Crude Oil ◽  
Type Strain ◽  
Gene Sequence ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Degrading Bacterium ◽  
Physiological Properties ◽  
Diamino Acid ◽  
The 16S Rrna Gene

The crude-oil-degrading strain BAS3T represents a novel Nocardioides species, according to a taxonomic study. The 16S rRNA gene sequence of strain BAS3T was most similar to that of Nocardioides ganghwensis (IMSNU 14028T; 99 % similarity), but the DNA–DNA relatedness to this type strain was only 32 %. The physiological properties of strain BAS3T differ from those of N. ganghwensis (IMSNU 14028T) and other species of Nocardioides. The diamino acid in the cell-wall peptidoglycan of strain BAS3T is ll-diaminopimelic acid and the major menaquinone is MK-8(H4). The name Nocardioides oleivorans sp. nov. is proposed for the novel Nocardioides species, since its type strain, BAS3T (=DSM 16090T=NCIMB 14004T), is able to degrade crude oil.

scholarly journals Paraburkholderia dioscoreae sp. nov., a novel plant associated growth promotor

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Johannes B. Herpell ◽  
Sarah Vanwijnsberghe ◽  
Charlotte Peeters ◽  
Florian Schindler ◽  
Lena Fragner ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Distinctive Features ◽  
Link Type ◽  
Novel Bacterium ◽  
A Genome ◽  
The 16S Rrna Gene

A novel bacterium, designated strain Msb3T, was recently isolated from leaves of the yam family plant Dioscorea bulbifera (Dioscoreaceae). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Paraburkholderia with Paraburkholderia xenovorans as nearest validly named neighbour taxon (99.3 % sequence similarity towards the P. xenovorans type strain). Earlier genome sequence analysis revealed a genome of 8.35 Mb in size with a G+C content of 62.5 mol%, which was distributed over two chromosomes and three plasmids. Here, we confirm that strain Msb3T represents a novel Paraburkholderia species. In silico DNA–DNA hybridization and average nucleotide identity (OrthoANIu) analyses towards P. xenovorans LB400T yielded 58.4 % dDDH and 94.5 % orthoANIu. Phenotypic and metabolic characterization revealed growth at 15 °C on tryptic soy agar, growth in the presence of 1 % NaCl and the lack of assimilation of phenylacetic acid as distinctive features. Together, these data demonstrate that strain Msb3T represents a novel species of the genus Paraburkholderia, for which we propose the name Paraburkholderia dioscoreae sp. nov. The type strain is Msb3T (=LMG 31881T, DSM 111632T, CECT 30342T).

scholarly journals Friedmanniella luteola sp. nov., Friedmanniella lucida sp. nov., Friedmanniella okinawensis sp. nov. and Friedmaniella sagamiharensis sp. nov., isolated from spiders

2010 ◽  
Vol 60 (1) ◽  
pp. 113-120 ◽  
Author(s):  
Kimika Iwai ◽  
Kazuo Aisaka ◽  
Makoto Suzuki
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Sequence Data ◽  
Chemical Properties ◽  
Rrna Gene ◽  
The Novel ◽  
Mycolic Acids ◽  
Isoprenoid Quinones ◽  
The 16S Rrna Gene ◽  
And Chemical Properties

Four Gram-positive, non-motile, aerobic actinobacteria were isolated from spiders and their webs. Their genetic, phenotypic and chemical properties were studied. The 16S rRNA gene sequence data suggested that the four novel isolates belonged to the genus Friedmanniella. Two strains (FA1T and FA2T) formed a cluster together with Friedmanniella capsulata and Friedmanniella lacustris and the other two strains (FB1T and FB2T) formed a cluster together with Friedmanniella antarctica and Friedmanniella spumicola. The cell-wall peptidoglycan contained ll-A2pm and mycolic acids were absent. Isoprenoid quinones were mainly composed of MK-9(H4), MK-9(H2) and MK-9 and the predominant fatty acids were 12-methyltetradecanoic acid (ai-C15 : 0) and 13-methyltetradecanoic acid (i-C15 : 0). The major polar lipids were phosphatidylinositol and phosphatidylglycerol. In addition, strain FA1T, FB1T, and FB2T contained diphosphatidylglycerol and phosphatidylcholine. The DNA G+C contents were: 72 mol%, 73 mol%, 74 mol% and 75 mol% for strains FA1T, FA2T, FB1T, and FB2T, respectively. DNA–DNA hybridization studies demonstrated that the novel strains showed low relatedness values to F. capsulata, F. lacustris, F. antarctica and F. spumicola. These data support the proposal that strains FA1T, FA2T, FB1T and FB2T represent novel species of the genus Friedmanniella. Therefore, the names Friedmanniella luteola (type strain FA1T=DSM 21741T=NBRC 104963T), Friedmanniella lucida (type strain FA2T=DSM 21742T=NBRC 104964T), Friedmanniella okinawensis (type strain FB1T=DSM 21744T=NBRC 104966T) and Friedmanniella sagamiharensis (type strain FB2T=DSM 21743T=NBRC 104965T) are proposed for these new strains.

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