scholarly journals Cultivation and description of Duncaniella dubosii sp. nov., Duncaniella freteri sp. nov. and emended description of the species Duncaniella muris

2020 ◽  
Vol 70 (5) ◽  
pp. 3105-3110 ◽  
Author(s):  
Sou Miyake ◽  
Yichen Ding ◽  
Melissa Soh ◽  
Adrian Low ◽  
Henning Seedorf
Keyword(s):  
Type Species ◽  
16S Rrna Genes ◽  
Morphological Properties ◽  
Rrna Genes ◽  
Bacterial Strains ◽  
Content Type ◽  
Phenotypic Differences ◽  
Link Type ◽  
Respective Type ◽  
Type Strains

Three bacterial strains, C9, H5 and TLL-A3, were isolated from fecal pellets of conventionally raised C57BL/6J mice. Analysis of 16S rRNA genes indicated that the strains belonged to the Muribaculaceae , and shared 91.6–99.9 % sequence identity with the recently described Duncaniella muris DSM 103720T. Genome-sequencing of the isolates was performed to compare average nucleotide identities (ANI) between strains. The ANI analysis revealed that all isolates shared highest ANI with D. muris DSM 103720T, with strain C9 being most similar (ANI: 98.0 %) followed by strains H5 (ANI: 76.4 %) and TLL-A3 (ANI: 74.4 %). Likewise, digital DNA–DNA hybridization (dDDH) indicated high similarity of strain C9 (dDDH: 86.6 %) to D. muris DSM 103720T, but strains H5 and TLL-A3 showed lower similarity (dDDH <35 %) to either of the three type species of the Muribaculaceae ( Muribaculum intestinale DSM 28989T , Paramuribaculum intestinale DSM 100749T, D. muris DSM 103720T). MK-10 and MK-11 were abundant in all three isolates, but concentrations varied between species. Based on genotypic, phylogenetic and phenotypic differences, the strains TLL-A3 and H5 are considered to represent novel species of the genus Duncaniella , for which the names Duncaniella freteri sp. nov., and Duncaniella dubosii sp. nov., are proposed. The respective type strains are TLL-A3T (=DSM 108168T=KCTC 15769T), and H5T (=DSM 107170T=KCTC 15734T). Strain C9 reveals limited sequence dissimilarity and minor differences in morphological properties with Duncaniella muris DSM 103720T and is therefore proposed to belong to the same species. The respective strain is C9 (=DSM 107165=KCTC 15733).

scholarly journals Rhizobium azibense sp. nov., a nitrogen fixing bacterium isolated from root-nodules of Phaseolus vulgaris

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1501-1506 ◽  
Author(s):  
Bacem Mnasri ◽  
Tian Yan Liu ◽  
Sabrine Saidi ◽  
Wen Feng Chen ◽  
Wen Xin Chen ◽  
...  
Keyword(s):  
Type Species ◽  
Root Nodules ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties ◽  
Microbial Strains ◽  
Type Strains

Three microbial strains isolated from common beans, 23C2T (Tunisia), Gr42 (Spain) and IE4868 (Mexico), which have been identified previously as representing a genomic group closely related to Rhizobium gallicum , are further studied here. Their 16S rRNA genes showed 98.5–99 % similarity with Rhizobium loessense CCBAU 7190BT, R. gallicum R602spT, Rhizobium mongolense USDA 1844T and Rhizobium yanglingense CCBAU 71623T. Phylogenetic analysis based on recA, atpD, dnaK and thrC sequences showed that the novel strains were closely related and could be distinguished from the four type strains of the closely related species. Strains 23C2T, Gr42 and IE4868 could be also differentiated from their closest phylogenetic neighbours by their phenotypic and physiological properties and their fatty acid contents. All three strains harboured symbiotic genes specific to biovar gallicum. Levels of DNA–DNA relatedness between strain 23C2T and the type strains of R. loessense , R. mongolense , R. gallicum and R. yanglingense ranged from 58.1 to 61.5 %. The DNA G+C content of the genomic DNA of strain 23C2T was 59.52 %. On the basis of these data, strains 23C2T, Gr42 and IE4868 were considered to represent a novel species of the genus Rhizobium for which the name Rhizobium azibense is proposed. Strain 23C2T ( = CCBAU 101087T = HAMBI3541T) was designated as the type strain.

scholarly journals Streptomyces herbaceus sp. nov., Streptomyces incanus sp. nov. and Streptomyces pratens sp. nov., isolated from the soil of a hay meadow

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1908-1913 ◽  
Author(s):  
Byung-Yong Kim ◽  
Xiaoying Rong ◽  
Tiago D. Zucchi ◽  
Avinash N. V. Bonda ◽  
Ying Huang ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Morphological Properties ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Respective Type ◽  
Type Strains

The taxonomic positions of three streptomycetes isolated from a soil sample from a hay meadow were determined using a polyphasic approach. The isolates had chemical and morphological properties typical of the genus Streptomyces and, in phylogenetic analyses based on 16S rRNA gene sequences, formed a distinct subclade that was most closely related to the Streptomyces prasinus subclade. DNA–DNA relatedness studies showed that the novel strains belonged to three different genomic species. The novel strains could be distinguished from one another and from the type strains of the species classified in the S. prasinus subclade using a combination of genotypic and phenotypic properties. On the basis of these data, it is proposed that the novel strains be assigned to the genus Streptomyces as Streptomyces herbaceus sp. nov., Streptomyces incanus sp. nov. and Streptomyces pratens sp. nov., with BK119T ( = KACC 21001T  = CGMCC 4.5797T), BK128T ( = KACC 21002T  = CGMCC 4.5799T) and BK138T ( = KACC 20904T  = CGMCC 4.5800T) as the respective type strains.

Bacteroides luhongzhouii sp. nov. and Bacteroides zhangwenhongii sp. nov., isolated from human faeces

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Yajun Ge ◽  
Gui Zhang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
...  
Keyword(s):  
Type Species ◽  
Cellular Fatty Acid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strictly Anaerobic ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Healthy Humans ◽  
Type Strains

Four unknown strains, characterized as Gram-stain-negative, strictly anaerobic, non-motile and rod-shaped, were isolated from fresh faeces of healthy humans in PR China. Pairwise sequence comparisons of the 16S rRNA genes showed that these isolates were separated into two clusters. Cluster I (strains HF-5141T and HF-106) was most closely related to Bacteroides xylanisolvens XB1AT (98.0–98.3 % similarity) and Bacteroides ovatus ATCC 8483T (97.3–97.5 %), whereas cluster II (strains HF-5287T and HF-5300) exhibited a similarity range of 96.8–97.0 % to Bacteroides finegoldii JCM 13345T, 96.7–96.9 % to Bacteroides faecis MAJ27T and 96.4–96.5 % to Bacteroides xylanisolvens XB1AT. The DNA G+C contents of type strains HF-5141T and HF-5287T were 41.5 and 42.6 mol%, respectively. These strains had anteiso-C15 : 0 as the major cellular fatty acid, MK-9 and MK-11 as the predominant respiratory quinones, and phosphatidylethanolamine, aminophospholipids and phospholipids as major polar lipids, which is typical for members of the genus Bacteroides . However, the average nucleotide identity and digital DNA–DNA hybridization values, accompanied by different phenotypic and biochemical characteristics, distinguished them from their corresponding closest relatives as well as from other recognized members of the genus Bacteroides . Therefore, strains HF-5141T and HF-5287T represent two novel species in the genus Bacteroides , for which the names Bacteroides luhongzhouii sp. nov. and Bacteroides zhangwenhongii sp. nov. are proposed, with HF-5141T (=CGMCC 1.16787T=GDMCC 1.1591T=JCM 33480T) and HF-5287T (=CGMCC 1.16724T=GDMCC 1.1590T=JCM 33481T) as type strains.

Hymenobacter koreensis sp. nov. and Hymenobacter saemangeumensis sp. nov., isolated from estuarine water

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4568-4573 ◽  
Author(s):  
Ji Young Kang ◽  
Jeesun Chun ◽  
Ahyoung Choi ◽  
Sung Hyun Moon ◽  
Jang-Cheon Cho ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Major Polar Lipid ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties

Two Gram-reaction-negative, rod-shaped, non-motile and red–pink-pigmented bacterial strains, designated GYR3077T and GSR0100T, were isolated from a water sample of the Mangyung estuary enclosed by the Saemangeum Embankment in JEOLlabuk-do, South Korea, and were characterized using a polyphasic approach. 16S rRNA genes of strains GYR3077T and GSR0100T exhibited sequence similarities of 95.9 % to Hymenobacter deserti ZLB-3T and 96.6 % to Hymenobacter soli PB17T, respectively, and indicated that these isolates belonged to the phylum Bacteroidetes . The major cellular fatty acids present in the two isolates were iso-C15 : 0, C16 : 1ω5c, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The major respiratory quinone and polyamine patterns were menaquinone-7 and sym-homospermidine, characteristic of the genus Hymenobacter . Flexirubin-type pigments were absent in both strains. The DNA G+C contents of strains GYR3077T and GSR0100T were 60.2 mol% and 61.9 mol%, respectively. The major polar lipid of strains GYR3077T and GSR0100T was phosphatidylethanolamine. Based on the morphological and physiological properties, strains GYR3077T and GSR0100T were considered to represent two novel species of the genus Hymenobacter , for which the names Hymenobacter koreensis sp. nov. (type strain GYR3077T = KACC 16451T = JCM 17924T) and Hymenobacter saemangeumensis sp. nov. (type strain GSR0100T = KACC 16452T = JCM 17923T) are proposed.

scholarly journals Capnocytophaga felis sp. nov. isolated from the feline oral cavity

2020 ◽  
Vol 70 (5) ◽  
pp. 3355-3360 ◽  
Author(s):  
Michio Suzuki ◽  
Kaoru Umeda ◽  
Masanobu Kimura ◽  
Koichi Imaoka ◽  
Shigeru Morikawa ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
Oral Cavity ◽  
Type Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
Cellular Fatty Acids ◽  
Link Type ◽  
Type Strains

Four strains, KC07070T, KC07105, 11 025B-8C and 11 026B-8-C, were isolated from the oral cavity of cats in 2007 or 2011 in Japan. These strains were Gram-stain-negative rods, exhibited gliding motility, grew in air with 5 % CO2 and showed catalase and oxidase activity. The sequences of 16S rRNA genes of the four strains were 100 % identical. Additionally, the sequences of 16S rRNA genes of KC07070T had identity to those of the type strains of Capnocytophaga canimorsus (97.7 %), Capnocytophaga cynodegmi (97.8 %) and Capnocytophaga canis (97.4 %) and 91.2–93.8% identity to those of other species of the genus Capnocytophaga . The major cellular fatty acids of KC07070T were iso-C15 : 0 (56.2 %) and summed feature 11 (14.9 %). The G+C content of the DNA from KC07070T was 35.6 mol%, and the genome size was 2.88 Mbp. KC07070T had digital DNA–DNA hybridization (dDDH) values of 26.2–27.6% and average nucleotide identity (ANI) values of 75.4–83.3 % to the type strains of the closest relatives, C. canimorsus , C. cynodegmi and C. canis . These results of phylogenetic analysis of 16S rRNA gene sequence, cellular fatty acids compositions and dDDH and ANI values indicate that strain KC07070T represents a novel species, for which we propose the name Capnocytophaga felis sp. nov., with type strain KC07070T (=JCM 32681T=DSM 107251T).

Description of Acidovorax wautersii sp. nov. to accommodate clinical isolates and an environmental isolate, most closely related to Acidovorax avenae

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2203-2206 ◽  
Author(s):  
Mario Vaneechoutte ◽  
Michèle Janssens ◽  
Véronique Avesani ◽  
Michel Delmée ◽  
Pieter Deschaght
Keyword(s):  
Nitrate Reduction ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phenol Red ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Three Gram-negative strains, NF 1078T, NF 1598 and NF 1715, were isolated from clinical (two) and environmental (one) samples, respectively. Sequence analysis of the 16S rRNA genes revealed similarity of 100 % among the three strains and next highest similarity to the type strain of Acidovorax avenae (98.16 %). The three strains were able to acidify lactose and rhamnose on low peptone phenol red agar and to alkalinize citrate on Simmons’ agar and were negative for nitrate reduction. The DNA G+C content of strain NF 1078T was 67.1 mol%. The level of DNA–DNA relatedness between this strain and the type strains of A. avenae (ATCC 19860T, LMG 2117T) was 29 %. Based on these phylogenetic, phenotypic and genotypic analyses, the three strains could be distinguished clearly from all other recognized Acidovorax species and should be classified as representatives of a novel species of the genus Acidovorax , for which the name Acidovorax wautersii sp. nov. is proposed. The type strain is NF 1078T ( = LMG 26971T = CCUG 62584T).

Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai‘i, and emended description of the genus Flavobacterium

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3280-3286 ◽  
Author(s):  
Iris Kuo ◽  
Jimmy Saw ◽  
Durrell D. Kapan ◽  
Stephanie Christensen ◽  
Kenneth Y. Kaneshiro ◽  
...  
Keyword(s):  
Type Species ◽  
Original Description ◽  
Gliding Motility ◽  
Rrna Gene ◽  
Content Type ◽  
Phenotypic Differences ◽  
Whole Cells ◽  
Link Type ◽  
Decaying Wood ◽  
Type Strains

Strain IK-1T was isolated from decaying tissues of the shrub Wikstroemia oahuensis collected on O‘ahu, Hawai‘i. Cells were rods that stained Gram-negative. Gliding motility was not observed. The strain was oxidase-negative and catalase-positive. Zeaxanthin was the major carotenoid. Flexirubin-type pigments were not detected. The most abundant fatty acids in whole cells of IK-1T grown on R2A were iso-C15 : 0 and one or both of C16 : 1ω7c and C16 : 1ω6c. Based on comparisons of the nucleotide sequence of the 16S rRNA gene, the closest neighbouring type strains were Flavobacterium rivuli WB 3.3-2T and Flavobacterium subsaxonicum WB 4.1-42T, with which IK-1T shares 93.84 and 93.67 % identity, respectively. The G+C content of the genomic DNA was 44.2 mol%. On the basis of distance from its nearest phylogenetic neighbours and phenotypic differences, the species Flavobacterium akiainvivens sp. nov. is proposed to accommodate strain IK-1T ( = ATCC BAA-2412T = CIP 110358T) as the type strain. The description of the genus Flavobacterium is emended to reflect the DNA G+C contents of Flavobacterium akiainvivens IK-1T and other species of the genus Flavobacterium described since the original description of the genus.

Streptomyces chlorus sp. nov. and Streptomyces viridis sp. nov., isolated from soil

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1728-1733 ◽  
Author(s):  
Byung-Yong Kim ◽  
Xiaoying Rong ◽  
Tiago D. Zucchi ◽  
Ying Huang ◽  
Michael Goodfellow
Keyword(s):  
Type Species ◽  
Aerial Mycelium ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Respective Type ◽  
Isoprenoid Quinones ◽  
Type Strains ◽  
Light Green

Two actinomycete strains, BK125T and BK199T, isolated from a hay meadow soil sample were investigated to determine their taxonomic position using a polyphasic approach. The isolates produced greenish-yellow and light green aerial mycelium on oatmeal agar, respectively. They contained anteiso-C15 : 0, iso-C15 : 0 and C16 : 0 as the major fatty acids, and MK-9 (H6) and MK-9 (H8) as the predominant isoprenoid quinones. Phylogenetic analysis of the 16S rRNA gene sequences showed that the isolates formed distinct phyletic lines towards the periphery of the Streptomyces prasinus subclade. Analysis of DNA–DNA relatedness between the two isolates showed that they belonged to different genomic species. The organisms were also distinguished from one another and from type strains of species classified in the S. prasinus subclade using a combination of genotypic and phenotypic properties. On the basis of these data, it is proposed that the isolates be assigned to the genus Streptomyces as Streptomyces chlorus sp. nov. and Streptomyces viridis sp. nov. with isolates BK125T ( = KACC 20902T = CGMCC 4.5798T) and BK199T ( = KACC 21003T = CGMCC 4.6824T) as the respective type strains.

Halobaculum magnesiiphilum sp. nov., a magnesium-dependent haloarchaeon isolated from commercial salt

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 861-866 ◽  
Author(s):  
Hirokazu Shimoshige ◽  
Tomoaki Yamada ◽  
Hiroaki Minegishi ◽  
Akinobu Echigo ◽  
Yasuhiro Shimane ◽  
...  
Keyword(s):  
Type Species ◽  
Lipid Analysis ◽  
Halophilic Archaea ◽  
Single Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
Link Type ◽  
Physiological And Biochemical Characteristics ◽  
Low Levels

Two extremely halophilic archaea, strains MGY-184T and MGY-205, were isolated from sea salt produced in Japan and rock salt imported from Bolivia, respectively. Both strains were pleomorphic, non-motile, Gram-negative and required more than 5 % (w/v) NaCl for growth, with optimum at 9–12 %, in the presence of 2 % (w/v) MgCl2 . 6H2O. In the presence of 18 % (w/v) MgCl2 . 6H2O, however, both strains showed growth even at 1.0 % (w/v) NaCl. Both strains possessed two 16S rRNA genes (rrnA and rrnB), and they revealed closest similarity to Halobaculum gomorrense JCM 9908T, the single species with a validly published name of the genus Halobaculum , with similarity of 97.8 %. The rrnA and rrnB genes of both strains were 100 % similar. The rrnA genes were 97.6 % similar to the rrnB genes in both strains. DNA G+C contents of strains MGY-184T and MGY-205 were 67.0 and 67.4 mol%, respectively. Polar lipid analysis revealed that the two strains contained phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester derived from C20C20 archaeol. The DNA–DNA hybridization value between the two strains was 70 % and both strains showed low levels of DNA–DNA relatedness (48–50 %) with Halobaculum gomorrense JCM 9908T. Physiological and biochemical characteristics allowed differentiation of strains MGY-184T and MGY-205 from Halobaculum gomorrense JCM 9908T. Therefore, strains MGY-184T and MGY-205 represent a novel species of the genus Halobaculum , for which the name Halobaculum magnesiiphilum sp. nov. is proposed; the type strain is MGY-184T ( = JCM 17821T = KCTC 4100T).

scholarly journals Mucilaginibacter koreensis sp. nov., isolated from leaf mould

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2274-2279 ◽  
Author(s):  
Cheol Su Park ◽  
Kyudong Han ◽  
Tae-Young Ahn
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

A Gram-staining-negative, strictly aerobic, rod-shaped, pale-pink pigmented bacterial strain, designated TF8T, was isolated from leaf mould in Cheonan, Republic of Korea. Its taxonomic position was determined through a polyphasic approach. Optimal growth occurred on R2A agar without NaCl supplementation, at 25–28 °C and at pH 6.0–7.0. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TF8T belongs to the genus Mucilaginibacter in the family Sphingobacteriaceae . The sequence similarity between 16S rRNA genes of strain TF8T and the type strains of other species of the genus Mucilaginibacter ranged from 92.1 to 94.7 %. The closest relatives of strain TF8T were Mucilaginibacter lutimaris BR-3T (94.7 %), M. soli R9-65T (94.5 %), M. litoreus BR-18T (94.5 %), M. rigui WPCB133T (94.0 %) and M. daejeonensis Jip 10T (93.8 %). The major isoprenoid quinone was MK-7 and the major cellular fatty acids were iso-C15 : 0 (33.0 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 24.8 %) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 13.0 %). The major polar lipids of TF8T were phosphatidylethanolamine and three unidentified aminophospholipids. The G+C content of the genomic DNA was 46.2 mol%. On the basis of the data presented here, strain TF8T is considered to represent a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter koreensis sp. nov. is proposed. The type strain is TF8T ( = KACC 17468T = JCM 19323T).

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