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 ◽  
...  

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.

Author(s):  
Nantawan Niemhom ◽  
Chanwit Suriyachadkun ◽  
Chokchai Kittiwongwattana

Two Gram-stain-negative, non-motile, rod-shaped bacterial strains were isolated from the surfaces of rice roots. They were designated as strains 1303T and 1310. Their colonies were circular, entire, opaque, convex and yellow. They were chitinase- and catalase-positive, reduced nitrate and grew at 16–37 °C (optimum, 30 °C), pH 5.0–10.0 (optimum, pH 7.0) and 0–2.0% NaCl (optimum, 1.0 %). Based on the 16S rRNA gene sequence analysis, they were classified as members of the genus Chitinophaga . Results of phylogenetic and phylogenomic analyses indicated that they formed a cluster with Chitinophaga eiseniae YC6729T, Chitinophaga qingshengii JN246T, Chitinophaga varians 10-7 W-9003T and Chitinophaga fulva G-6-1-13T. When the genomic sequences of strains 1303T and 1310 were compared with their close relatives, the average nucleotide identity and digital DNA–DNA hybridization values were below the cut-off levels. Phosphatidylethanolamine was the major polar lipid. MK-7 was the major respiratory quinone. iso-C15 : 0, C16 : 1  ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c) were the predominant fatty acids. Differential characteristics between both strains and their close relatives were also observed. Based on the distinctions in genotypic, phenotypic and chemotypic features, strains 1303T and 1310 represent members of a novel species of the genus Chitinophaga , for which the name Chitinophaga oryzae sp. nov. is proposed. The type strain is 1303T (=KACC 22075T=TBRC 12926T).


2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1501-1506 ◽  
Author(s):  
Bacem Mnasri ◽  
Tian Yan Liu ◽  
Sabrine Saidi ◽  
Wen Feng Chen ◽  
Wen Xin Chen ◽  
...  

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.


2020 ◽  
Vol 70 (4) ◽  
pp. 2369-2381 ◽  
Author(s):  
Dmitriy V. Volokhov ◽  
Dénes Grózner ◽  
Miklós Gyuranecz ◽  
Naola Ferguson-Noel ◽  
Yamei Gao ◽  
...  

In 1983, Mycoplasma sp. strain 1220 was isolated in Hungary from the phallus lymph of a gander with phallus inflammation. Between 1983 and 2017, Mycoplasma sp. 1220 was also identified and isolated from the respiratory tract, liver, ovary, testis, peritoneum and cloaca of diseased geese in several countries. Seventeen studied strains produced acid from glucose and fructose but did not hydrolyse arginine or urea, and all grew under aerobic, microaerophilic and anaerobic conditions at 35 to 37 ˚C in either SP4 or pleuropneumonia-like organism medium supplemented with glucose and serum. Colonies on agar showed a typical fried-egg appearance and transmission electron microscopy revealed a typical mycoplasma cellular morphology. Molecular characterization included analysis of the following genetic loci: 16S rRNA, 23S rRNA, 16S–23S rRNA ITS, rpoB, rpoC, rpoD, uvrA, parC, topA, dnaE, fusA and pyk. The genome was sequenced for type strain 1220T. The 16S rRNA gene sequences of studied strains of Mycoplasma sp. 1220 shared 99.02–99.19 % nucleotide similarity with M. anatis strains but demonstrated ≤95.00–96.70 % nucleotide similarity to the 16S rRNA genes of other species of the genus Mycoplasma . Phylogenetic, average nucleotide and amino acid identity analyses revealed that the novel species was most closely related to Mycoplasma anatis . Based on the genetic data, we propose a novel species of the genus Mycoplasma , for which the name Mycoplasma anserisalpingitidis sp. nov. is proposed with the type strain 1220T (=ATCC BAA-2147T=NCTC 13513T=DSM 23982T). The G+C content is 26.70 mol%, genome size is 959110 bp.


2020 ◽  
Vol 70 (11) ◽  
pp. 5627-5633 ◽  
Author(s):  
Yong Li ◽  
Shengkun Wang ◽  
Ju-pu Chang ◽  
Dan-ran Bian ◽  
Li-min Guo ◽  
...  

Two Gram-stain-negative, aerobic, non-motile bacterial strains, 36D10-4-7T and 30C10-4-7T, were isolated from bark canker tissue of Populus × euramericana, respectively. 16S rRNA gene sequence analysis revealed that strain 36D10-4-7T shows 98.0 % sequence similarity to Sphingomonas adhaesiva DSM 7418T, and strain 30C10-4-7T shows highest sequence similarity to Sphingobacterium arenae H-12T (95.6 %). Average nucleotide identity analysis indicates that strain 36D10-4-7T is a novel member different from recognized species in the genus Sphingomonas . The main fatty acids and respiratory quinone detected in strain 36D10-4-7T are C18 : 1  ω7c and/or C18 : 1  ω6c and Q-10, respectively. The polar lipids are diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, aminolipid, phosphatidylethanolamine, sphingoglycolipid, two uncharacterized phospholipids and two uncharacterized lipids. For strain 30C10-4-7T, the major fatty acids and menaquinone are iso-C15 : 0, C16 : 1  ω7c and/or C16 : 1  ω6c and iso-C17 : 0 3-OH and MK-7, respectively. The polar lipid profile includes phosphatidylethanolamine, phospholipids, two aminophospholipids and six unidentified lipids. Based on phenotypic and genotypic characteristics, these two strains represent two novel species within the genera Sphingomonas and Sphingobacterium . The name Sphingomonas corticis sp. nov. (type strain 36D10-4-7T=CFCC 13112T=KCTC 52799T) and Sphingobacterium corticibacterium sp. nov. (type strain 30C10-4-7T=CFCC 13069T=KCTC 52797T) are proposed.


2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 497-503 ◽  
Author(s):  
Yin Shan Jiao ◽  
Hui Yan ◽  
Zhao Jun Ji ◽  
Yuan Hui Liu ◽  
Xin Hua Sui ◽  
...  

Five bacterial strains representing 45 isolates originated from root nodules of the medicinal legume Sophora flavescens were defined as two novel groups in the genus Rhizobium based on their phylogenetic relationships estimated from 16S rRNA genes and the housekeeping genes recA, glnII and atpD. These groups were distantly related to Rhizobium leguminosarum USDA 2370T (95.6 % similarity for group I) and Rhizobium phaseoli ATCC 14482T (93.4 % similarity for group II) in multilocus sequence analysis. In DNA–DNA hybridization experiments, the reference strains CCBAU 03386T (group I) and CCBAU 03470T (group II) showed levels of relatedness of 17.9–57.8 and 11.0–42.9 %, respectively, with the type strains of related species. Both strains CCBAU 03386T and CCBAU 03470T contained ubiquinone 10 (Q-10) as the major respiratory quinone and possessed 16 : 0, 18 : 0, 19 : 0 cyclo ω8c, summed feature 8 and summed feature 2 as major fatty acids, but did not contain 20 : 3 ω6,8,12c. Phenotypic features distinguishing both groups from all closely related species of the genus Rhizobium were found. Therefore, two novel species, Rhizobium sophorae sp. nov. for group I (type strain CCBAU 03386T = E5T = LMG 27901T = HAMBI 3615T) and Rhizobium sophoriradicis sp. nov. for group II (type strain CCBAU 03470T = C-5-1T = LMG 27898T = HAMBI 3510T), are proposed. Both groups were able to nodulate Phaseolus vulgaris and their hosts of origin (Sophora flavescens) effectively and their nodulation gene nodC was phylogenetically located in the symbiovar phaseoli.


2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 438-443 ◽  
Author(s):  
R. Nomoto ◽  
F. Maruyama ◽  
S. Ishida ◽  
M. Tohya ◽  
T. Sekizaki ◽  
...  

In order to clarify the taxonomic position of serotypes 20, 22 and 26 of Streptococcus suis , biochemical and molecular genetic studies were performed on isolates (SUT-7, SUT-286T, SUT-319, SUT-328 and SUT-380) reacted with specific antisera of serotypes 20, 22 or 26 from the saliva of healthy pigs as well as reference strains of serotypes 20, 22 and 26. Comparative recN gene sequencing showed high genetic relatedness among our isolates, but marked differences from the type strain S. suis NCTC 10234T, i.e. 74.8–75.7 % sequence similarity. The genomic relatedness between the isolates and other strains of species of the genus Streptococcus , including S. suis, was calculated using the average nucleotide identity values of whole genome sequences, which indicated that serotypes 20, 22 and 26 should be removed taxonomically from S. suis and treated as a novel genomic species. Comparative sequence analysis revealed 99.0–100 % sequence similarities for the 16S rRNA genes between the reference strains of serotypes 20, 22 and 26, and our isolates. Isolate STU-286T had relatively high 16S rRNA gene sequence similarity with S. suis NCTC 10234T (98.8 %). SUT-286T could be distinguished from S. suis and other closely related species of the genus Streptococcus using biochemical tests. Due to its phylogenetic and phenotypic similarities to S. suis we propose naming the novel species Streptococcus parasuis sp. nov., with SUT-286T ( = JCM 30273T = DSM 29126T) as the type strain.


Author(s):  
Ming-Sheng Chen ◽  
Bao-Quan Pang ◽  
Shao-Wei Liu ◽  
Fei-Na Li ◽  
Xiao-Rui Yan ◽  
...  

A Gram-stain-positive, aerobic, non-motile, non-endospore-forming and rod-shaped actinobacterium, designated strain CMS6Z-2T, was isolated from a surface-sterilized branch of Kandelia candel collected from the Maowei Sea, Guangxi Zhuang Autonomous Region, PR China. Strain CMS6Z-2T grew at 10–37 °C (optimum, 37 °C), pH 6.0–9.0 (optimum, pH 7.0–8.0) and in the presence of 0–10.0 % (w/v) NaCl (optimum, 0–1.0 %). Strain CMS6Z-2T possessed meso-diaminopimelic acid as the diamino acid of the peptidoglycan and MK-8 (H4) as the predominant menaquinone. The major fatty acids were iso-C15 : 0, C16 : 0 and C18 : 1  ω9c. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unknown phospholipids. The G+C content of the genomic DNA was 74.1 mol%. Comparative analysis of 16S rRNA genes showed that strain CMS6Z-2T should be assigned to the genus Phycicoccus and its closest relative was Phycicoccus endophyticus IP6SC6T with 98.3 % similarity. Phylogenetic analyses based on 16S rRNA gene sequence and phylogenomic analysis based on core proteomes alignment revealed that strain CMS6Z-2T belonged to the genus Phycicoccus and formed a robust cluster with Phycicoccus endophyticus IP6SC6T within the genus Phycicoccus . The average nucleotide identity value and estimated digital DNA–DNA hybridization value between strain CMS6Z-2T and the type strain of Phycicoccus endophyticus were 81.5 and 23.9 %, respectively. On the basis of phylogenetic, phenotypic and chemotaxonomic characteristics, strain CMS6Z-2T represents a novel species of the genus Phycicoccus , for which the name Phycicoccus flavus sp. nov. is proposed. The type strain is CMS6Z-2T (=KCTC 49240T=CGMCC4.7549T).


2020 ◽  
Vol 70 (8) ◽  
pp. 4838-4842 ◽  
Author(s):  
Fabiana Tonial ◽  
Felipe Guella ◽  
Luciane Maria Pereira Passaglia ◽  
Fernando Hayashi Sant’Anna

Bacteria of the genus Paenibacillus are relevant to humans, animals and plants. The species Paenibacillus massiliensis and Paenibacillus panacisoli are Gram-stain-positive and endospore-forming bacilli isolated from a blood culture of a leukemia patient and from soil of a ginseng field, respectively. Comparative analyses of their 16S rRNA genes revealed that the two Paenibacillus species could be synonyms (99.3% sequence identity). In the present study we performed different genomic analyses in order to evaluate the phylogenetic relationship of these micro-organisms. Paenibacillus massiliensis DSM 16942T and P. panacisoli DSM 21345T presented a difference in their G+C content lower than 1 mol%, overall genome relatedness index values higher than the species circumscription thresholds (average nucleotide identity, 95.57 %; genome-wide ANI, =96.51 %; and orthologous ANI, 96.25 %), and a monophyletic grouping pattern in the phylogenies of the 16S rRNA gene and the proteome core. Considering that these strains present differential biochemical capabilities and that their computed digital DNA–DNA hybridization value is lower than the cut-off for bacterial subspecies circumscription, we suggest that each of them form different subspecies of P. massiliensis , Paenibacillus massiliensis subsp. panacisoli subsp. nov. (type strain DSM 21345T) and Paenibacillus massiliensis subsp. massiliensis subsp. nov. (type strain DSM 16942T).


2020 ◽  
Vol 70 (5) ◽  
pp. 3105-3110 ◽  
Author(s):  
Sou Miyake ◽  
Yichen Ding ◽  
Melissa Soh ◽  
Adrian Low ◽  
Henning Seedorf

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).


2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1779-1785 ◽  
Author(s):  
David Frasson ◽  
Matije Udovičić ◽  
Beat Frey ◽  
Aleš Lapanje ◽  
De-Chao Zhang ◽  
...  

Psychrophilic bacterial strains were isolated from alpine glaciers in Switzerland and characterized taxonomically. On the basis of phylogenetic analysis of partial 16S rRNA and rpoB genes, three of those strains, strain 79 ( = CCOS 247), strain 4/58 ( = CCOS 250) and strain 4/56 ( = CCOS 258) clustered together with strain Cr9-12T and separately from the type strains Glaciimonas immobilis Cr9-30T and Glaciimonas singularis LMG 27070T. Strain Cr9-12T has been previously described as a strain of G. immobilis . The three newly isolated strains were compared phenotypically with strain Cr9-12T and with the type strains of the species G. immobilis and G. singularis . Cr9-12T and the three novel strains from an alpine glacier in Switzerland were Gram-stain-negative, non-motile, rod-shaped and psychrophilic and showed good growth throughout a temperature range of 1–20 °C and characteristically oxidized d-mannitol, l-fucose and bromosuccinic acid. The predominant cellular fatty acids of strain Cr9-12T and the three novel strains were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. The respiratory quinone of these strains was ubiquinone 8 (UQ-8). The genomic DNA G+C content of Cr9-12T was 49.2 mol%. The combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies strongly support the reclassification of strain Cr9-12T as representing a novel species. This strain and the isolates 79 ( = CCOS 247), 4/58 ( = CCOS 250) and 4/56 ( = CCOS 258) are representatives of a novel species of the genus Glaciimonas , for which the name Glaciimonas alpina sp. nov. is proposed. The type strain of Glaciimonas alpina is Cr9-12T ( = CCOS 761T = DSM 22814T).


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