scholarly journals Revisiting Corynebacterium glyciniphilum (ex Kubota et al., 1972) sp. nov., nom. rev., isolated from putrefied banana

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 177-182 ◽  
Author(s):  
Arwa Al-Dilaimi ◽  
Hanna Bednarz ◽  
Alexander Lömker ◽  
Karsten Niehaus ◽  
Jörn Kalinowski ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Morphological Characterization ◽  
Content Type ◽  
Phylogenetic Characterization ◽  
Ph Values ◽  
Link Type

A strain of a species of the genus Corynebacterium , designated AJ 3170T, was isolated during the 1980s from putrefied bananas. Since then, there have been no further updates on the description of the strain or its phylogenetic classification. However, phylogenetic analysis of this strain using 16S rRNA and in silico DNA–DNA hybridization has confirmed that it is a member of the genus Corynebacterium and that strain AJ 3170T clusters with Corynebacterium variabile DSM 44702T, Corynebacterium terpenotabidum Y-11T and Corynebacterium nuruki S6-4T in one subgroup. Furthermore, a combination of enzymatic, chemical, and morphological characterization techniques was applied in order to describe strain AJ 3170T further. The strain grew well at pH values of 6–10 and at temperatures of 30–41 °C. The major fatty acids were C16 : 0 (42.15 %), C18 : 1ω9c (41.6 %) and C18 : 0 10-methyl (TBSA) (8.56 %). The whole-cell sugars were determined to comprise galactose, arabinose and ribose. On the basis of this phenotypic, chemotaxonomic and phylogenetic characterization, it is proposed that strain AJ 3170T represents a novel species, for which the name Corynebacterium glyciniphilum sp. nov. is proposed; the type strain is AJ 3170T ( = DSM 45795T = ATCC 21341T).

scholarly journals Xanthomonas hydrangeae sp. nov., a novel plant pathogen isolated from Hydrangea arborescens

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Nay C. Dia ◽  
Johan Van Vaerenbergh ◽  
Cinzia Van Malderghem ◽  
Jochen Blom ◽  
Theo H. M. Smits ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Close Relation ◽  
Genome Sequences ◽  
Content Type ◽  
Phylogenetic Characterization ◽  
Link Type ◽  
Amplification Assay

This paper describes a novel species isolated in 2011 and 2012 from nursery-grown Hydrangea arborescens cultivars in Flanders, Belgium. After 4 days at 28 °C, the strains yielded yellow, round, convex and mucoid colonies. Pathogenicity of the strains was confirmed on its isolation host, as well as on Hydrangea quercifolia. Analysis using MALDI-TOF MS identified the Hydrangea strains as belonging to the genus Xanthomonas but excluded them from the species Xanthomonas hortorum . A phylogenetic tree based on gyrB confirmed the close relation to X. hortorum . Three fatty acids were dominant in the Hydrangea isolates: anteiso-C15 : 0, iso-C15 : 0 and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c). Unlike X. hortorum pathovars, the Hydrangea strains were unable to grow in the presence of lithium chloride and could only weakly utilize d-fructose-6-PO4 and glucuronamide. Phylogenetic characterization based on multilocus sequence analysis and phylogenomic characterization revealed that the strains are close to, yet distinct from, X. hortorum . The genome sequences of the strains had average nucleotide identity values ranging from 94.35–95.19 % and in silico DNA–DNA hybridization values ranging from 55.70 to 59.40 % to genomes of the X. hortorum pathovars. A genomics-based loop-mediated isothermal amplification assay was developed which was specific to the Hydrangea strains for its early detection. A novel species, Xanthomonas hydrangeae sp. nov., is proposed with strain LMG 31884T (=CCOS 1956T) as the type strain.

Mucilaginibacter soyangensis sp. nov., isolated from a lake

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 413-419 ◽  
Author(s):  
Yochan Joung ◽  
Haneul Kim ◽  
Heeyoung Kang ◽  
Beom-Il Lee ◽  
Tae-Seok Ahn ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Yellow Orange

A non-motile, yellow–orange-pigmented bacterial strain, designated HME6664T, was isolated from Lake Soyang, Republic of Korea. The major fatty acids of strain HME6664T were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c; 44.7 %) and iso-C15 : 0 (20.2 %). The DNA G+C content was 40.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME6664T formed a lineage within the genus Mucilaginibacter . Strain HME6664T was closely related to Mucilaginibacter ximonensis (96.7 %), Mucilaginibacter dorajii (96.5 %) and Mucilaginibacter lappiensis (96.3 %). On the basis of the evidence presented in this study, strain HME6664T represents a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter soyangensis sp. nov., is proposed. The type strain is HME6664T ( = KCTC 23261T = CECT 7824T).

Enterococcus saccharolyticus subsp. taiwanensis subsp. nov., isolated from broccoli

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4691-4697 ◽  
Author(s):  
Yi-sheng Chen ◽  
Yu-hsuan Lin ◽  
Shwu-fen Pan ◽  
Si-hua Ji ◽  
Yu-chung Chang ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Phenotypic Traits ◽  
Strain Atcc ◽  
Content Type ◽  
Cellular Fatty Acids ◽  
Link Type ◽  
Emended Description

A coccal strain isolated from fresh broccoli was initially identified as Enterococcus saccharolyticus ; however, molecular identification and phenotypic traits did not support this identification. DNA–DNA hybridization with the type strain of E. saccharolyticus (76.4 % relatedness), DNA G+C content (35.7 mol%), phylogenetic analysis based on 16S rRNA, pheS and rpoA gene sequences, rep-PCR fingerprinting and profiles of cellular fatty acids, whole-cell proteins and enzyme activities, together with carbohydrate metabolism characteristics, indicated that this strain is distinct and represents a novel subspecies, for which the name Enterococcus saccharolyticus subsp. taiwanensis subsp. nov. is proposed. The type strain is 812T ( = NBRC 109476T = BCRC 80575T). Furthermore, we present an emended description of Enterococcus saccharolyticus and proposal of Enterococcus saccharolyticus subsp. saccharolyticus subsp. nov. (type strain ATCC 43076T = CCUG 27643T = CCUG 33311T = CIP 103246T = DSM 20726T = JCM 8734T = LMG 11427T = NBRC 100493T = NCIMB 702594T).

Arenimonas daechungensis sp. nov., isolated from the sediment of a eutrophic reservoir

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 484-489 ◽  
Author(s):  
Hangsak Huy ◽  
Long Jin ◽  
Young-Ki Lee ◽  
Keun Chul Lee ◽  
Jung-Sook Lee ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Genetic Data ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Gram Negative ◽  
Content Type ◽  
Link Type

A Gram-negative, non-motile, non-spore-forming and rod-shaped bacterial strain, CH15-1T, was isolated from a sediment sample taken from Daechung Reservoir, South Korea, during the late-blooming period of cyanobacteria. Strain CH15-1T grew optimally at pH 7.0 and 30 °C. A phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain CH15-1T belongs to the genus Arenimonas with the similarity range from 92.6–97.4 % and is closely related to Arenimonas oryziterrae YC6267T (97.4 %), Arenimonas composti TR7-09T (95.4 %), Arenimonas metalli CF5-1T (94.7 %), Arenimonas malthae CC-JY-1T (94.6 %) and Arenimonas donghaensis HO3-R19T (92.6 %). However, the DNA–DNA hybridization between strain CH15-1T and the closest strain, Arenimonas oryziterrae YC6267T, was 8.9–12.9 %. The DNA G+C content was 63.9 mol% compared to A. oryziterrae YC626T, 65.8 mol%. Strain CH15-1T included Q-8 as the major ubiquinone and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylmonomethylethanolamine as the major polar lipids. The major fatty acids (>5 %) were iso-C15 : 0, iso-C16 : 0, iso-C14 : 0, iso-C11 : 0 3-OH, iso-C17 : 0 and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl). On the basis of phylogenetic, phenotypic and genetic data, strain CH15-1T was classified in the genus Arenimonas as a member of a novel species, for which the name Arenimonas daechungensis sp. nov. is proposed. The type strain is CH15-1T ( = KCTC 23553T = DSM 24763T).

Actinokineospora bangkokensis sp. nov., isolated from rhizospheric soil

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2655-2660 ◽  
Author(s):  
Bungonsiri Intra ◽  
Atsuko Matsumoto ◽  
Yuki Inahashi ◽  
Satoshi Ōmura ◽  
Yōko Takahashi ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
Rhizospheric Soil ◽  
Content Type ◽  
Link Type

A novel actinomycete, strain 44EHWT, was isolated from rhizospheric soil under an Elephant ear plant (Colocasia esculenta) in Bangkok, Thailand. Strain 44EHWT produced long branching hyphae and abundant aerial mycelia with chains of rod-shaped spores. Whole-cell hydrolysates contained galactose, glucose, arabinose, ribose, mannose and rhamnose as diagnostic sugars. meso-Diaminopimelic acid was the diamino acid and glycine, alanine and glutamic acid were present in the cell-wall peptidoglycan with the acyl type of the peptidoglycan being acetyl. Phospholipids consisted of phosphatidylethanolamine, phosphatidylethanolamine with hydroxy fatty acids and diphosphatidylglycerol, as well as other unknown phospholipids; however, no mycolic acids were detected. The predominant menaquinone observed was MK-9(H4) and major fatty acids were iso-C16 : 0 and 2-OH iso-C16 : 0. The G+C content of genomic DNA was 74 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that this isolate was most similar to Actinokineospora enzanensis NBRC 16517T. However, DNA–DNA hybridization revealed a low relatedness between this isolate and A. enzanensis NBRC 16517T, indicating that this isolate represented a novel species in the genus Actinokineospora . On the basis of 16S rRNA gene sequence analysis, phenotypic characteristics and DNA–DNA hybridization data, we propose that strain 44EHWT represents a novel species in the genus Actinokineospora , Actinokineospora bangkokensis. The type strain is 44EHWT ( = BCC 53155T = NBRC 108932T).

Novosphingobium lindaniclasticum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2160-2167 ◽  
Author(s):  
Anjali Saxena ◽  
Shailly Anand ◽  
Ankita Dua ◽  
Naseer Sangwan ◽  
Fazlurrahman Khan ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Phylogenetic Analysis ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium

A yellow-pigmented, Gram-negative, aerobic, non-motile, non-spore-forming, rod-shaped-bacterium, LE124T, was isolated from a hexachlorocyclohexane (HCH) dumpsite located in Lucknow, India. The type strain LE124T grew well with hexachlorocyclohexane as a sole carbon source, degrading it within 24 h of incubation. Phylogenetic analysis of strain LE124T showed highest 16S rRNA gene sequence similarity to Novosphingobium barchaimii LL02T (98.5 %), Novosphingobium panipatense SM16T (98.1 %), Novosphingobium soli CC-TPE-1T (97.9 %), Novosphingobium naphthalenivorans TUT562T (97.6 %), Novosphingobium mathurense SM117T (97.5 %) and Novosphingobium resinovorum NCIMB 8767T (97.5 %) and lower sequence similarity (<97 %) to all other members of the genus Novosphingobium . The DNA–DNA relatedness between strain LE124T and N. barchaimii LL02T and other related type strains was found to vary from 15 % to 45 % confirming that it represents a novel species. The genomic DNA G+C content of strain LE124T was 60.7 mol%. The predominant fatty acids were summed feature 8 (C18 : 1ω7c, 49.1 %), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c, 19.9 %), C16 : 0 (6.7 %), C17 : 1ω6c (4.9 %) and a few hydroxyl fatty acids, C14 : 0 2-OH (9.4 %) and C16 : 0 2-OH (2.1 %). Polar lipids consisted mainly of phosphatidyldimethylethanolamine, phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, sphingoglycolipid and some unidentified lipids. The major respiratory quinone was ubiquinone Q-10. Spermidine was the major polyamine observed. Phylogenetic analysis, DNA–DNA hybridization, chemotaxonomic and phenotypic analysis support the conclusion that strain LE124T represents a novel species within the genus Novosphingobium for which we propose the name Novosphingbium lindaniclasticum sp. nov. The type strain is LE124T ( = CCM 7976T = DSM 25409T).

Sphingopyxis rigui sp. nov. and Sphingopyxis wooponensis sp. nov., isolated from wetland freshwater, and emended description of the genus Sphingopyxis

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1297-1303 ◽  
Author(s):  
Keun Sik Baik ◽  
Han Na Choe ◽  
Seong Chan Park ◽  
Yeoung Min Hwang ◽  
Eun Mi Kim ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Emended Description

Two yellow-pigmented, Gram-reaction-negative strains, designated 01SU5-PT and 03SU3-PT, were isolated from the freshwater of Woopo wetland, Republic of Korea. Both strains were aerobic, non-motile and catalase-negative. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates belong to the genus Sphingopyxis , showing the highest level of sequence similarity with respect to Sphingopyxis witflariensis W-50T (95.4–95.7 %). The two novel isolates shared 99.4 % sequence similarity. DNA–DNA hybridization between the isolates and the type strain of S. witflariensis clearly suggested that strains 01SU5-PT and 03SU3-PT represent two separate novel species in the genus Sphingopyxis . The two strains displayed different fingerprints after PCR analysis using the repetitive primers BOX, ERIC and REP. Several phenotypic characteristics served to differentiate these two isolates from recognized members of the genus Sphingopyxis . The data from the polyphasic study presented here indicated that strains 01SU5-PT and 03SU3-PT should be classified as representing novel species in the genus Sphingopyxis , for which the names Sphingopyxis rigui sp. nov. and Sphingopyxis wooponensis sp. nov., respectively, are proposed. The type strain of Sphingopyxis rigui sp. nov. is 01SU5-PT ( = KCTC 23326T = JCM 17509T) and the type strain of Sphingopyxis wooponensis sp. nov. is 03SU3-PT ( = KCTC 23340T = JCM 17547T).

scholarly journals Re-examination of the taxonomic status of Enterobacter helveticus, Enterobacter pulveris and Enterobacter turicensis as members of the genus Cronobacter and their reclassification in the genera Franconibacter gen. nov. and Siccibacter gen. nov. as Franconibacter helveticus comb. nov., Franconibacter pulveris comb. nov. and Siccibacter turicensis comb. nov., respectively

2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3402-3410 ◽  
Author(s):  
Roger Stephan ◽  
Christopher J. Grim ◽  
Gopal R. Gopinath ◽  
Mark K. Mammel ◽  
Venugopal Sathyamoorthy ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Biochemical Characterization ◽  
Novel Species ◽  
Taxonomic Status ◽  
New Genera ◽  
Content Type ◽  
Link Type ◽  
Genome Scale

Recently, a taxonomical re-evaluation of the genus Enterobacter , based on multi-locus sequence typing (MLST) analysis, has led to the proposal that the species Enterobacter pulveris , Enterobacter helveticus and Enterobacter turicensis should be reclassified as novel species of the genus Cronobacter . In the present work, new genome-scale analyses, including average nucleotide identity, genome-scale phylogeny and k-mer analysis, coupled with previously reported DNA–DNA hybridization values and biochemical characterization strongly indicate that these three species of the genus Enterobacter are not members of the genus Cronobacter , nor do they belong to the re-evaluated genus Enterobacter . Furthermore, data from this polyphasic study indicated that all three species constitute two new genera. We propose reclassifying Enterobacter pulveris and Enterobacter helveticus in the genus Franconibacter gen. nov. as Franconibacter pulveris comb. nov. (type strain 601/05T = LMG 24057T = DSM 19144T) and Franconibacter helveticus comb. nov. (type strain 513/05T = LMG 23732T = DSM 18396T), respectively, and Enterobacter turicensis in the genus Siccibacter gen. nov. as Siccibacter turicensis comb. nov. (type strain 508/05T = LMG 23730T = DSM 18397T).

scholarly journals Leptospira mayottensis sp. nov., a pathogenic species of the genus Leptospira isolated from humans

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4061-4067 ◽  
Author(s):  
Pascale Bourhy ◽  
Louis Collet ◽  
Sylvain Brisse ◽  
Mathieu Picardeau
Keyword(s):  
Sequence Analysis ◽  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Leptospira Borgpetersenii

A group of strains representing species of the genus Leptospira, isolated from patients with leptospirosis in Mayotte (Indian Ocean), were previously found to be considerably divergent from other known species of the genus Leptospira . This was inferred from sequence analysis of rrs (16S rRNA) and other genetic loci and suggests that they belong to a novel species. Two strains from each serogroup currently identified within this novel species were studied. Spirochaete, aerobic, motile, helix-shaped strains grew well at 30–37 °C, but not at 13 °C or in the presence of 8-azaguanine. Draft genomes of the strains were also analysed to study the DNA relatedness with other species of the genus Leptospira . The new isolates formed a distinct clade, which was most closely related to Leptospira borgpetersenii , in multilocus sequence analysis using concatenated sequences of the genes rpoB, recA, fusA, gyrB, leuS and sucA. Analysis of average nucleotide identity and genome-to-genome distances, which have recently been proposed as reliable substitutes for classical DNA–DNA hybridization, further confirmed that these isolates should be classified as representatives of a novel species. The G+C content of the genomic DNA was 39.5 mol%. These isolates are considered to represent a novel species, for which the name Leptospira mayottensis sp. nov. is proposed, with 200901116T ( = CIP 110703T = DSM 28999T) as the type strain.

Pectobacterium quasiaquaticum sp. nov., isolated from waterways

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Hajar Ben Moussa ◽  
Jacques Pédron ◽  
Claire Bertrand ◽  
Amandine Hecquet ◽  
Marie-Anne Barny
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Core Genome ◽  
Novel Species ◽  
Taxonomic Status ◽  
Artificial Lake ◽  
Content Type ◽  
Link Type ◽  
Rivers And Lakes

Through this study, we established the taxonomic status of seven strains belonging to the genus Pectobacterium (A477-S1-J17T, A398-S21-F17, A535-S3-A17, A411-S4-F17, A113-S21-F16, FL63-S17 and FL60-S17) collected from four different river streams and an artificial lake in south-east France between 2016 and 2017. Ecological surveys in rivers and lakes pointed out different repartition of strains belonging to this clade compared to the closest species, Pectobacterium aquaticum . The main phenotypic difference observed between these strains and the P. aquaticum type strain was strongly impaired growth with rhamnose as the sole carbon source. This correlates with three different forms of pseudogenization of the l-rhamnose/proton symporter gene rhaT in the genomes of strains belonging to this clade. Phylogenetic analysis using gapA gene sequences and multi locus sequence analysis of the core genome showed that these strains formed a distinct clade within the genus Pectobacterium closely related to P. aquaticum. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values showed a clear discontinuity between the new clade and P. aquaticum . However, the calculated values are potentially consistent with either splitting or merging of this new clade with P. aquaticum . In support of the split, ANI coverages were higher within this new clade than between this new clade and P. aquaticum . The split is also consistent with the range of observed ANI or dDDH values that currently separate several accepted species within the genus Pectobacterium . On the basis of these data,strains A477-S1-J17T, A398-S21-F17, A535-S3-A17, A411-S4-F17, A113-S21-F16, FL63-S17 and FL60-S17 represent a novel species of the genus Pectobacterium , for which the name Pectobacterium quasiaquaticum sp. nov. is proposed. The type strain is A477-S1-J17T (=CFBP 8805T=LMG 32181T).

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