scholarly journals Corynebacterium silvaticum sp. nov., a unique group of NTTB corynebacteria in wild boar and roe deer

2020 ◽  
Vol 70 (6) ◽  
pp. 3614-3624 ◽  
Author(s):  
Alexandra Dangel ◽  
Anja Berger ◽  
Jörg Rau ◽  
Tobias Eisenberg ◽  
Peter Kämpfer ◽  
...  

A total of 34 Corynebacterium sp. strains were isolated from caseous lymph node abscesses of wild boar and roe deer in different regions of Germany. They showed slow growth on Columbia sheep blood agar and sparse growth on Hoyle’s tellurite agar. Cellular fatty acid analysis allocated them in the C. diphtheriae group of genus Corynebacterium . MALDI-TOF MS using specific database extensions and rpoB sequencing resulted in classification as C. ulcerans . Their quinone system is similar to C. ulcerans , with major menaquinone MK-8(H2). Their complex polar lipid profile includes major lipids phosphatidylinositol, phosphatidylinositol-mannoside, diphosphatidylglycerol, but also unidentified glycolipids, distinguishing them clearly from C. ulcerans . They ferment glucose, ribose and maltose (like C. ulcerans ), but do not utilise d-xylose, mannitol, lactose, sucrose and glycogen (like C. pseudotuberculosis ). They showed activity of catalase, urease and phospholipase D, but variable results for alkaline phosphatase and alpha-glucosidase. All were non-toxigenic, tox gene bearing and susceptible to clindamycin, penicillin and erythromycin. In 16SrRNA gene and RpoB protein phylogenies the strains formed distinct brancheswith C. ulcerans as nearest relative.Whole genome sequencing revealed the unique sequence type 578, a distinctbranch in pangenomic core genome MLST, average nucleotide identities <91%, enhancedgenome sizes (2.55 Mbp) and G/C content (54.4 mol%) compared to related species.These results suggest that the strains represent a novel species, for which wepropose the name Corynebactriumsilvaticum sp. nov., based on their first isolation from forest-dwellinggame animals. The type strain isKL0182T (= CVUAS 4292T = DSM 109166T = LMG 31313T= CIP 111 672T).

Author(s):  
Soo-Yeon Choi ◽  
Ji-Sung Oh ◽  
Dong-Hyun Roh

A Gram-stain-negative, aerobic, yellow-pigmented and non-motile rod-shaped bacterium, designated as GrpM-11T, was isolated from coastal seawater collected from the East Sea, Republic of Korea. Strain GrpM-11T could grow at 10–40 °C (optimum, 35 °C), at pH 5.5–9.5 (optimum, pH 7.0) and in the presence of 0–8 % (w/v) NaCl (optimum, 3–4 %). Cells hydrolysed aesculin, gelatin and casein, but could not reduce nitrate to nitrite. The 16S rRNA gene sequence analysis showed that this strain formed a distinct phylogenic lineage with Parasphingopyxis algicola ATAX6-5T (96.2 % sequence identity) and Parasphingopyxis lamellibrachiae DSM 26725T (96.2 % identity) and belonged to the genus Parasphingopyxis . The predominant isoprenoid quinone was ubiquinone-10. The polar lipid profile of strain GrpM-11T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and three unknown glycolipids. Cellular fatty acid analysis indicated that summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c; 42.8 %), C16 : 0 (19.0 %), C18 : 1 ω7c 11-methyl (13.3 %) and C18 : 1 ω7c (8.0 %) were the major fatty acids. The DNA G+C content of strain GrpM-11T was 63.7 mol%. Through whole genome sequence comparisons, the digital DNA–DNA hybridization and average nucleotide identity values between strain GrpM-11T and two species of the genus Parasphingopyxis were revealed to be in the ranges of 19.0–22.0 % and 76.3–79.7 %, respectively. Based on the results of polyphasic analysis, strain GrpM-11T represents a novel species of the genus Parasphingopyxis , for which the name Parasphingopyxis marina sp. nov. is proposed. The type strain is GrpM-11T (KCCM 43343T=JCM 34665T).


Author(s):  
Xiunuan Chen ◽  
Bingxia Dong ◽  
Ting Chen ◽  
Na Ren ◽  
Jing Wang ◽  
...  

Aniline blue-decolourizing bacterial strain 502str22T, isolated from sediment collected in the East Pacific, was subjected to characterization by a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 502str22T belongs to the genus Novosphingobium , with closely related type strains ‘ Novosphingobium profundi ’ F72T (97.6%), N. mathurense SM117T (97.1%) and N. arvoryzae Jyi-02T (97.0%). Digital DNA–DNA hybridization and average nucleotide identity values between strain 502str22T and closely related type strains were 20.3–24.8% and 74.1–81.9%, respectively. The major cellular fatty acid (>10%) was C18:1 ω7c. The polar lipid profile consisted of a mixture of phosphatidylcholine, one sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The DNA G+C content of strain 502str22T was 65.5 mol%. The polyphasic taxonomic results indicated that strain 502str22T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium decolorationis sp. nov is proposed. The type strain is 502str22T (=KCTC 82134T= MCCC 1K04799 T).


2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1525-1530 ◽  
Author(s):  
Claire M. Grison ◽  
Stephen Jackson ◽  
Sylvain Merlot ◽  
Alan Dobson ◽  
Claude Grison

A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming bacterium (ChimEc512T) was isolated from 56 host seedlings of the hyperaccumulating Anthyllis vulneraria legume, which was on an old zinc mining site at Les Avinières, Saint-Laurent-Le-Minier, Gard, South of France. On the basis of 16S rRNA gene sequence similarities, strain ChimEc512T was shown to belong to the genus Rhizobium and to be most closely related to Rhizobium endophyticum CCGE 2052T (98.4 %), Rhizobium tibeticum CCBAU 85039T (98.1 %), Rhizobium grahamii CCGE 502T (98.0 %) and Rhizobium mesoamericanum CCGE 501T (98.0 %). The phylogenetic relationships of ChimEc512T were confirmed by sequencing and analyses of recA and atpD genes. DNA–DNA relatedness values of strain ChimEc512T with R. endophyticum CCGE 2052T, R. tibeticum CCBAU 85039T, R. mesoamericanum CCGE 52T, Rhizobium grahamii CCGE 502T, Rhizobium etli CCBAU 85039T and Rhizobium radiobacter KL09-16-8-2T were 27, 22, 16, 18, 19 and 11 %, respectively. The DNA G+C content of strain ChimEc512T was 58.9 mol%. The major cellular fatty acid was C18 : 1ω7c, characteristic of the genus Rhizobium . The polar lipid profile included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine and moderate amounts of aminolipids, phospholipid and sulfoquinovosyl diacylglycerol. Although ChimEc512T was able to nodulate A. vulneraria, the nodC and nifH genes were not detected by PCR. The rhizobial strain was tolerant to high concentrations of heavy metals: up to 35 mM Zn and up to 0.5 mM Cd and its growth kinetics was not impacted by Zn. The results of DNA–DNA hybridizations and physiological tests allowed genotypic and phenotypic differentiation of strain ChimEc512T from species of the genus Rhizobium with validly published names. Strain ChimEc512T, therefore, represents a novel species, for which the name Rhizobium metallidurans sp. nov. is proposed, with the type strain ChimEc512T ( = DSM 26575 = CIP 110550T).


2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4271-4276 ◽  
Author(s):  
Vishnuvardhan Reddy Sultanpuram ◽  
Tushar Dilipchand Lodha ◽  
Venkata Ramana Chintalapati ◽  
Sasikala Chintalapati

Two novel Gram-stain-negative, motile, catalase-negative and oxidase-positive strains of bacteria (JC131T and JC112) were isolated from Lonar, a soda lake in India. Based on 16S rRNA gene sequence similarity studies, strains JC131T and JC112 belong to the family Cohaesibacteraceae of the class Alphaproteobacteria and were most closely related to Cohaesibacter marisflavi DQHS21T (98.0 %) and Cohaesibacter gelatinilyticus CL-GR15T (96.0 %). Polar lipids of strains JC131T and JC112 include phosphatidylglycerol, phosphatidylethnolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and two unidentified lipids (L1 and L2). Both strains have diplopterol, diploptene, an unidentified hopane (UH) and bacteriohopane derivatives (BHD1 and 2) as major hopanoids and an unidentified pigment (P1). The predominant isoprenoid quinone of both strains was ubiquinone-10 (Q10). Whole-cell fatty acid analysis of both strains revealed that C18 : 1ω7c was the predominant cellular fatty acid and significant proportions of C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), 11-methyl C18 : 1ω7c, C18 : 1ω9c, C18 : 0 and C20 : 1ω7c were also detected. The DNA G+C content of strains JC131T and JC112 was 54.6 and 53.8 mol%, respectively. The genome reassociation (based on DNA–DNA hybridization) of strains JC131T and JC112 with Cohaesibacter marisflavi NCCB 100300T ( = DQHS21T) was about 58 %, while between JC131T and JC112 it was about 87 %. On the basis of physiological, biochemical and chemotaxonomical properties, strains JC131T and JC112 are differentiated from the other two members of the genus Cohaesibacter . Strains JC131T and JC112 represent a novel species of the genus Cohaesibacter , for which the name Cohaesibacter haloalkalitolerans sp. nov. is proposed. The type strain is JC131T ( = KCTC 32038T = NBRC 109022T). An emended description of the genus Cohaesibacter is presented.


2020 ◽  
Vol 70 (12) ◽  
pp. 6213-6219
Author(s):  
Onuma Kaewkla ◽  
Wilaiwan Koomsiri ◽  
Arinthip Thamchaipenet ◽  
Christopher Milton Mathew Franco

An endophytic actinobacterium, strain CLES2T, was discovered from the surface-sterilized stem of a Thai medicinal plant, Clausena excavala Burm. f., collected from the Phujong-Nayoa National Park, Ubon Ratchathani Province, Thailand. The results of a polyphasic taxonomic study identified this strain as a member of the genus Microbispora and a Gram-stain-positive, aerobic actinobacterium. It had well-developed substrate mycelia, which were non-motile and possessed paired spores. A phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this strain in the family Streptosporangiaceae , being most closely related to Microbispora bryophytorum NEAU-TX2-2T (99.4 %), Microbispora camponoti 2C-HV3T (99.2 %), Microbispora catharanthi CR1-09T (99.2 %) and Microbispora amethystogenes JCM 3021T and Microbispora fusca NEAU-HEGS1-5T (both at 99.1 %). The major cellular fatty acid of this strain was iso-C16 : 0 and major menaquinone was MK-9(H4). The polar lipid profile of strain CLES2T contained diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol and phosphatidylinositol dimannosides. These chemotaxonomic data confirmed the affiliation of strain CLES2T to the genus Microbispora . The DNA G+C content of this strain was 70 mol%. Digital DNA–DNA hybridization and average nucleotide identity blast values between strain CLES2T and M. catharanthi CR1-09T were 62.4 and 94.0 %, respectively. The results of the polyphasic study allowed the genotypic and phenotypic differentiation of strain CLES2T from its closest species with valid names. The name proposed for the new species is Microbispora clausenae sp. nov. The type strain is CLES2T (=DSM 101759T=NRRL B-65340T).


2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3341-3345 ◽  
Author(s):  
Jia-Fa Wu ◽  
Jie Li ◽  
Zhi-Qing You ◽  
Si Zhang

A novel Gram-stain-positive actinobacterium, designated strain SCSIO 11529T, was isolated from tissues of the stony coral Galaxea fascicularis, and characterized by using a polyphasic approach. The temperature range for growth was 22–50 °C (optimum 28–45 °C), the pH range for growth was 6.0–8.0 (optimum pH 7.0), and the NaCl concentration range for growth was 0–7 % (w/v) NaCl. The polar lipid profile contained diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and an unknown polar lipid. The predominant menaquinone was MK-9(H4). The major fatty acids (>10 %) were iso-C16 : 0, iso-C17 : 1ω6c, iso-C16 : 1 H and C16 : 1ω7c/iso-C15 : 0 2-OH. The DNA G+C content of strain SCSIO 11529T was 70.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SCSIO 11529T belongs to the genus Prauserella , with the closest neighbours being Prauserella marina MS498T (97.0 % 16S rRNA gene sequence similarity), Prauserella rugosa DSM 43194T (96.4 %) and Prauserella flava YIM 90630T (95.9 %). Based on the evidence of the present study, strain SCSIO 11529T is considered to represent a novel species of the genus Prauserella , for which the name Prauserella coralliicola sp. nov. is proposed. The type strain is SCSIO 11529T ( = DSM 45821T = NBRC 109418T).


2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 934-938 ◽  
Author(s):  
Wen-Ming Chen ◽  
Rey-Chang Chang ◽  
Chih-Yu Cheng ◽  
Yu-Wen Shiau ◽  
Shih-Yi Sheu

A novel bacterium, designated strain JchiT, was isolated from soil in Taiwan and characterized using a polyphasic approach. Cells of strain JchiT were aerobic, Gram-stain-negative, motile and rod-shaped. They contained poly-β-hydroxybutyrate granules and formed dark-yellow colonies. Growth occurred at 20–37 °C (optimum between 25 and 30 °C), at pH 6.0–8.0 (optimum between pH 7.0 and pH 8.0) and with 0–2 % NaCl (optimum between 0 and 1 %). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain JchiT belonged to the genus Jeongeupia and that its closest neighbour was Jeongeupia naejangsanensis BIO-TAS4-2T (98.0 % sequence similarity). The major fatty acids (>10 %) of strain JchiT were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major cellular hydroxy fatty acid was C12 : 0 3-OH. The isoprenoid quinone was Q-8 and the genomic DNA G+C content was 66.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine and two unidentified phospholipids. The DNA–DNA relatedness value between strain JchiT and J. naejangsanensis BIO-TAS4-2T was about 41.0 %. On the basis of the genotypic and phenotypic data, strain JchiT represents a novel species in the genus Jeongeupia , for which the name Jeongeupia chitinilytica sp. nov. is proposed. The type strain is JchiT ( = BCRC 80367T  = KCTC 23701T).


Author(s):  
Veeraya Weerawongwiwat ◽  
Seokmin Yoon ◽  
Jong-Hwa Kim ◽  
Jung-Hoon Yoon ◽  
Jung Sook Lee ◽  
...  

A Gram-stain-negative, aerobic, motile, short rod-shaped, catalase-negative and oxidase-positive bacterium, strain CAU 1568T, was isolated from marine sediment sand sampled at Sido Island in the Republic of Korea. The optimum conditions for growth were at 25–30 °C, at pH 6.5–8.5 and with 0–4.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CAU 1568T was a member of the genus Photobacterium with high similarity to Photobacterium salinisoli JCM 30852T (97.7 %), Photobacterium halotolerans KACC 17089T (97.3 %) and Photobacterium galatheae LMG F28894T (97.3 %). The predominant cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c) and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), with Q-8 as the major of isoprenoid quinone. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerols, phosphatidylcholine, phosphatidylethanolamine, phospholipid, two aminophospholipids and three unidentified lipids. The whole genome size of strain CAU 1568T was 4.8 Mb with 50.1 mol% G+C content; including 38 contigs and 4233 protein-coding genes. These taxonomic data support CAU 1568T as representing a novel Photobacterium species, for which the name Photobacterium arenosum sp. nov. is proposed. The type strain of this novel species is CAU 1568T (=KCTC 82404T=MCCC 1K05668T).


Author(s):  
Juan Du ◽  
Yang Liu ◽  
Tao Pei ◽  
Ming-Rong Deng ◽  
Honghui Zhu

A novel Gram-stain-negative, aerobic and rod-shaped bacterial strain designated as 6D45AT was isolated from mangrove soil and characterized using a polyphasic taxonomic approach. Strain 6D45AT was found to grow at 10–37 °C (optimum, 28 °C), at pH 6.0–9.0 (optimum, 7.0) and in 0–5 % (w/v) NaCl (optimum, 2%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 6D45AT fell into the genus Salipiger and shared 99.1 % identity with the closest type strain Salipiger pacificus CGMCC 1.3455T and less than 97.2 % identity with other type strains of this genus. The 34.8 % digital DNA–DNA hybridization (dDDH) and 88.3 % average nucleotide identity (ANI) values between strain 6D45AT and the closest relative above were well below recognized thresholds of 70 % DDH and 95–96 % ANI for species definition, implying that strain 6D45AT should represent a novel genospecies. The phylogenomic analysis indicated that strain 6D45AT formed an independent branch distinct from reference strains. The predominant cellular fatty acid of strain 6D45AT was summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c, 66.9 %); the polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, two unidentified glycolipids and an unknown lipid; the respiratory quinone was Q-10. The genomic DNA G+C content was 66.5 mol %. Based on the phenotypic and genotypic characteristics, strain 6D45AT is concluded to represent a novel species of the genus Salipiger , for which the name Salipiger mangrovisoli sp. nov., is proposed. The type strain of the species is 6D45AT (=GDMCC 1.1960T=KCTC 82334T). We also propose the reclassification of Paraphaeobacter pallidus as Salipiger pallidus comb. nov. and ‘ Pelagibaca abyssi ’ as a species of the genus Salipiger .


2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 754-759 ◽  
Author(s):  
Paulina Corral ◽  
Angela Corcelli ◽  
Antonio Ventosa

An extremely haloalkaphilic archaeon, strain T26T, belonging to the genus Halostagnicola , was isolated from sediment of the soda lake Bange in the region of Tibet, China. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain T26T was closely related to Halostagnicola alkaliphila 167-74T (98.4 %), Halostagnicola larsenii XH-48T (97.5 %) and Halostagnicola kamekurae 194-10T (96.8 %). Strain T26T grew optimally in media containing 25 % (w/v) salts, at pH 9.0 and 37 °C in aerobic conditions. Mg2+ was not required for growth. The cells were motile, pleomorphic and Gram-stain-variable. Colonies of this strain were pink pigmented. Hypotonic treatment caused cell lysis. The polar lipids of the isolate consisted of C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and minor phospholipids components. Glycolipids were not detected, in contrast to the two neutrophilic species of this genus. The genomic DNA G+C content of strain T26T was 60.1 mol% and DNA–DNA hybridization showed a relatedness of 19 and 17 % with Halostagnicola alkaliphila CECT 7631T and Halostagnicola larsenii CECT 7116T, respectively. The comparison of 16S rRNA gene sequences, detailed phenotypic characterization, polar lipid profile and DNA–DNA hybridization studies revealed that strain T26T belongs to the genus Halostagnicola , and represents a novel species for which the name Halostagnicola bangensis sp. nov. is proposed. The type strain is T26T ( = CECT 8219T = IBRC-M 10759T = JCM 18750T).


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