Phreatobacter oligotrophus gen. nov., sp. nov., an alphaproteobacterium isolated from ultrapure water of the water purification system of a power plant

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 839-845 ◽  
Author(s):  
E. M. Tóth ◽  
A. Vengring ◽  
Z. G. Homonnay ◽  
Zs. Kéki ◽  
C. Spröer ◽  
...  
Keyword(s):  
Power Plant ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Rrna Gene ◽  
Ultrapure Water ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strains of a novel alphaproteobacterium were isolated from ultrapure water of a Hungarian power plant on a newly developed medium. Phylogenetic analysis of the 16S rRNA gene sequences of the novel strains showed that these bacteria belong to a distinct lineage far from any known taxa. Based on the 16S rRNA gene sequences, strains PI_31, PI_25 and PI_21T exhibited the highest sequence similarity to Bosea minatitlanensis AMX51T (93.43 %) and Bosea thiooxidans DSM 9653T (93.36 %); similarity to all other taxa was less than 93.23 %. Fatty acid profiles, matrix-assisted laser-desorption/ionization time-of-flight mass spectra of cell extracts as well as physiological and biochemical characteristics indicated that our strains represent a novel genus and species within the class Alphaproteobacteria . The major isoprenoid quinone of the strains was Q-10, the major cellular fatty acids were C18 : 1ω7c and 11-methyl C18 : 1ω7c and the polar lipid profiles of the strains contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and several unknown phospholipids and other lipids. The characteristic diamino acid in their cell wall was meso-diaminopimelic acid. The G+C content of DNA of the proposed type strain PI_21T was 68.9 mol%. A new genus and species, Phreatobacter oligotrophus gen. nov., sp. nov., is proposed to accommodate the strains. Strain PI_21T ( = DSM 25521T = NCAIM B 02510T) is the type strain of Phreatobacter oligotrophus.

Taxonomic status of the species Clostridium methoxybenzovorans Mechichi et al. 1999

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Hisami Kobayashi ◽  
Yasuhiro Tanizawa ◽  
Mitsuo Sakamoto ◽  
Moriya Ohkuma ◽  
Masanori Tohno
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

The taxonomic status of the species Clostridium methoxybenzovorans was assessed. The 16S rRNA gene sequence, whole-genome sequence and phenotypic characterizations suggested that the type strain deposited in the American Type Culture Collection ( C. methoxybenzovorans ATCC 700855T) is a member of the species Eubacterium callanderi . Hence, C. methoxybenzovorans ATCC 700855T cannot be used as a reference for taxonomic study. The type strain deposited in the German Collection of Microorganism and Cell Cultures GmbH (DSM 12182T) is no longer listed in its online catalogue. Also, both the 16S rRNA gene and the whole-genome sequences of the original strain SR3T showed high sequence identity with those of Lacrimispora indolis (recently reclassified from Clostridium indolis ) as the most closely related species. Analysis of the two genomes showed average nucleotide identity based on blast and digital DNA–DNA hybridization values of 98.3 and 87.9 %, respectively. Based on these results, C. methoxybenzovorans SR3T was considered to be a member of L. indolis .

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).

scholarly journals Proposed reclassification of Pasteurella lymphangitidis Sneath & Stevens 1990 as Yersinia pseudotuberculosis

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3927-3929 ◽  
Author(s):  
Olivier Gaillot ◽  
Olivier Lemenand ◽  
Michaël Marceau ◽  
Michel Simonet
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Yersinia Pseudotuberculosis ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

The 16S rRNA gene sequences of Pasteurella lymphangitidis , Yersinia pseudotuberculosis and Yersinia pestis were found to be identical and multilocus sequence analysis could not discriminate between the three species. The susceptibility to a Y. pseudotuberculosis phage and the presence of the Y. pseudotuberculosis -specific invasin gene in P. lymphangitidis indicate that the latter should be reclassified as Y. pseudotuberculosis .

scholarly journals Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov.

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 894-900 ◽  
Author(s):  
D. P. Labeda ◽  
J. R. Doroghazi ◽  
K.-S. Ju ◽  
W. W. Metcalf
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Streptomyces Albus

In phylogenetic analyses of the genus Streptomyces using 16S rRNA gene sequences, Streptomyces albus subsp . albus NRRL B-1811T forms a cluster with five other species having identical or nearly identical 16S rRNA gene sequences. Moreover, the morphological and physiological characteristics of these other species, including Streptomyces almquistii NRRL B-1685T, Streptomyces flocculus NRRL B-2465T, Streptomyces gibsonii NRRL B-1335T and Streptomyces rangoonensis NRRL B-12378T are quite similar. This cluster is of particular taxonomic interest because Streptomyces albus is the type species of the genus Streptomyces . The related strains were subjected to multilocus sequence analysis (MLSA) utilizing partial sequences of the housekeeping genes atpD, gyrB, recA, rpoB and trpB and confirmation of previously reported phenotypic characteristics. The five strains formed a coherent cluster supported by a 100 % bootstrap value in phylogenetic trees generated from sequence alignments prepared by concatenating the sequences of the housekeeping genes, and identical tree topology was observed using various different tree-making algorithms. Moreover, all but one strain, S. flocculus NRRL B-2465T, exhibited identical sequences for all of the five housekeeping gene loci sequenced, but NRRL B-2465T still exhibited an MLSA evolutionary distance of 0.005 from the other strains, a value that is lower than the 0.007 MLSA evolutionary distance threshold proposed for species-level relatedness. These data support a proposal to reclassify S. almquistii , S. flocculus , S. gibsonii and S. rangoonensis as later heterotypic synonyms of S. albus with NRRL B-1811T as the type strain. The MLSA sequence database also demonstrated utility for quickly and conclusively confirming that numerous strains within the ARS Culture Collection had been previously misidentified as subspecies of S. albus and that Streptomyces albus subsp. patho cidicus should be redescribed as a novel species, Streptomyces pathocidini sp. nov., with the type strain NRRL B-24287T.

Ilumatobacter nonamiense sp. nov. and Ilumatobacter coccineum sp. nov., isolated from seashore sand

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3404-3408 ◽  
Author(s):  
Atsuko Matsumoto ◽  
Hiroaki Kasai ◽  
Yoshihide Matsuo ◽  
Yoshikazu Shizuri ◽  
Natsuko Ichikawa ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Seashore Sand ◽  
The 16S Rrna Gene

Bacterial strains YM16-303T and YM16-304T were isolated from a sample of seashore sand using a medium with an artificial seawater base. Both isolates grew slowly on marine agar, and were found to be Gram-reaction-positive, aerobic, non-motile and rod-shaped. The cell-wall peptidoglycan contained ll-diaminopimelic acid, glycine, alanine and hydroxyglutamic acid, and the acyl type of the muramic acid was glycolyl. The predominant menaquinone was MK-9(H8). The 16S rRNA gene sequences of strains YM16-303T and YM16-304T were most similar to that of Ilumatobacter fluminis YM22-133T, and phylogenetic analyses also indicated that they belong to the genus Ilumatobacter . Ilumatobacter fluminis YM22-133T and strains YM16-303T and YM16-304T should be classified as distinct species in the genus Ilumatobacter , however, since the 16S rRNA gene sequence similarity between them was low and the major cellular fatty acids and some physiological properties were different. Moreover, average nucleotide identity and maximal unique exact matches index values also supported the conclusion that they represent different species. On the basis of the above analyses, two novel species, Ilumatobacter nonamiense sp. nov. (type strain YM16-303T = NBRC 109120T = KCTC 29139T) and Ilumatobacter coccineum sp. nov. (type strain YM16-304T = NBRC 103263T = KCTC 29153T), are proposed. The order Acidimicrobiales , which contains the genus Ilumatobacter , currently includes six genera and only six species, and they are phylogenetically very far from each other. Phylogenetic analyses revealed that strains YM16-303T and YM16-304T clustered with closely related uncultured actinobacteria but not Ilumatobacter fluminis YM22-133T, suggesting that many uncultured bacteria related to these isolates exist in the environment. This is the first report on interspecies relationships in the order Acidimicrobiales .

Flavobacterium lotistagni sp. nov. and Flavobacterium celericrescens sp. nov., isolated from freshwater habitats

2021 ◽  
Author(s):  
Jia-Hong Wu ◽  
Ya-Xiu You ◽  
Chiu-Chung Young ◽  
Soon-Wo Kwon ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Freshwater Habitats

This study presents taxonomic descriptions of strains CYK-4T and TWA-26T isolated from freshwater habitats in Taiwan. Both strains were Gram-stain-negative, strictly aerobic, motile by gliding and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that both strains belonged to the genus Flavobacterium . Analysis of 16S rRNA gene sequences showed that strains CYK-4T and TWA-26T shared 92.7 % sequence similarity and were most closely related to Flavobacterium ovatum W201ET (95.6 %) and Flavobacterium aquaticum JC164T (96.7 %), respectively. Both strains shared common chemotaxonomic characteristics comprising MK-6 as the main isoprenoid quinone, iso-C15 : 0 and iso-C15 : 1 G as the predominant fatty acids, phosphatidylethanolamine as the principal polar lipid, and homospermidine as the major polyamine. The DNA G+C contents of strains CYK-4T and TWA-26T were 41.5 and 31.8 mol%, respectively. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between these two novel isolates and their closest relatives were below the cut-off values of 95–96, 90 and 70 %, respectively, used for species demarcation. On the basis of phenotypic and genotypic properties and phylogenetic inference, both strains should be classified as novel species within the genus Flavobacterium , for which the names Flavobacterium lotistagni sp. nov. (type strain CYK-4T=BCRC 81192T=LMG 31330T) and Flavobacterium celericrescens sp. nov. (type strain TWA-26T=BCRC 81200T=LMG 31333T) are proposed.

scholarly journals Serratia myotis sp. nov. and Serratia vespertilionis sp. nov., isolated from bats hibernating in caves

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 90-94 ◽  
Author(s):  
P. García-Fraile ◽  
M. Chudíčková ◽  
O. Benada ◽  
J. Pikula ◽  
M. Kolařík
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

During the study of bacteria associated with bats affected by white-nose syndrome hibernating in caves in the Czech Republic, we isolated two facultatively anaerobic, Gram-stain-negative bacteria, designated strains 12T and 52T. Strains 12T and 52T were motile, rod-like bacteria (0.5–0.6 µm in diameter; 1–1.3 µm long), with optimal growth at 20–35 °C and pH 6–8. On the basis of the almost complete sequence of their 16S rRNA genes they should be classified within the genus Serratia ; the closest relatives to strains 12T and 52T were Serratia quinivorans DSM 4597T (99.5 % similarity in 16S rRNA gene sequences) and Serratia ficaria DSM 4569T (99.5 % similarity in 16S rRNA gene sequences), respectively. DNA–DNA relatedness between strain 12T and S. quinivorans DSM 4597T was only 37.1 % and between strain 52T and S. ficaria DSM 4569T was only 56.2 %. Both values are far below the 70 % threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Serratia as representatives of Serratia myotis sp. nov. (type strain 12T = CECT 8594T = DSM 28726T) and Serratia vespertilionis sp. nov. (type strain 52T = CECT 8595T = DSM 28727T).

Survey of 150 strains belonging to the Mycobacterium terrae complex and description of Mycobacterium engbaekii sp. nov., Mycobacterium heraklionense sp. nov. and Mycobacterium longobardum sp. nov.

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 401-411 ◽  
Author(s):  
Enrico Tortoli ◽  
Zoe Gitti ◽  
Hans-Peter Klenk ◽  
Stefania Lauria ◽  
Roberta Mannino ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Reductase Activity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Genotypic Analysis ◽  
The 16S Rrna Gene

A thorough phenotypic and genotypic analysis of 150 strains belonging to the Mycobacterium terrae complex resulted in the identification of a number of previously unreported sequevars (sqvs) within the species known to belong to the complex. For the species Mycobacterium arupense , three sqvs were detected in the 16S rRNA gene, six sqvs in the hsp65 gene and 15 sqvs in the rpoB gene; in Mycobacterium senuense two sqvs were present in each of the three genetic regions; in Mycobacterium kumamotonense four, two and nine sqvs were found, respectively, and in M. terrae three, four and six sqvs were found, respectively. The inappropriate inclusion of Mycobacterium triviale within the M. terrae complex was confirmed. The limited utility of biochemical tests and of mycolic acid analyses for the differentiation of the members of M. terrae complex was also confirmed. The survey allowed the recognition of three previously undescribed species that were characterized by unique sequences in the 16S rRNA, hsp65 and rpoB genes. Mycobacterium engbaekii sp. nov. (proposed previously 40 years ago but never validly published) was characterized by pink photochromogenic pigmentation and rapid growth; phylogenetically it was related to Mycobacterium hiberniae . The type strain of this species, of which eight strains were investigated, is ATCC 27353T ( = DSM 45694T). A cluster of 24 strains was the basis for the description of Mycobacterium heraklionense sp. nov., which has an intermediate growth rate and is unpigmented; nitrate reductase activity is typically strong. Closely related to M. arupense with respect to the 16S rRNA gene, M. heraklionense sp. nov. could be clearly differentiated from the latter species in the other genetic regions investigated. The type strain is NCTC 13432T ( = LMG 24735T = CECT 7509T). Mycobacterium longobardum sp. nov., represented in the study by seven strains, was characterized by a unique phylogenetic location within the M. terrae complex, clearly divergent from any other species. The type strain is DSM 45394T ( = CCUG 58460T).

Bacillus composti sp. nov. and Bacillus thermophilus sp. nov., two thermophilic, Fe(III)-reducing bacteria isolated from compost

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3030-3036 ◽  
Author(s):  
Guiqin Yang ◽  
Ming Chen ◽  
Zhen Yu ◽  
Qin Lu ◽  
Shungui Zhou
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Two novel thermophilic bacteria, designated SgZ-9T and SgZ-10T, were isolated from compost. Cells of the two strains were catalase-positive, endospore-forming and Gram-staining-positive rods. Strain SgZ-9T was oxidase-positive and non-motile, and strain SgZ-10T was oxidase-negative and motile. The highest 16S rRNA gene sequence similarity for both strains SgZ-9T and SgZ-10T was observed with Bacillus fortis (97.5 % and 96.9 %, respectively). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SgZ-9T formed a cluster with B. fortis R-6514T and Bacillus fordii R-7190T, and SgZ-10T formed a cluster with Bacillus farraginis R-6540T. The DNA–DNA pairing studies showed that SgZ-9T displayed 41.6 % and 30.7 % relatedness to the type strains of B. fortis and B. fordii , respectively. The 16S rRNA gene sequence similarity between strains SgZ-9T and SgZ-10T was 97.2 %, and the level of DNA–DNA relatedness between them was 39.2 %. The DNA G+C content of SgZ-9T and SgZ-10T was 45.3 and 47.9 mol%, respectively. Chemotaxonomic analysis revealed that both strains contained the menaquinone 7 (MK-7) as the predominant respiratory quinone. The major cellular fatty acids (>5 %) were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C17 : 0 in SgZ-9T and iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0, anteiso-C17 : 0 and iso-C16 : 0 in SgZ-10T. Based on the phenotypic characteristics, chemotaxonomic features, DNA–DNA hybridization with the nearest phylogenetic neighbours and phylogenetic analysis based on the 16S rRNA gene sequences, the two strains were determined to be two distinct novel species in the genus Bacillus , and the names proposed are Bacillus composti sp. nov. SgZ-9T ( = CCTCC AB2012109T = KACC 16872T) and Bacillus thermophilus sp. nov. SgZ-10T (CCTCC AB2012110T = KACC 16873T).

Methylophaga nitratireducenticrescens sp. nov. and Methylophaga frappieri sp. nov., isolated from the biofilm of the methanol-fed denitrification system treating the seawater at the Montreal Biodome

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2216-2222 ◽  
Author(s):  
Céline Villeneuve ◽  
Christine Martineau ◽  
Florian Mauffrey ◽  
Richard Villemur
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Vitamin B ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Ribulose Monophosphate Pathway ◽  
The 16S Rrna Gene

Two bacterial strains, designated JAM1T and JAM7T, were isolated from a methanol-fed denitrification system treating seawater at the Montreal Biodome, Canada. They were affiliated within the genus Methylophaga of the Gammaproteobacteria by analysis of the 16S rRNA gene sequences. Strain JAM1T had the capacity to grow under denitrifying conditions by reducing nitrate into nitrite which is unique among the species of the genus Methylophaga . Major fatty acids were C16 : 1ω7c or ω6c, C16 : 0 and C18 : 1ω7c or ω6c. The major ubiquinone was Q8. Both strains required vitamin B12 and Na+ ions for growth. The genomes of strains JAM1T and JAM7T have been completely sequenced and showed a DNA G+C content of 44.7 mol% and 47.8 mol%, respectively. Growth occurred at pH 6–11 and at 0.5–8 % NaCl. Both genomes contained predicted ORFs encoding the key enzymes of the ribulose monophosphate pathway. Also, operons encoding two nitrate reductases (Nar), two nitric oxide reductases (Nor), one nitrous oxide reductase (Nos) and one truncated nitrite reductase (NirK) were clustered in a 67 kb chromosomal region in strain JAM1T. No such operons were found in strain JAM7T. These results supported the affiliation of the two strains as novel species within the genus Methylophaga . The names Methylophaga nitratireducenticrescens sp. nov. for type strain JAM1T ( = DSM 25689T = ATCC BAA-2433T) and Methylophaga frappieri sp. nov. for type strain JAM7T ( = DSM 25690T = ATCC BAA-2434T) are proposed.

Sign in / Sign up

Export Citation Format

Share Document