Description of two new species ofHalomonas:Halomonas israelensissp.nov. andHalomonas canadensissp.nov.

1995 ◽  
Vol 41 (12) ◽  
pp. 1124-1131 ◽  
Author(s):  
J. Hansel Huval ◽  
Roger Latta ◽  
Rebecca Wallace ◽  
Donn J. Kushner ◽  
Russell H. Vreeland
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Bacterial Species ◽  
Distinct Species ◽  
Jaccard Coefficient ◽  
Salt Tolerant ◽  
Halotolerant Bacteria ◽  
Phenotypic Characters ◽  
Halomonas Elongata ◽  
Halomonas Species

Six well-known strains of halotolerant bacteria, including two strains previously identified only as NRCC 41227 and Ba1have been compared using 125 phenotypic characters and DNA–DNA hybridization. Although these strains represent some of the most heavily studied salt-tolerant bacteria, they have never been taxonomically compared. The data presented show that these bacteria form a relatively homogeneous group related at the genus level. The taxonomic comparison showed that these six organisms represented four distinct species all related above the 65% Jaccard coefficient level. In addition to two previously identified bacterial species, Halomonas elongata (ATCC 33173T) and Halomonas halodurans (ATCC 29686T), the strains included in this study represent two previously unnamed Halomonas species. These two new taxa have been assigned the names Halomonas israelensis (ATCC 43985T) and Halomonas canadensis (NRCC 41227T = ATCC 43984). DNA–DNA hybridizations show that these two species are related to the type species H. elongata at 54.9 and 48.9%, respectively.Key words: Halomonas, taxonomy, israelensis, canadensis, halotolerant.

scholarly journals Pseudomonas granadensis sp. nov., a new bacterial species isolated from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 625-632 ◽  
Author(s):  
Javier Pascual ◽  
Marina García-López ◽  
Gerald F. Bills ◽  
Olga Genilloud
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Bacterial Species ◽  
Phenotypic Traits ◽  
Terminal Electron Acceptor ◽  
Content Type ◽  
Link Type ◽  
Natural Park ◽  
Fatty Acid Compositions

During the course of screening bacterial isolates as sources of as-yet unknown bioactive compounds with pharmaceutical applications, a chemo-organotrophic, Gram-negative bacterium was isolated from a soil sample taken from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain. Strain F-278,770T was oxidase- and catalase-positive, aerobic, with a respiratory type of metabolism with oxygen as the terminal electron acceptor, non-spore-forming and motile by one polar flagellum, although some cells had two polar flagella. Phylogenetic analysis of the 16S rRNA, gyrB, rpoB and rpoD genes revealed that strain F-278,770T belongs to the Pseudomonas koreensis subgroup (Pseudomonas fluorescens lineage), with Pseudomonas moraviensis , P. koreensis , P. baetica and P. helmanticensis as its closest relatives. Chemotaxonomic traits such as polar lipid and fatty acid compositions and G+C content of genomic DNA corroborated the placement of strain F-278,770T in the genus Pseudomonas . DNA–DNA hybridization assays and phenotypic traits confirmed that this strain represents a novel species of the genus Pseudomonas , for which the name Pseudomonas granadensis sp. nov. is proposed. The type strain is F-278,770T ( = DSM 28040T = LMG 27940T).

scholarly journals Genome analysis-based reclassification of Pseudomonas fuscovaginae and Pseudomonas shirazica as later heterotypic synonyms of Pseudomonas asplenii and Pseudomonas asiatica, respectively

2020 ◽  
Vol 70 (5) ◽  
pp. 3547-3552 ◽  
Author(s):  
Mari Tohya ◽  
Shin Watanabe ◽  
Tatsuya Tada ◽  
Htay Htay Tin ◽  
Teruo Kirikae
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Bacterial Species ◽  
Taxonomic Status ◽  
Species Delineation ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Group Species

This study was conducted to clarify the taxonomic status of the species Pseudomonas fuscovaginae and Pseudomonas shirazica . Whole genome sequences for the type strains of P. fuscovaginae and P. shirazica were compared against the closely related type strains of the Pseudomonas putida group and the Pseudomonas fluorescens group species. Average nucleotide identity and digital DNA–DNA hybridization values between P. fuscovaginae LMG 2158T and Pseudomonas asplenii ATCC 23835T were 98.4 and 85.5 %, and between P. shirazica VM14T and Pseudomonas asiatica RYU5T were 99.3 and 95.3 %. These values were greater than recognized thresholds for bacterial species delineation, indicating that they belong to the same genomospecies, respectively. Therefore, P. fuscovaginae and P. shirazica should be reclassified as later heterotypic synonyms of P. asplenii and P. asiatica , respectively.

scholarly journals Pseudomonas yangonensis sp. nov., isolated from wound samples of patients in a hospital in Myanmar

2020 ◽  
Vol 70 (6) ◽  
pp. 3597-3605 ◽  
Author(s):  
Mari Tohya ◽  
Shin Watanabe ◽  
Kanae Teramoto ◽  
Tatsuya Tada ◽  
Kyoko Kuwahara-Arai ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Quinic Acid ◽  
Distinct Species ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
Genome Comparisons

Strains of a Gram-negative, aerobic, rod-shaped, non-spore-forming bacterium, designated MY50T, MY63 and MY101, were isolated from wound samples of three hospitalized patients in Yangon, Myanmar. Strains MY50T, MY63 and MY101 grew at temperatures of 4–44 °C, in media containing 1.0–7.0 % (w/v) NaCl and at pH 6.0–9.5. Phylogenetic analysis based on 16S rRNA gene and whole genome sequences showed that these strains belonged to the genus Pseudomonas and were part of the Pseudomonas oleovorans group and located close to Pseudomonas guguanensis and Pseudomonas mendocina . Whole-genome comparisons, using average nucleotide identity and digital DNA–DNA hybridization analyses, confirmed that strains MY50T, MY63 and MY101 were the same strain and they were a distinct species in the P. oleovorans group. Results of phenotypic characterization tests demonstrated that utilization of p-hydroxy-phenylacetic acid, glycerol, l-pyroglutamic acid and quinic acid could distinguish these strains from other species of the P. oleovorans group. These genetic and phenotypic characteristics suggest that they should be classified as representing a novel species, under the proposed name Pseudomonas yangonensis sp. nov. The type strain is MY50T (=LMG 31602T,=JCM 33396T), with a DNA G+C content of 62.82 mol%.

Acidithiobacillus ferridurans sp. nov., an acidophilic iron-, sulfur- and hydrogen-metabolizing chemolithotrophic gammaproteobacterium

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4018-4025 ◽  
Author(s):  
Sabrina Hedrich ◽  
D. Barrie Johnson
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Ferric Iron ◽  
Iron Oxidation ◽  
Distinct Species ◽  
Content Type ◽  
Link Type ◽  
Iron Sulfur ◽  
Anoxic Environments ◽  
Acidic Sites

Twelve strains of iron-oxidizing acidithiobacilli isolated from acidic sites throughout the world, including some previously shown by multi-locus sequence analyses and DNA–DNA hybridization to comprise a distinct species, were characterized in terms of their physiologies. The bacteria were shown to be obligately chemolithotrophic, acidophilic and mesophilic, and grew in both oxic and anoxic environments, using ferrous iron, reduced sulfur or hydrogen as electron donors and oxygen or ferric iron as electron acceptors. Some of the strains grew at lower pH than those reported for the two recognized iron-oxidizing Acidithiobacillus species, Acidithiobacillus ferrooxidans and Acidithiobacillus ferrivorans . Tolerance of transition metals and aluminium, and also specific rates of iron oxidation and reduction, were more similar to those of A. ferrooxidans (to which the strains are more closely related) than to A. ferrivorans . The name Acidithiobacillus ferridurans sp. nov. is proposed to accommodate the 12 strains, with the type strain being JCM 18981T ( = ATCC 33020T).

scholarly journals Genome analysis-based reclassification of Lelliottia aquatilis as a later heterotypic synonym of Lelliottia jeotgali

2019 ◽  
Vol 69 (4) ◽  
pp. 998-1000 ◽  
Author(s):  
Wenjing Wu ◽  
Zhiyong Zong
Keyword(s):  
Genome Analysis ◽  
Dna Hybridization ◽  
Type Species ◽  
Bacterial Species ◽  
Whole Genome ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type ◽  
Type Strains

The aim of this study was to further clarify the taxonomic relationship between the two recently described bacterial species, Lelliottia jeotgali sp. nov. and Lelliottia aquatilis sp. nov. Whole genome sequences of types strains of the two species are available for analysis. Average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) values between the two type strains were determined. The ANI and isDDH values between type strains of the two species are 98.7 and 91.0 %, respectively, which are higher than cut-offs to define a bacterial species. It is therefore clear that the two species actually belong to the same species. The name of L.aquatilis was published at an earlier date than that of L. aquatilis . We therefore propose that L. aquatilis is a later heterotypic synonym of L. jeotgali .

scholarly journals Comparative genomics suggests a taxonomic revision of the Staphylococcus cohnii species complex

2021 ◽  
Author(s):  
Anna Lavecchia ◽  
Matteo Chiara ◽  
Caterina De Virgilio ◽  
Caterina Manzari ◽  
Carlo Pazzani ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Species Complex ◽  
Large Scale ◽  
Genomic Sequence ◽  
Bacterial Species ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
The Novel ◽  
Staphylococcus Cohnii ◽  
Taxonomic Assignments

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

scholarly journals Cyclobacterium qasimii sp. nov., a psychrotolerant bacterium isolated from Arctic marine sediment

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2133-2139 ◽  
Author(s):  
S. Shivaji ◽  
P. Vishnu Vardhan Reddy ◽  
S. S. S. Nageshwara Rao ◽  
Zareena Begum ◽  
Poorna Manasa ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Marine Sediment ◽  
Dna Hybridization ◽  
Type Species ◽  
Unsaturated Fatty Acids ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Sequence Similarities

A novel Gram-stain-negative, horseshoe-shaped, non-motile bacterium, designated strain M12-11BT, was isolated from a marine sediment sample collected at a depth of 200 m from Kongsfjorden, Svalbard. The colony colour was orangish red due to the presence of carotenoids. Fatty acids were dominated by branched and unsaturated fatty acids (90.8 %), with a high abundance of iso-C15 : 0 (14.9 %), anteiso-C15 : 0 (11.4 %), iso-C15 : 1 G (13.1 %), C15 : 1ω6c (5.4 %), C17 : 1ω6c (6.7 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 9.3 %) and summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c; 5.9 %). Strain M12-11BT contained MK-7 as the major respiratory quinone. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, one unidentified aminolipid and three unidentified lipids. Based on 16S rRNA gene sequence similarities, the type strains of Cyclobacterium amurskyense , Cyclobacterium marinum and Cyclobacterium lianum were most closely related to M12-11BT with sequence similarities of 98.2, 96.8 and 93.3 %, respectively. Other members of the family Cyclobacteriaceae had sequence similarities of <92.0 %. However, DNA–DNA hybridization with Cyclobacterium amurskyense KCTC 12363T and Cyclobacterium marinum DSM 745T showed relatedness values of only 24.5 and 32.5 % with respect to strain M12-11BT. Based on the results of DNA–DNA hybridization experiments and phenotypic and chemotaxonomic data, it appears that strain M12-11BT represents a novel species of the genus Cyclobacterium , for which the name Cyclobacterium qasimii sp. nov. is proposed; the type strain is M12-11BT ( = KCTC 23011T = NBRC 106168T) and it has a DNA G+C content of 40.5 mol%.

Morphological and molecular evidence places Maronina into synonymy with Protoparmelia (Ascomycota: Lecanorales)

2011 ◽  
Vol 43 (6) ◽  
pp. 561-567 ◽  
Author(s):  
K. PAPONG ◽  
G. KANTVILAS ◽  
H. T. LUMBSCH
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Distinct Species ◽  
Genetic Distances ◽  
Molecular Evidence ◽  
New Combinations ◽  
Secondary Chemistry ◽  
Phenotypic Characters ◽  
Dna Sequence Data ◽  
Phylogenetic Placement

AbstractThe phylogenetic placement of the genus Maronina was studied, based chiefly on phenotypic characters such as thallus colour and anatomy, secondary chemistry, the anatomy of the excipulum and the ascus-type. DNA sequence data of mitochondrial and nuclear ribosomal loci from some of the species support the hypothesis that Maronina is nested within Protoparmelia. Hence, Maronina is reduced to synonymy with Protoparmelia. Comparison of genetic distances suggests that the two varieties within M. orientalis should be regarded as distinct species. Consequently, the new combinations Protoparmelia australiensis (Hafellner & R. W. Rogers) Kantvilas et al., P. corallifera (Kantvilas & Papong) Kantvilas et al., P. hesperia (Kantvilas & Elix) Kantvilas et al., P. multifera (Nyl.) Kantvilas et al., and P. orientalis (Kantvilas & Papong) Kantvilas et al. are proposed.

Peptoniphilus Colimassiliensis sp. nov. and Peptoniphilus Urinimassiliensis sp. nov., Two New Species Isolated From Humans

2021 ◽  
Author(s):  
Babacar Mbaye ◽  
Cheikh Ibrahima LO ◽  
Niokhor Dione ◽  
Sarah Benabdelkader ◽  
Maryam Tidjani Alou ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Dna Hybridization ◽  
Kidney Transplant Recipient ◽  
Bacterial Species ◽  
Hexadecanoic Acid ◽  
Anaerobic Conditions ◽  
New Members ◽  
Two New Species ◽  
Type Strains ◽  
Gram Positive Cocci

Abstract Strains Marseille-P3761 and Marseille-P3195 are representatives of two bacterial species isolated from human specimens. Strain Marseille-P3761 was isolated from the stool of a healthy volunteer, while strain Marseille-P3915 was cultivated from the urine of a kidney transplant recipient. Both strains are anaerobic Gram-positive cocci bacteria. Both are catalase-negative and oxidase-negative and grow optimally at 37°C in anaerobic conditions. They also metabolize carbohydrates such as galactose, glucose, fructose, and glycerol. The major fatty acids were hexadecanoic acid for both strains, Marseille-P3761 (38%) and Marseille-P3195 (31%). The highest DNA-DNA hybridization values of Marseille-P3761 and Marseille-P3195 strains when compared to their closest phylogenetic relatives were 52.3% and 56.4%, respectively. The morphological, biochemical, phenotypic and genomic characteristics strongly support that these strains are new members of the Peptoniphilus genus. Thus, we suggest that strains Marseille-P3761 (CSUR P3761 = CCUG71569) and Marseille-P3195 (CSUR P3195 = DSM 103468) are the type strains of two new Peptoniphilus species, for which we propose the names Peptoniphilus colimassiliensis sp. nov. and Peptoniphilus urinimassiliensis sp. nov., respectively.

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