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 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 Re-identification of strains deposited as Pseudomonas aeruginosa, Pseudomonas fluorescens and Pseudomonas putida in GenBank based on whole genome sequences

2020 ◽  
Vol 70 (11) ◽  
pp. 5958-5963
Author(s):  
Yuh Morimoto ◽  
Mari Tohya ◽  
Zulipiya Aibibula ◽  
Tadashi Baba ◽  
Hiroyuki Daida ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genome Sequencing ◽  
Dna Hybridization ◽  
Type Species ◽  
Whole Genome ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type

The taxonomic classification of Pseudomonas species has been revised and updated several times. This study utilized average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) cutoff values of 95 and 70 %, respectively, to re-identify the species of strains deposited in GenBank as P. aeruginosa , P. fluorescens and P. putida . Of the 264 deposited P. aeruginosa strains, 259 were correctly identified as P. aeruginosa , but the remaining five were not. All 28 deposited P. fluorescens strains had been incorrectly identified as P. fluorescens . Four of these strains were re-identified, including two as P. kilonensis and one each as P. aeruginosa and P. brassicacearum , but the remaining 24 could not be re-identified. Similarly, all 35 deposited P. putida strains had been incorrectly identified as P. putida . Nineteen of these strains were re-identified, including 12 as P. alloputida , four as P. asiatica and one each as P. juntendi , P. monteilii and P. mosselii . These results strongly suggest that Pseudomonas bacteria should be identified using ANI and dDDH analyses based on whole genome sequencing when Pseudomonas species are initially deposited in GenBank/DDBJ/EMBL databases.

Proposal of Streptomyces aureorectus (ex Taig et al. 1969) Taig and Solovieva 1986 as a later heterotypic synonym of Streptomyces calvus Backus et al. 1957 (Approved Lists 1980) on the basis of a polyphasic taxonomic approach

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Kaiqin Li ◽  
Siren Hu ◽  
Yinfeng Wang ◽  
Yihui Guo ◽  
Meiliang Zhou ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Species Boundaries ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Genomic Species ◽  
Comprehensive Comparison ◽  
Taxonomic Approach ◽  
Type Strains

As two separate genomic species, Streptomyces calvus and Streptomyces aureorectus were approved in 1980 and 1986, respectively. However, recently, it has been found that the average nucleotide identity and digital DNA–DNA hybridization values between S. calvus JCM 4326T and S. aureorectus DSM 41692T were 99.19 and 92.70 %, respectively, much higher than 95–96 and 70  % cut-off points proposed and the generally accepted species boundaries. These data indicated that they should be classified as the same genomic species. Furthermore, this result was also supported by a comprehensive comparison of phenotypic, chemotaxonomic and physio-biochemical characteristics between the two type strains. All these data indicated that S. calvus and S. aureorectus had the same taxonomic position. In accordance with the principle of priority, it is proposed that S. aureorectus is a later heterotypic synonyms of S. calvus .

Yersinia occitanica is a later heterotypic synonym of Yersinia kristensenii subsp. rochesterensis and elevation of Yersinia kristensenii subsp. rochesterensis to species status

2021 ◽  
Author(s):  
Scott Van Nguyen ◽  
Scott A. Cunningham ◽  
Patricio Jeraldo ◽  
Anthony Tran ◽  
Robin Patel
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Average Nucleotide Identity ◽  
Species Status ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Genomic Relatedness

The taxonomic position of Yersinia kristensenii subsp. rochesterensis and Yersinia occitanica was re-evaluated by genomic analysis. Average nucleotide identity (ANI), digital DNA–DNA hybridization values, and phylogenetic analyses of the type strains indicate that Y. kristensenii subsp. rochesterensis and Y. occitanica are the same genospecies. Additionally, the overall genomic relatedness index (OGRI) values reveal that Y. kristensenii subsp. rochesterensis should be elevated to species status as Yersinia rochesterensis sp. nov.

scholarly journals Pseudomonas izuensis sp. nov., a novel species isolated from Izu Oshima, Japan

2020 ◽  
Vol 70 (7) ◽  
pp. 4212-4216 ◽  
Author(s):  
Yu Jie Lu ◽  
Yuh Morimoto ◽  
Mari Tohya ◽  
Tomomi Hishinuma ◽  
Keiichi Hiramatsu ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
Whole Genome ◽  
Gram Stain ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type ◽  
Pseudomonas Jessenii ◽  
Type Strains

An aerobic, Gram-stain-negative, rod-shaped bacterial strain, IzPS43_3003T, was isolated from Izu Oshima, an active volcanic island located 22 km east of the Izu Peninsula, Japan. The sequence of its 16S rRNA gene indicated that IzPS43_3003T belongs to the Pseudomonas fluorescens lineage, with its sequence being most similar to that of Pseudomonas vancouverensis DhA-51T (99.79 %). Phylogenetic analysis based on whole genome sequences showed that IzPS43_3003T was a member of the Pseudomonas jessenii subgroup. The average nucleotide identity values and genome-to genome distances between the whole genome sequences of IzPS43_3003T and other type strains showed that the highest correlations were with Pseudomonas moorei DSM 12647T (87.3 and 33.5% respectively). These genotypic and phenotypic analyses indicated that IzPS43_3003T belongs to a novel species, Pseudomonas izuensis sp. nov. Its type strain is IzPS43_3003T (=LMG 31527T,=CECT 9963T).

scholarly journals Proposal for the creation of a new genus Musicola gen. nov., reclassification of Dickeya paradisiaca (Samson et al. 2005) as Musicola paradisiaca comb. nov. and description of a new species Musicola keenii sp. nov.

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Nicole Hugouvieux-Cotte-Pattat ◽  
Cécile Jacot des-Combes ◽  
Jérôme Briolay ◽  
Leighton Pritchard
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Plant Pathogens ◽  
Phenotypic Analysis ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
A New Species ◽  
Laboratory Collection

The Pectobacteriaceae family of important plant pathogens includes the genus Dickeya . There are currently 12 described species of Dickeya , although some are poorly characterized at the genomic level. Only two genomes of Dickeya paradisiaca , the type strain CFBP 4178T and strain Ech703, have previously been sequenced. Members of this species are mostly of tropical or subtropical origin. During an investigation of strains present in our laboratory collection we sequenced the atypical strain A3967, registered as CFBP 722, isolated from Solanum lycopersicum (tomato) in the South of France in 1965. The genome of strain A3967 shares digital DNA–DNA hybridization and average nucleotide identity (ANI) values of 68 and 96 %, respectively, with the D. paradisiaca type strain CFBP 4178T. However, ANI analysis showed that D. paradisiaca strains are significantly dissimilar to the other Dickeya species, such that less than one third of their genomes align to any other Dickeya genome. On phenotypic, phylogenetic and genomic grounds, we propose a reassignment of D. paradisiaca to the genus level, for which we propose the name Musicola gen. nov., with Musicola paradisiaca as the type species and CFBP 4178T (NCPPB 2511T) as the type strain. Phenotypic analysis showed differences between strain A3967T and CFBP 4178T, such as for the assimilation of melibiose, raffinose and myo-inositol. These results support the description of two novel species, namely Musicola paradisiaca comb. nov. and Musicola keenii sp. nov., with CFBP 4178T (NCPPB 2511T=LMG 2542T) and A3967T (CFBP 8732T=LMG 31880T) as the type strains, respectively.

Companilactobacillus pabuli sp. nov., a lactic acid bacterium isolated from animal feed

2021 ◽  
Author(s):  
Ji Young Jung ◽  
Hye Kyeong Kang ◽  
Hyun Mi Jin ◽  
Sang-Soo Han ◽  
Young Chul Kwon ◽  
...  
Keyword(s):  
Lactic Acid ◽  
16S Rrna ◽  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

A Gram-positive, facultative anaerobic, catalase-negative, non-motile, non-spore-forming and rod-shaped lactic acid bacterium strain, denoted as NFFJ11T and isolated from total mixed fermentation feed in the Republic of Korea, was characterized through polyphasic approaches, including sequence analyses of the 16S rRNA gene and housekeeping genes (rpoA and pheS), determination of average nucleotide identity and in silico DNA–DNA hybridization, fatty acid methyl ester analysis, and phenotypic characterization. Phylogenetic analyses based on 16S rRNA, rpoA and pheS gene sequences revealed that strain NFFJ11T belonged to the genus Companilactobacillus . The 16S rRNA gene sequence of strain NFFJ11T exhibited high similarity to Companilactobacillus formosensis S215T (99.66 %), Companilactobacillus farciminis Rv4 naT (99.53 %), Companilactobacillus crustorum LMG 23699T (99.19 %), Companilactobacillus futsaii YM 0097T (99.06 %), Companilactobacillus zhachilii HBUAS52074T (98.86 %) and Companilactobacillus heilongiiangensis S4-3T (98.66 %). However, average nucleotide identity and in silico DNA–DNA hybridization values for these type strains were in the range of 79.90–92.93 % and 23.80–49.30 %, respectively, which offer evidence that strain NFFJ11T belongs to a novel species of the genus Companilactobacillus . The cell-wall peptidoglycan type was A4α (l-Lys–d-Asp) and the G+C content of the genomic DNA was 35.7 mol%. The main fatty acids of strain NFFJ11T were C18 : 1  ω9c (43.3 %), C16 : 0 (20.1 %) and summed feature 7 (18.3 %; comprising any combination of C19 : 1  ω7c, C19 : 1  ω6c and C19 : 0 cyclo ω10c). Through polyphasic taxonomic analysis, it was observed that strain NFFJ11T represents a novel species belonging to the genus Companilactobacillus , for which the name Companilactobacillus pabuli sp. nov. is proposed. The type strain is NFFJ11T (= KACC 21771T= JCM 34088T).

Nocardioides donggukensis sp. nov. and Hyunsoonleella aquatilis sp. nov., isolated from Jeongbang Waterfall on Jeju Island

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Inhyup Kim ◽  
Geeta Chhetri ◽  
Jiyoun Kim ◽  
Minchung Kang ◽  
Yoonseop So ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Bacterial Species ◽  
Jeju Island ◽  
Nucleotide Identity ◽  
Rrna Gene ◽  
Average Nucleotide Identity ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

Two bacterial strains, designated MJB4T and SJ7T, were isolated from water samples collected from Jeongbang Falls on Jeju Island, Republic of Korea. Phylogenetic analysis of 16S rRNA gene sequences indicated that the two strains belonged to the genera Nocardioides and Hyunsoonleella , owing to their high similarities to Nocardioides jensenii DSM 29641T (97.5 %) and Hyunsoonleella rubra FA042 T (96.3 %), respectively. These values are much lower than the gold standard for bacterial species (98.7 %). The average nucleotide identity values between strains MJB4T, SJ7T and the reference strains, Nocardioides jensenii DSM 29641T, Nocardioides daejeonensis MJ31T and Hyunsoonleella flava T58T were 77.2, 75.9 and 75.4 %, respectively. Strains MJB4T and SJ7T and the type strains of the species involved in system incidence have average nucleotide identity and average amino acid threshold values of 60.1–82.6 % for the species boundary (95–96 %), which confirms that strains MJB4T and SJ7T represent two new species of genus Nocardioides and Hyunsoonleella , respectively. Based on phylogenetic and phenotypic data, strains MJB4T and SJ7T are considered to represent novel species of the genus Nocardioides and Hyunsoonleella , respectively, for which the names Nocardioides donggukensis sp. nov. (type strain MJB4T=KACC 21724T=NBRC 114402T) and Hyunsoonleella aquatilis sp. nov., (type strain SJ7T=KACC 21715T=NBRC 114486T) have been proposed.

scholarly journals Descriptions of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov. and Rhodopseudomonas pseudopalustris sp. nov., and emended description of Rhodopseudomonas palustris

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1790-1798 ◽  
Author(s):  
V. Venkata Ramana ◽  
S. Kalyana Chakravarthy ◽  
P. Shalem Raj ◽  
B. Vinay Kumar ◽  
E. Shobha ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Rhodopseudomonas Palustris ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Geographical Regions ◽  
Emended Description ◽  
Type Strains

Four strains (JA310T, JA531T, JA447 and JA490) of red to reddish brown pigmented, rod-shaped, motile and budding phototrophic bacteria were isolated from soil and freshwater sediment samples from different geographical regions of India. All strains contained bacteriochlorophyll a and carotenoids of the spirilloxanthin series. The major cellular fatty acid of strains JA310T and JA531T was C18 : 1ω7c, the quinone was Q-10 and polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an aminohopanoid and an unidentified aminolipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that all strains clustered with species of the genus Rhodopseudomonas in the class Alphaproteobacteria . Strains JA531T, JA447 and JA490 were genotypically (>80 % related based on DNA–DNA hybridization) and phenotypically closely related to each other and the three strains were distinct from strain JA310T (33 % related). Furthermore, all four strains had less than 48 % relatedness (DNA–DNA hybridization) with type strains of members of the genus Rhodopseudomonas , i.e. Rhodopseudomonas palustris ATCC 17001T, Rhodopseudomonas faecalis JCM 11668T and Rhodopseudomonas rhenobacensis DSM 12706T. The genomic DNA G+C contents of strains JA310T and JA531T were 63.8 and 62.4 mol%, respectively. On the basis of phenotypic, chemotaxonomic and molecular genetic evidence, it is proposed that strains JA310T ( = NBRC 106083T = KCTC 5839T) and JA531T ( = NBRC 107575T = KCTC 5841T) be classified as the type strains of two novel species of the genus Rhodopseudomonas , Rhodopseudomonas parapalustris sp. nov. and Rhodopseudomonas harwoodiae sp. nov., respectively. In addition, we propose that strain DSM 123T ( = NBRC 100419T) represents a novel species, Rhodopseudomonas pseudopalustris sp. nov., since this strain differs genotypically and phenotypically from R. palustris ATCC 17001T and other members of the genus Rhodopseudomonas . An emended description of R. palustris is also provided.

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).

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