scholarly journals Description of Klebsiella quasipneumoniae sp. nov., isolated from human infections, with two subspecies, Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and Klebsiella quasipneumoniae subsp. similipneumoniae subsp. nov., and demonstration that Klebsiella singaporensis is a junior heterotypic synonym of Klebsiella variicola

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3146-3152 ◽  
Author(s):  
Sylvain Brisse ◽  
Virginie Passet ◽  
Patrick A. D. Grimont
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Carbon Sources ◽  
Biochemical Properties ◽  
Nucleotide Identity ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Human Infections ◽  
Human Blood Cultures

Strains previously classified as members of Klebsiella pneumoniae phylogroups KpI, KpII-A, KpII-B and KpIII were characterized by 16S rRNA (rrs) gene sequencing, multilocus sequence analysis based on rpoB, fusA, gapA, gyrA and leuS genes, average nucleotide identity and biochemical characteristics. Phylogenetic analysis demonstrated that KpI and KpIII corresponded to K. pneumoniae and Klebsiella variicola , respectively, whereas KpII-A and KpII-B formed two well-demarcated sequence clusters distinct from other members of the genus Klebsiella . Average nucleotide identity between KpII-A and KpII-B was 96.4 %, whereas values lower than 94 % were obtained for both groups when compared with K. pneumoniae and K. variicola . Biochemical properties differentiated KpII-A, KpII-B, K. pneumoniae and K. variicola , with acid production from adonitol and l-sorbose and ability to use 3-phenylproprionate, 5-keto-d-gluconate and tricarballylic acid as sole carbon sources being particularly useful. Based on their genetic and phenotypic characteristics, we propose the names Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and K. quasipneumoniae subsp. similipneumoniae subsp. nov. for strains of KpII-A and KpII-B, respectively. The type strain of K. quasipneumoniae sp. nov. and of K. quasipneumoniae subsp. quasipneumoniae subsp. nov. is 01A030T ( = SB11T = CIP 110771T = DSM 28211T). The type strain of K. quasipneumoniae subsp. similipneumoniae subsp. nov. is 07A044T ( = SB30T = CIP 110770T = DSM 28212T). Both strains were isolated from human blood cultures. This work also showed that Klebsiella singaporensis is a junior heterotypic synonym of K. variicola .

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 Leptospira dzianensis and Leptospira putramalaysiae are later heterotypic synonyms of Leptospira yasudae and Leptospira stimsonii

2021 ◽  
Author(s):  
Arnau Casanovas-Massana ◽  
Antony T. Vincent ◽  
Pascale Bourhy ◽  
Vasantha Kumari Neela ◽  
Frederic J. Veyrier ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Nucleotide Identity ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Genome Comparisons

Leptospira dzianensis and Leptospira putramalaysiae were recently described as novel species and published almost concurrently with Leptospira yasudae and Leptospira stimsonii . Genome comparisons based on average nucleotide identity of the type strain genomes indicate that L. dzianensis and L. putramalaysiae are conspecific with L. yasudae and L. stimsonii , respectively. Based on the rules of priority, L. dzianensis should be reclassified as a later heterotypic synonym of L. yasudae , and L. putramalaysiae should be reclassified as a later heterotypic synonym of L. stimsonii .

Genome analysis reveals that the correct name of type strain Adlercreutzia caecicola DSM 22242T is Parvibacter caecicola Clavel et al. 2013

2021 ◽  
Vol 71 (5) ◽  
Author(s):  
Dominic A. Stoll ◽  
Nicolas Danylec ◽  
Christina Grimmler ◽  
Sabine E. Kulling ◽  
Melanie Huch
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Draft Genome ◽  
Amino Acid Identity ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Genome Wide ◽  
Average Amino Acid Identity ◽  
Biochemical Analyses

The strain Adlercreutzia caecicola DSM 22242T (=CCUG 57646T=NR06T) was taxonomically described in 2013 and named as Parvibacter caecicola Clavel et al. 2013. In 2018, the name of the strain DSM 22242T was changed to Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 due to taxonomic investigations of the closely related genera Adlercreutzia, Asaccharobacter and Enterorhabdus within the phylum Actinobacteria . However, the first whole draft genome of strain DSM 22242T was published by our group in 2019. Therefore, the genome was not available within the study of Nouioui et al. (2018). The results of the polyphasic approach within this study, including phenotypic and biochemical analyses and genome-based taxonomic investigations [genome-wide average nucleotide identity (gANI), alignment fraction (AF), average amino acid identity (AAI), percentage of orthologous conserved proteins (POCP) and genome blast distance phylogeny (GBDP) tree], indicated that the proposed change of the name Parvibacter caecicola to Adlercreutzia caecicola was not correct. Therefore, it is proposed that the correct name of Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 strain DSM 22242T is Parvibacter caecicola Clavel et al. 2013.

scholarly journals Cohnella fermenti sp. nov., isolated from a fermentation process

2020 ◽  
Vol 70 (4) ◽  
pp. 2602-2610 ◽  
Author(s):  
Shih-Yao Lin ◽  
Wen-Ming Chen ◽  
Asif Hameed ◽  
Guan-Hua Huang ◽  
Mei-Hua Hung ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Nucleotide Identity ◽  
Whole Genome Sequencing Data ◽  
Rrna Gene ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Vegetable Sample

A novel Gram-stain-positive, aerobic, motile with peritrichous flagella, rod-shaped bacterium, designated CC-MHH1044T, was isolated from a preserved vegetable sample. A polyphasic taxonomic approach was applied to the isolates in order to clarify its taxonomic position. Growth of the strain CC-MHH1044T occurred at 15–50 °C (optimum, 30 °C), pH 6.0–8.0 (optimum, pH 7.0) and with 0–2.0 % (w/v) NaCl (optimum, 1 %, w/v). The genome of strain CC-MHH1044T consisted of 8.5 Mb and the genomic DNA G+C content was 58.5 mol%. Comparison of the 16S rRNA gene sequences showed that CC-MHH1044T belonged to the genus Cohnella and showed a close relationship with the type strains of Cohnella damuensis (96.2 %) and Cohnella panacarvi (95.9 %), and lower sequence similarity to other species. Average nucleotide identity values calculated from whole-genome sequencing data proved that CC-MHH1044T represents a distinct Cohnella species. The dominant cellular fatty acids (>5 %) included iso-C14 : 0(7.4 %), iso-C15 : 0 (6.4 %), anteiso-C15 : 0(40.3 %), C16 : 0 (6.6 %) and iso-C16 : 0 (27.0 %). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified aminophospholipids, one unidentified phospholipid and glycolipid. The major polyamine was spermidine. The predominant isoprenoid quinone was menaqinone 7 (MK-7). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits, together with results of comparative 16S rRNA gene sequence, average nucleotide identity and digital DNA–DNA hybridization analyses, we conclude that strain CC-MHH1044T represents a novel member of the genus Cohnella , for which the name Cohnella fermenti sp. nov. is proposed. The type strain is CC-MHH1044T (=BCRC 81147T=JCM 32834T).

Chryseobacterium lecithinasegens sp. nov., a siderophore-producing bacterium isolated from soil at the bottom of a pond

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Ryo Kutsuna ◽  
Izumi Mashima ◽  
Tohru Miyoshi-Akiyama ◽  
Yuki Muramatsu ◽  
Junko Tomida ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Nucleotide Identity ◽  
Phylogenetic Study ◽  
Species Discrimination ◽  
Rrna Gene ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type

Bacterial strain PAGU 2197T, which was isolated from soil collected from the bottom of a pond in Japan, is characterized in this study. Cells of strain PAGU 2197T were aerobic, Gram-negative, short rod-shaped, non-motile, flexirubin-producing, oxidase-positive, catalase-positive and lecithinase-negative. A phylogenetic study based on 16S rRNA gene sequences and multilocus sequence analysis (gyrB, rpoB and rpoD) indicated that strain PAGU 2197T belongs to the genus Chryseobacterium and is a member of an independent lineage including Chryseobacterium tructae CCUG 60111T (sequence similarity, 95.9 %), Chryseobacterium lactis CCUG 60566T (93.4 %) and Chryseobacterium viscerum CCUG 60103T (91.6 %). The average nucleotide identity values were 80.83–85.04 %. Because average nucleotide identity values of 95–96 % exceed the 70 % DNA–DNA hybridization cutoff value for species discrimination, strain PAGU 2197T represents a novel species in the genus Chryseobacterium . The genome of strain PAGU 2197T was 4 967 738 bp with a G+C content of 35.5 mol%. The sole respiratory quinone of strain PAGU 2197T was MK-6; the major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3OH, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 9 (iso-C17 : 1  ω9c and/or C16 : 0 10-methyl); and the major polar lipids were phosphoglycolipids and phosphatidylethanolamine. These results indicate that strain PAGU 2197T should be classified as representing a novel species in the genus Chryseobacterium , for which the name Chryseobacterium lecithinasegens sp. nov. is proposed, with strain PAGU 2197T (=NBRC 114264T=CCUG 75150T) as the type strain.

scholarly journals Description of Paenibacillus tepidiphilus sp. nov., isolated from a tepid spring

2020 ◽  
Vol 70 (3) ◽  
pp. 1977-1981 ◽  
Author(s):  
Manik Prabhu Narsing Rao ◽  
Zhou-Yan Dong ◽  
Yu Kan ◽  
Lei Dong ◽  
Shuai Li ◽  
...  
Keyword(s):  
Type Species ◽  
Hot Springs ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Nucleotide Identity ◽  
Rrna Gene ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type

China is a hotspot for hot springs and during microbial diversity analysis of Tengchong hot spring, Yunnan province, south-west PR China, two strains designated SYSU G01001T and SY-13 were isolated. SYSU G01001T and SY-13 were Gram-stain-positive, motile and spore-forming. Colonies were white, circular, raised and punctiform. SYSU G01001T and SY-13 grew at pH 6.0–9.0 (optimum pH 8.0) and at 23–37 °C (optimum 28 °C). The 16S rRNA gene sequence similarity between SYSU G01001T and SY-13 was 99.6 % but these strains shared low sequence similarity with Paenibacillus azotifigens (97.5 %) indicating that they represented a novel species. On the basis of the results, SYSU G01001T was selected for further investigations and SY-13 was considered to represent a second strain of the species. The cell wall peptidoglycan of SYSU G01001T was meso-2,6-diaminopimelic acid and MK-7 was the only respiratory quinone. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two unidentified aminolipids (AL), two unidentified amino phospholipids (APL), an unidentified phospholipid (PL) and an unidentified polar lipid (L). The G+C content of the genomic DNA was 53.9 mol%. The average nucleotide identity (ANIb and ANIm) values between SYSU G01001T and Paenibacillus azotifigens LMG 29963T were below the cut-off level (95–96 %) recommended as the average nucleotide identity (ANI) criterion for interspecies identity. On the basis of the above results strain SYSU G01001T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus tepidiphilus sp. nov. is proposed. The type strain is SYSU G01001T (=KCTC 33952T=CGMCC 1.13870T).

scholarly journals Proposal for transfer of Defluviimonas alba to the genus Frigidibacter as Frigidibacter mobilis nom. nov

2020 ◽  
Vol 70 (5) ◽  
pp. 3553-3558 ◽  
Author(s):  
Yang Liu ◽  
Tao Pei ◽  
Jun Zhang ◽  
Fan Yang ◽  
Honghui Zhu
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Amino Acid Identity ◽  
Biochemical Properties ◽  
Rrna Gene ◽  
Separate Species ◽  
Content Type ◽  
Link Type ◽  
Close Relationship ◽  
Exact Position

A polyphasic taxonomic study was undertaken to clarify the exact position of the type strain cai42T of the species Defluviimonas alba Pan et al. 2015. The results of the 16S rRNA gene sequence analysis indicated that the two sequences from cai42T shared 99.6 and 99.7 % similarity to that of the type strain SP32T of the species Frigidibacter albus and formed a coherent clade in the phylogenetic tree. Whole genomic comparison between cai42T and SP32T yielded a digital DNA–DNA hybridization estimate of 36.3 %, an average nucleotide identity of 88.8 % and an average amino acid identity of 89.8 %, clearly indicating that the two strains should belong to two genospecies of the same genus. The close relationship between the two strains was underpinned by the results of genome-based phylogenetic analysis. Although cai42T and SP32T shared similar physiological and biochemical properties, some striking differences, such as mobility, the temperature range for growth and the polar lipid components, could distinguish them as separate species. Therefore, the comparative phenotypic and genotypic analyses supported the incorporation of Defluviimonas alba into the genus Frigidibacter as Frigidibacter mobilis nom. nov. with the type strain cai42T (=CGMCC 1.12518T=LMG 27406T).

scholarly journals Vibrio metoecus sp. nov., a close relative of Vibrio cholerae isolated from coastal brackish ponds and clinical specimens

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3208-3214 ◽  
Author(s):  
Paul C. Kirchberger ◽  
Maryann Turnsek ◽  
Dana E. Hunt ◽  
Bradd J. Haley ◽  
Rita R. Colwell ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Type Species ◽  
The United States ◽  
Nucleotide Identity ◽  
Close Relative ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
The Past ◽  
Link Type ◽  
Close Resemblance

A Gram-staining-negative, curved-rod-shaped bacterium with close resemblance to Vibrio cholerae , the aetiological agent of cholera, was isolated over the course of several years from coastal brackish water (17 strains) and from clinical cases (two strains) in the United States. 16S rRNA gene identity with V. cholerae exceeded 98 % yet an average nucleotide identity based on genome data of around 86 % and multi locus sequence analysis of six housekeeping genes (mdh, adk, gyrB, recA, pgi and rpoB) clearly delineated these isolates as a distinct genotypic cluster within the V. cholerae – V. mimicus clade. Most standard identification techniques do not differentiate this cluster of isolates from V. cholerae . Only amplification of the ompW gene using V. cholerae -specific primers and a negative Voges–Proskauer test showed a difference between the two clusters. Additionally, all isolated strains differed phenotypically from V. cholerae in their ability to utilize N-acetyl-d-galactosamine and d-glucuronic acid as sole carbon sources. Furthermore, they were generally unable to infect the slime mould Dictyostelium discoideum, a widespread ability in V. cholerae . Based on these clear phenotypic differences that are not necessarily apparent in standard tests as well as average nucleotide identity and phylogeny of protein-coding genes, we propose the existence of a novel species, Vibrio metoecus sp. nov. with the type strain OP3HT ( = LMG 27764T = CIP 110643T). Due to its close resemblance to V. cholerae and the increasing number of strains isolated over the past several years, we suggest that V. metoecus sp. nov. is a relatively common species of the genus Vibrio , isolates of which have been identified as atypical isolates of V. cholerae in the past. Its isolation from clinical samples also indicates that strains of this species, like V. cholerae , are opportunistic pathogens.

scholarly journals Streptomyces apocyni sp. nov., an endogenous actinomycete isolated from Apocynum venetum

2020 ◽  
Vol 70 (9) ◽  
pp. 4883-4889 ◽  
Author(s):  
Wen-Xiang Liu ◽  
Li-Ran Ma ◽  
Zhan-Feng Xia ◽  
Hong Zeng ◽  
Xiao-Xia Luo ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Nucleotide Identity ◽  
Rrna Gene ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Apocynum Venetum ◽  
Taxonomic Approach

A novel actinomycete, designated strain TRM 66233T, was isolated from Apocynum venetum L. collected from the Xinjiang Uygur Autonomous Region of China and characterized using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain TRM 66233T with the genus Streptomyces . Strain TRM 66233T showed a high similarity value to Streptomyces bikiniensis NRRL B-1049T (98.07 %) based on the 16S rRNA gene phylogenetic tree. The whole-cell sugar pattern of TRM 66233T consisted of glucose, galactose, mannose and ribose. The predominant menaquinones were MK-9(H2), MK-9(H6), MK-9(H8) and MK-9(H10). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and four unidentified lipids. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, C16 : 0 and iso-C17 : 0. The G+C content of the DNA was 70.35 mol%. The DNA–DNA relatedness and average nucleotide identity values as well as evolutionary distances based on multilocus (atpD, gyrB, recA, rpoB and trpB) sequences between strain TRM 66233T and closely related type strains were significantly lower than the recommended threshold values. The whole-genome average nucleotide identity and digital DNA–DNA hybridization values between strain TRM 66233T and S. bikiniensis NRRL B-1049T were 78.86 and 23.2 %, respectively. On the basis of evidence from this polyphasic study, strain TRM 66233T should represent a novel species of the genus Streptomyces , for which the name Streptomyces apocyni sp. nov. is proposed. The type strain is TRM 66233T (=CCTCC AA 2019056T=LMG 31559T).

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.

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