Reclassification of Streptomyces costaricanus and Streptomyces phaeogriseichromatogenes as later heterotypic synonyms of Streptomyces murinus

2021 ◽  
Author(s):  
Hisayuki Komaki
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Biosynthetic Gene ◽  
Rrna Gene Sequence ◽  
Biosynthetic Gene Clusters ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

This study aimed to clarify the taxonomic relationships among Streptomyces costaricanus , Streptomyces graminearus, Streptomyces murinus and Streptomyces phaeogriseichromatogenes . These strains share the same 16S rRNA gene sequence. Multilocus sequence analysis revealed that S. costaricanus , S. murinus and S. phaeogriseichromatogenes belong to the same species, but S. graminearus does not. Digital DNA–DNA relatedness and average nucleotide identity among S. costaricanus, S. murinus and S. phaeogriseichromatogenes were 70.9–74.6% and 96.5–97.0 %, respectively. In addition to the previously reported phenotypic data, the presence of a similar set of secondary metabolite-biosynthetic gene clusters for polyketides and nonribosomal peptides supported the similarity among the three species. Therefore, S. costaricanus and S. phaeogriseichromatogenes should be reclassified as later heterotypic synonyms of S. murinus .

scholarly journals Reclassification of Streptomyces fulvissimus as a later heterotypic synonym of Streptomyces microflavus

2020 ◽  
Vol 70 (9) ◽  
pp. 5156-5162 ◽  
Author(s):  
Hisayuki Komaki ◽  
Tomohiko Tamura
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biosynthetic Gene Clusters ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Type Strains

We investigated the taxonomic relationships among Streptomyces fulvissimus , Streptomyces fulvorobeus and Streptomyces microflavus . These type strains shared the same 16S rRNA gene sequence. Digital DNA–DNA relatedness and average nucleotide identity analyses using whole genome sequences suggested that S. fulvissimus and S. microflavus belong to the same genomospecies, whereas S. fulvorobeus does not. In addition to previously reported phenotypic data, the presence of almost the same set of secondary metabolite-biosynthetic gene clusters for polyketides and nonribosomal peptides also supported the synonymy between S. fulvissimus and S. microflavus . Therefore, S. fulvissimus should be reclassified as a later heterotypic synonym of S. microflavus .

scholarly journals Faecalicoccus acidiformans gen. nov., sp. nov., isolated from the chicken caecum, and reclassification of Streptococcus pleomorphus (Barnes et al. 1977), Eubacterium biforme (Eggerth 1935) and Eubacterium cylindroides (Cato et al. 1974) as Faecalicoccus pleomorphus comb. nov., Holdemanella biformis gen. nov., comb. nov. and Faecalitalea cylindroides gen. nov., comb. nov., respectively, within the family Erysipelotrichaceae

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3877-3884 ◽  
Author(s):  
Celine De Maesschalck ◽  
Filip Van Immerseel ◽  
Venessa Eeckhaut ◽  
Siegrid De Baere ◽  
Margo Cnockaert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Strains LMG 27428T and LMG 27427 were isolated from the caecal content of a chicken and produced butyric, lactic and formic acids as major metabolic end products. The genomic DNA G+C contents of strains LMG 27428T and LMG 27427 were 40.4 and 38.8 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were most closely related to the generically misclassified Streptococcus pleomorphus ATCC 29734T. Strain LMG 27428T could be distinguished from S. pleomorphus ATCC 29734T based on production of more lactic acid and less formic acid in M2GSC medium, a higher DNA G+C content and the absence of activities of acid phosphatase and leucine, arginine, leucyl glycine, pyroglutamic acid, glycine and histidine arylamidases, while strain LMG 27428 was biochemically indistinguishable from S. pleomorphus ATCC 29734T. The novel genus Faecalicoccus gen. nov. within the family Erysipelotrichaceae is proposed to accommodate strains LMG 27428T and LMG 27427. Strain LMG 27428T ( = DSM 26963T) is the type strain of Faecalicoccus acidiformans sp. nov., and strain LMG 27427 ( = DSM 26962) is a strain of Faecalicoccus pleomorphus comb. nov. (type strain LMG 17756T = ATCC 29734T = DSM 20574T). Furthermore, the nearest phylogenetic neighbours of the genus Faecalicoccus are the generically misclassified Eubacterium cylindroides DSM 3983T (94.4 % 16S rRNA gene sequence similarity to strain LMG 27428T) and Eubacterium biforme DSM 3989T (92.7 % 16S rRNA gene sequence similarity to strain LMG 27428T). We present genotypic and phenotypic data that allow the differentiation of each of these taxa and propose to reclassify these generically misnamed species of the genus Eubacterium formally as Faecalitalea cylindroides gen. nov., comb. nov. and Holdemanella biformis gen. nov., comb. nov., respectively. The type strain of Faecalitalea cylindroides is DSM 3983T = ATCC 27803T = JCM 10261T and that of Holdemanella biformis is DSM 3989T = ATCC 27806T = CCUG 28091T.

Patulibacter medicamentivorans sp. nov., isolated from activated sludge of a wastewater treatment plant

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2588-2593 ◽  
Author(s):  
Bárbara Almeida ◽  
Ivone Vaz-Moreira ◽  
Peter Schumann ◽  
Olga C. Nunes ◽  
Gilda Carvalho ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Treatment Plant ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A Gram-positive, aerobic, non-motile, non-endospore-forming rod-shaped bacterium with ibuprofen-degrading capacity, designated strain I11T, was isolated from activated sludge from a wastewater treatment plant. The major respiratory quinone was demethylmenaquinone DMK-7, C18 : 1 cis9 was the predominant fatty acid, phosphatidylglycerol was the predominant polar lipid, the cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the G+C content of the genomic DNA was 74.1 mol%. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain I11T were Patulibacter ginsengiterrae CECT 7603T (96.8 % similarity), Patulibacter minatonensis DSM 18081T (96.6 %) and Patulibacter americanus DSM 16676T (96.6 %). Phenotypic characterization supports the inclusion of strain I11T within the genus Patulibacter (phylum Actinobacteria) . However, distinctive features and 16S rRNA gene sequence analysis suggest that is represents a novel species, for which the name Patulibacter medicamentivorans sp. nov. is proposed. The type strain is I11T ( = DSM 25962T = CECT 8141T).

Caldicellulosiruptor diazotrophicus sp. nov., a thermophilic, nitrogen-fixing fermentative bacterium isolated from a terrestrial hot spring in Japan

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Yuxin Chen ◽  
Arisa Nishihara ◽  
Takao Iino ◽  
Moriya Ohkuma ◽  
Shin Haruta
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Cellular Fatty Acids ◽  
Link Type ◽  
The 16S Rrna Gene

A novel nitrogen-fixing fermentative bacterium, designated as YA01T, was isolated from Nakabusa hot springs in Japan. The short-rod cells of strain YA01T were Gram-positive and non-sporulating. Phylogenetic trees of the 16S rRNA gene sequence and concatenated sequences of 40 single-copy ribosomal genes revealed that strain YA01T belonged to the genus Caldicellulosiruptor and was closely related to Caldicellulosiruptor hydrothermalis 108T, Caldicellulosiruptor bescii DSM 6725T and Caldicellulosiruptor kronotskyensis 2002T. The 16S rRNA gene sequence of strain YA01T shares less than 98.1 % identity to the known Caldicellulosiruptor species. The G+C content of the genomic DNA was 34.8 mol%. Strain YA01T shares low genome-wide average nucleotide identity (90.31–91.10 %), average amino acid identity (91.45–92.10 %) and <70 % digital DNA–DNA hybridization value (41.8–44.2 %) with the three related species of the genus Caldicellulosiruptor . Strain YA01T grew at 50–78 °C (optimum, 70 °C) and at pH 5.0–9.5 (optimum, pH 6.5). Strain YA01T mainly produced acetate by consuming d(+)-glucose as a carbon source. The main cellular fatty acids were iso-C17 : 0 (35.7 %), C16 : 0 (33.3 %), DMA16 : 0 (6.6 %) and iso-C15 : 0 (5.9 %). Based on its distinct phylogenetic position, biochemical and physiological characteristics, and the major cellular fatty acids, strain YA01T is considered to represent a novel species of the genus Caldicellulosiruptor for which the name Caldicellulosiruptor diazotrophicus sp. nov. is proposed (type strain YA01T=DSM 112098T=JCM 34253T).

scholarly journals Pseudomonas piscis sp. nov., isolated from the profound head ulcers of farmed Murray cod (Maccullochella peelii peelii)

2020 ◽  
Vol 70 (4) ◽  
pp. 2732-2739 ◽  
Author(s):  
Yang Liu ◽  
Qiuhua Rao ◽  
Jochen Blom ◽  
Qiu Lin ◽  
Tuyan Luo
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Murray Cod

A Gram-stain-negative, strictly aerobic, motile, rod-shaped bacterium with monopolar flagella, designated as MC042T, was isolated from the profound head ulcers of farmed Murray cod sampled from Zhejiang Province, China. Analysis of its 16S rRNA gene sequence and multilocus sequence analysis phylogeny showed that strain MC042T belonged to the genus Pseudomonas , showing the highest 16S rRNA gene sequence similarity to Pseudomonas juntendi BML3T (98.9 %), and less than 98.8 % similarity to other Pseudomonas species with validly published names. Whole-genome sequencing and phylogenetic reconstruction based on a core set of 1563 Pseudomonas genes further indicated that strain MC042T was most closely related to the clade formed by Pseudomonas protegens CHA0T and Pseudomonas saponiphila DSM 975T and distantly related to any of the validly published species of the genus Pseudomonas . Furthermore, strain MC042T could be distinguished from its closely related species of the genus Pseudomonas by its ability to assimilate maltose, d-xylose and melibiose, but not d-mannitol. The principal fatty acids were C16 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The respiratory quinone was Q-9. Polar lipids of strain MC042T comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, unidentified glycolipids, an unidentified lipid, an unknown glycolipid and aminolipid. Based on its phenotypic, chemotaxonomic and phylogenetic features, strain MC042T is considered to represent a novel species, for which the name Pseudomonas piscis sp. nov. is proposed. The type strain is MC042T (=KCTC 72033T=MCCC 1K03575T).

scholarly journals Cellulomonas rhizosphaerae sp. nov., a novel actinomycete isolated from soil

2019 ◽  
Vol 69 (4) ◽  
pp. 1001-1008 ◽  
Author(s):  
Yuanyuan Tian ◽  
Chuanyu Han ◽  
Jiangmeihui Hu ◽  
Junwei Zhao ◽  
Chen Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A novel actinomycete, designated strain NEAU-TCZ24T, was isolated from soil and characterized using a polyphasic approach. The results of phylogenetic analysis based on the 16S rRNA gene sequence indicated that the organism should be assigned to the genus Cellulomonas and formed a stable clade with its closest relatives Cellulomonas terrae JCM 14899T (98.4 % 16S rRNA gene sequence similarity), Cellulomonas xylanilytica JCM 14281T (97.9 %) and Cellulomonas humilata JCM 11945T (97.7 %). The major menaquinones were identified as MK-9(H4) and MK-8(H4). The phospholipid profile was found to contain diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositolmannoside, a ninhydrin-positiveglycolipid, an unidentified phosphoglycolipid, an unidentified phospholipid and an unidentified lipid. The major fatty acids were identified as anteiso-C15 : 0, C18 : 1ω9c, C16 : 0 and anteiso-C17 : 0. Moreover, morphological and chemotaxonomic properties of NEAU-TCZ24T also confirmed the affiliation of the isolate to the genus Cellulomonas . However, multilocus sequence analysis based on five other house-keeping genes (gyrB, rpoB, recA, relA and atpD), DNA–DNA relatedness, physiological and biochemical data indicated that NEAU-TCZ24T could be distinguished from its closest relatives. Therefore, it is proposed that NEAU-TCZ24T represents a novel species of the genus Cellulomonas , for which the name Cellulomonas rhizosphaerae sp. nov. is proposed. The type strain is NEAU-TCZ24T (=CCTCC AA 2018042T=JCM 32383T).

Pedobacter tournemirensis sp. nov., isolated from a fault water sample of a deep Toarcian argillite layer

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 303-308 ◽  
Author(s):  
Laurent Urios ◽  
Laurent Intertaglia ◽  
Michel Magot
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Subsurface Water ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A Gram-negative bacterium, designated TF5-37.2-LB10T, was isolated from subsurface water of the Toarcian geological layer of Tournemire, France. Cells were non-motile straight rods that formed cream to light pink colonies on 10-fold diluted LB agar. Strain TF5-37.2-LB10T contained menaquinone 7 and its major fatty acids were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 0 3-OH and iso-C17 : 1ω9c. The G+C content of the genomic DNA was 46 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed strain TF5-37.2-LB10T within the genus Pedobacter , family Sphingobacteriaceae . Pedobacter composti TR6-06T and Pedobacter oryzae DSM 19973T were the closest phylogenetic relatives (93.5 and 93.3 % 16S rRNA gene sequence similarity, respectively). On the basis of 16S rRNA gene sequence comparison and physiological and biochemical characteristics, strain TF5-37.2-LB10T represents a novel species of the genus Pedobacter , for which the name Pedobacter tournemirensis sp. nov. is proposed. The type strain is TF5-37.2-LB10T ( = DSM 23085T = CIP 110085T = MOLA 820T).

scholarly journals Sphingomonas starnbergensis sp. nov., isolated from a prealpine freshwater lake

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1017-1023 ◽  
Author(s):  
Hong Chen ◽  
Mareike Jogler ◽  
Brian J. Tindall ◽  
Hans-Peter Klenk ◽  
Manfred Rohde ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A novel type of freshwater bacterium was isolated from the prealpine mesotrophic Starnberger See (Bavaria, southern Germany). Cells of strain 382T were Gram-negative and rod-shaped, motile and creamy-white. The isolate was strictly aerobic, catalase- and oxidase-positive, and grew at pH values of 6–9 (optimum, pH 7) and temperatures of 10–37 °C (optimum, 28 °C). The genomic G+C content of strain 382T was 64.1 mol%. Based on 16S rRNA gene sequence analyses, strain 382T belongs to the family Sphingomonadaceae and clusters within the genus Sphingomonas . Sphingomonas histidinilytica UM 2T and Sphingomonas wittichii DSM 6014T were the closest relatives, as indicated by the highest 16S rRNA gene sequence similarities (97.1 % and 96.8 %, respectively). Sphingomonas paucimobilis DSM 1098T (the type species of the genus Sphingomonas ) exhibited 95.3 % sequence similarity. This affiliation of strain 382T to the genus Sphingomonas is confirmed by the presence of Q-10 as the major respiratory quinone, two sphingoglycolipids, C14 : 0 2-OH as the major 2-hydroxy fatty acid and sym-homospermidine as the major polyamine. The main cellular fatty acids of strain 382T were C18 : 1ω7c (39 %), C16 : 1ω7c (21 %), C16 : 0 (10 %) and C14 : 0 2-OH (10 %). Based on the phylogenetic distance from other species of the genus Sphingomonas and its unusually high C16 : 1ω7c content, strain 382T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas starnbergensis is proposed. The type strain is 382T ( = DSM 25077T  = LMG 26763T).

Rhodococcus spelaei sp. nov., isolated from a cave, and proposals that Rhodococcus biphenylivorans is a later synonym of Rhodococcus pyridinivorans, Rhodococcus qingshengii and Rhodococcus baikonurensis are later synonyms of Rhodococcus erythropolis, and Rhodococcus percolatus and Rhodococcus imtechensis are later synonyms of Rhodococcus opacus

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Soon Dong Lee ◽  
In Seop Kim
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rhodococcus Erythropolis ◽  
Rhodococcus Opacus ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two novel actinobacterial strains, designated C9-5T and C3-43, were isolated from soil samples of a cave in Jeju Island, Republic of Korea, and subjected to taxonomic study by a polyphasic approach. The organisms exhibited a typical rod–coccus developmental cycle during growth and grew at 10–30 °C, pH 5–9 and 0–3 % (w/v) NaCl. In 92 single-copy core gene sequence analysis, strain C9-5T was loosely associated with Rhodococcus tukisamuensis , albeit sharing low 16S rRNA gene sequence similarity (97.4 %). A combination of morphological and chemotaxonomic characteristics supported assignment with the genus Rhodococcus . With respect to 16S rRNA gene sequence similarity, the novel isolates showed the highest identity to the type strain of Rhodococcus subtropicus (98.7 % sequence similarity), followed by Rhodococcus olei (98.5 %) and Rhodococcus pedocola (98.4 %).The average nucleotide identity and digital DNA–DNA hybridization values between strain C9-5T and members of the genus Rhodococcus were ≤81.5 and ≤37.1 %, respectively. A set of physiological and chemotaxonomic properties together with overall genomic relatedness differentiated the novel isolates from members of the genus Rhodococcus , for which the name Rhodococcus spelaei sp. nov. is proposed. The type strain is C9-5T (=KACC 19822T=DSM 107558T). Based on genome analysis performed here, it is also proposed that Rhodococcus biphenylivorans Su et al. 2015 is a later heterotypic synonym of Rhodococcus pyridinivorans Yoon et al. 2000, Rhodococcus qingshengii Xu et al. 2007 and Rhodococcus baikonurensis Li et al. 2004 are later heterotypic synonyms of Rhodococcus erythropolis (Gray and Thornton 1928) Goodfellow and Alderson 1979 (Approved Lists 1980), and Rhodococcus percolatus Briglia et al. 1996 and Rhodococcus imtechensis Ghosh et al. 2006 are later heterotypic synonyms of Rhodococcus opacus Klatte et al. 1995.

Paenibacillus allorhizosphaerae sp. nov., from soil of the rhizosphere of Zea mays

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Dominique Clermont ◽  
Alexis Criscuolo ◽  
...  
Keyword(s):  
Zea Mays ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A Gram-stain-positive, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays, was studied for its detailed taxonomic allocation. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-447T was shown to be a member of the genus Paenibacillus , most closely related to the type strain of Paenibacillus solanacearum (97.8 %). The 16S rRNA gene sequence similarity values to all other Paenibacillus species were below 97.0 %. DNA–DNA hybridization (DDH) values with the type strain of P. solanacearum were 35.9 % (reciprocal 27%), respectively. The average nucleotide identity and in silico DDH values with the type strain of P. solanacearum were 84.86 and 28.9 %, respectively. The quinone system of strain JJ-447T consisted exclusively of menaquinones and the major component was MK-7 (96.4 %) but minor amounts of MK–6 (3.6 %) were detected as well. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. Major fatty acids were iso- and anteiso-branched with the major compounds anteiso-C15 : 0 and iso-C15 : 0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-447T from the most closely related species on the basis of d-glucose, l-arabinose and d-mannose assimilation and other physiological tests. Thus, JJ-447T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus allorhizosphaerae sp. nov. is proposed, with JJ-447T (=LMG 31601T=CCM 9021T=CIP 111802T) as the type strain.

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