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 .

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 Deinococcus xibeiensis Wang et al. 2010 as a heterotypic synonym of Deinococcus wulumuqiensis Wang et al. 2010

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 1083-1085 ◽  
Author(s):  
Sunhee Hong ◽  
Christine E. Farrance ◽  
Anne Russell ◽  
Hana Yi
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Taxonomic Status ◽  
Single Species ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Genomic Relatedness

Two species of the genus Deinococcus , namely Deinococcus wulumuqiensis Wang et al. 2010 and Deinococcus xibeiensis Wang et al. 2010, were simultaneously proposed and described in the same publication. However, the identical 16S rRNA gene sequence of the two type strains strongly raised the probability of their relatedness at the species level. Thus, the genomic relatedness of the two species of the genus Deinococcus was investigated here to clarify their taxonomic status. The high (99.9 %) average nucleotide identity (ANI) between the genome sequences of the two type strains suggested that the two species are synonymous. Additional phenotypic data including enzymic activities and substrate-utilization profiles showed no pronounced differences between the type strains of the two species. Data from this study demonstrated that the two taxa constitute a single species. According to Rule 42 of the Bacteriological Code, we propose that D. xibeiensis Wang et al. 2010 should be reclassified as a subjective heterotypic synonym of D. wulumuqiensis Wang et al. 2010.

scholarly journals Lysinibacillus macroides sp. nov., nom. rev.

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1121-1127 ◽  
Author(s):  
An Coorevits ◽  
Anna E. Dinsdale ◽  
Jeroen Heyrman ◽  
Peter Schumann ◽  
Anita Van Landschoot ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Cow Dung ◽  
Rrna Gene ◽  
Pairwise Similarity ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Type Strains

‘Bacillus macroides’ ATCC 12905T ( = DSM 54T = LMG 18474T), isolated in 1947 from cow dung, was not included in the Approved Lists of Bacterial Names and so it lost standing in bacteriological nomenclature. Reinvestigation of the strain, including DNA–DNA relatedness experiments, revealed that ‘Bacillus macroides’ is genomically distinct from its closest relatives Lysinibacillus xylanilyticus , Lysinibacillus boronitolerans and Lysinibacillus fusiformis (as determined by 16S rRNA gene sequence analysis, with pairwise similarity values of 99.2, 98.8 and 98.5 %, respectively, with the type strains of these species). Further analysis showed that ‘Bacillus macroides’ shares the A4α l-Lys–d-Asp peptidoglycan type with other members of the genus Lysinibacillus and can thus be attributed to this genus. These results, combined with additional phenotypic data, justify the description of strain LMG 18474T ( = DSM 54T = ATCC 12905T) as Lysinibacillus macroides sp. nov., nom. rev.

scholarly journals Flavobacterium panici sp. nov. isolated from the rhizosphere of the switchgrass Panicum virgatum

2020 ◽  
Vol 70 (11) ◽  
pp. 5824-5831 ◽  
Author(s):  
Peter Kämpfer ◽  
S. P. Glaeser ◽  
John A. McInroy ◽  
Jia Xu ◽  
Hans-Jürgen Busse ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Panicum Virgatum ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-staining-negative non endospore-forming strain, PXU-55T, was isolated from the rhizosphere of the switchgrass Panicum virgatum and studied in detail to determine its taxonomic position. The results of 16S rRNA gene sequence analysis indicated that the isolate represented a member of the genus Flavobacterium . The isolate shared highest 16S rRNA gene sequence similarities with the type strains of Flavobacterium chungangense (98.78 %) and Flavobacterium chilense (98.64 %). The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) values between the PXU-55T genome assembly and the ones of the most closely related type strains of species of the genus Flavobacterium were 87.3 and 31.9% ( Flavobacterium defluvii ), and 86.1 and 29.9% ( Flavobacterium johnsoniae ). Menaquinone MK-6 was the major respiratory quinone. As major polar lipids, phosphatidylethanolamine, an ornithine lipid and the unidentified polar lipids L2, L3 and L4 lacking a functional group were found. Moderate to minor amounts of another ornithine lipid, the unidentified lipid L1 and a glycolipid were present, as well. The major polyamine is sym-homospermidine. The fatty acid profiles contained major amounts of iso-C15:0, iso-C15:0 3-OH, iso-C17:0 3-OH, C15:0, summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) and various hydroxylated fatty acids in smaller amounts, among them iso C16:0 3-OH, C16:0 3-OH and C15:0 3-OH, which supported the classification of the isolate as a member of the genus Flavobacterium . Physiological and biochemical characterisation and ANI calculations with the type strains of the most closely related species allowed a clear phenotypic and genotypic differentiation of the strain. For this reason, we propose that strain PXU-55T (=CIP 111646T=CCM 8914T) represents a novel species with the name Flavobacterium panici sp. nov.

scholarly journals Pseudooceanicola aestuarii sp. nov., isolated from the Jiulong River Estuary in PR China

2020 ◽  
Vol 70 (12) ◽  
pp. 6220-6225 ◽  
Author(s):  
Yanyan Li ◽  
Yu Wang ◽  
Yina Wang ◽  
Fang Lin ◽  
Hongmei Zhu ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
River Estuary ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Jiulong River Estuary ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Type Strains

A novel Gram-stain-negative, rod-shaped, aerobic, oxidase-positive and catalase-positive bacterium of the genus Pseudooceanicola , designated strain E2-1T, was isolated from surface water of Jiulong River Estuary, PR China. Cells of strain E2-1T grew in medium containing 0.5–12 % NaCl (w/v; optimum, 2–4 %), at 15–45 °C (optimum, 28–33 °C) and at pH 7.0–9.0 (optimum, pH 7.0–8.0). Comparative analyses of the 16S rRNA gene sequence revealed that strain E2-1T had the highest similarity to Pseudooceanicola nitratireducens JLT1210T (97.3 %) and Pseudooceanicola batsensis HTCC2597T (97.1 %), and had less than 97.0 % 16S rRNA gene sequence similarity to other type strains within the genus Pseudooceanicola . The DNA G+C content of strain E2-1T was 65.7 mol%. The average nucleotide identity and digital DNA–DNA hybridization relatedness values between E2-1T and related type strains were 75.0 and 20.1 % with P. nitratireducens JLT1210T and 75.6 and 20.4 % with P. batsensis HTCC2597T, respectively. The sole isoprenoid quinone was Q-10; the predominant polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids and six unidentified lipids; the major cellular fatty acids were C16 : 0 (17.5 %), C19 : 0 cyclo ω8c (22.7 %) and summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c; 10.1 %). According to the phylogenetic and genotypic results, strain E2-1T represents a novel species in the genus Pseudooceanicola , for which the name Pseudooceanicola aestuarii sp. nov. is proposed. The type strain is E2-1T (=MCCC 1K03742T=KCTC 72107T).

Micromonospora humida sp. nov., exhibiting antimicrobial potential, isolated from riverside soil

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Jun Sik Ra ◽  
Min Ji Kim ◽  
Dong Hyeon Lee ◽  
Ji Won Jeong ◽  
Seung Bum Kim
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Clusters ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Biosynthetic Gene Clusters ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
The 16S Rrna Gene

An actinobacterial strain designated MMS20-R1-14T was isolated from a riverside soil sample. Colonies on agar plates were orange to strong orange brown in colour, which later became black. The cells grew at 10–40 °C (optimum, 37 °C), pH 5.0–11.0 (pH 8.0) and in the presence of 0–4 % NaCl (1 %). The 16S rRNA gene sequence of strain MMS20-R1-14T showed highest similarities to Micromonospora wenchangensis CCTCC AA 2012002T (99.51 %) and Micromonospora rifamycinica AM105T (99.37 %). The orthoANI values between strain MMS20-R1-14T and the two type strains were 95.72 and 90.99 %, and the digital DNA–DNA hybridization values were 63.6 and 40.8 %, respectively, thus confirming the distinction of strain MMS20-R1-14T from its mostly related species. The DNA G+C content of strain MMS20-R1-14T was 72.9 mol%. The strain contained meso-diaminopimelic acid as the major cell-wall amino acid, and the characteristic whole-cell sugars were arabinose, xylose, glucose, ribose and rhamnose. The main cellular fatty acids were C18 : 1  ω9c, iso-C15 : 0 and iso-C16 : 0, the diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the predominant menaquinones were MK-10(H4) and MK-10(H6), all of which were consistent with those of Micromonospora . Strain MMS20-R1-14T showed antimicrobial activity against a range of bacterial and yeast species. The genome of the strain was found to contain 33 potential biosynthetic gene clusters for secondary metabolites, thus showing a high potential as a producer of bioactive compounds. On the basis of these phenotypic, genotypic and chemotaxonomic data, strain MMS20-R1-14T merits recognition as representing a novel species of the genus Micromonospora , for which the name Micromonospora humida sp. nov. (type strain=MMS20 R1-14T=KCTC 49541T=JCM 34494T) is proposed.

Devosia equisanguinis sp. nov., isolated from horse blood

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
Dominique Clermont ◽  
Alexis Criscuolo ◽  
Stefanie P. Glaeser
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Horse Blood ◽  
Type Strains

A Gram-stain-negative, aerobic, non-endospore-forming organism isolated from horse blood was studied for its taxonomic allocation. On the basis of 16S rRNA gene sequence similarity comparisons, strain M6-77T grouped within the genus Devosia and was most closely related to Devosia elaeis (97.6 %) and Devosia indica (97.55 %). The 16S rRNA gene sequence similarity to type strains of other Devosia species was below 97.5 %. The average nucleotide identity and digital DNA–DNA hybridization values between the M6-77T genome assembly and those of the closest relative Devosia type strains were <85 and <25 %, respectively. Strain M6-77T grew optimally at 25–37 °C (range: 10–36 °C), at a pH range of pH 6.5–10.5 and in the presence of up to 3 % (w/v) NaCl. The fatty acid profile from whole-cell hydrolysates supported the allocation of the strain to the genus Devosia . Major fatty acids were C18 : 1  ω7c, 11-methyl C18 : 1  ω7c and C16 : 0. The quinone system consisted exclusively of ubiquinone Q-10. The polar lipid profile was composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol and three unidentified glycolipids. In the polyamine pattern, putrescine was predominant and spermidine was detected in moderate amounts. The diamino acid of the peptidoglycan was meso-diaminopimelic acid. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain M6-77T from the closely related species. Hence, M6-77T represents a new species of the genus Devosia , for which we propose the name Devosia equisanguinis sp. nov., with M6-77T (=CIP 111628T=LMG 30659T=CCM 8868T) as the type strain.

Jannaschia faecimaris sp. nov., isolated from a tidal flat sediment

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 945-951 ◽  
Author(s):  
Yong-Taek Jung ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, non-motile, rod- or coccoid-shaped bacterial strain, designated HD-22T, belonging to the class Alphaproteobacteria , was isolated from a tidal flat sediment of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain HD-22T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain HD-22T fell within the clade comprising species of the genus Jannaschia , clustering with the type strains of Jannaschia helgolandensis , Jannaschia donghaensis and Jannaschia rubra , with which it exhibited highest 16S rRNA gene sequence similarity (97.6–98.2 %). Levels of 16S rRNA gene sequence similarity between strain HD-22T and the type strains of the other species of the genus Jannaschia were in the range 94.4–97.5 %. The DNA G+C content was 64.6 mol% and mean DNA–DNA relatedness values between strain HD-22T and the type strains of J. helgolandensis , J. donghaensis and J. rubra were 42.1, 40.1 and 27.0 %, respectively. Strain HD-22T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, demonstrated that strain HD-22T is distinguishable from recognized species of the genus Jannaschia . On the basis of the data presented, strain HD-22T is considered to represent a novel species of the genus Jannaschia , for which the name Jannaschia faecimaris sp. nov. is proposed. The type strain is HD-22T ( = KCTC 32179T = CCUG 63415T).

Microbacterium lemovicicum sp. nov., a bacterium isolated from a natural uranium-rich soil

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2600-2606 ◽  
Author(s):  
Laure Mondani ◽  
Laurie Piette ◽  
Richard Christen ◽  
Dipankar Bachar ◽  
Catherine Berthomieu ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Natural Uranium ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Type Strains

An actinobacterial strain, designated ViU22T, was isolated from a natural uranium-rich soil and was studied using a polyphasic approach. Cells formed orange-pigmented colonies, were rod-shaped, Gram-positive (non-staining method), non-motile and non-spore-forming. This organism grew in 0–4.5 % (w/v) NaCl and at 15–37 °C, with optimal growth occurring in 0.5 % (w/v) NaCl and at 30 °C. Comparative 16S rRNA gene sequence analysis revealed that the strain ViU22T belonged to the genus Microbacterium . It exhibited highest 16S rRNA gene sequence similarity with the type strains of Microbacterium testaceum (98.14 %) and Microbacterium binotii (98.02 %). The DNA–DNA relatedness of strains ViU22T with the most closely related type strains Microbacterium testaceum and Microbacterium binotii DSM 19164T was 20.10 % (±0.70) and 28.05 % (±0.35), respectively. Strain ViU22T possessed a type B2β peptidoglycan with partial substitution of glutamic acid by 3-hydroxy glutamic acid. The major menaquinones were MK-11 and MK-12. Major polar lipids detected in the strain ViU22T were diphosphatidylglycerol, phosphatidylglycerol, an unknown phospholipid and unknown glycolipids. The predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, a pattern reported for other Microbacterium species. The major cell-wall sugars were galactose, xylose and mannose and the DNA G+C content was 71 mol%. Together, the DNA–DNA hybridization results and the differentiating phenotypic characteristics, showed that strain ViU22T should be classified as the type strain of a novel species within the genus Microbacterium , for which the name Microbacterium lemovicicum sp. nov. is proposed. The type strain is ViU22T ( = ATCC BAA-2396T = CCUG 62198T = DSM 25044T).

Loktanella sediminilitoris sp. nov., isolated from tidal flat sediment

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4118-4123 ◽  
Author(s):  
Sooyeon Park ◽  
Yong-Taek Jung ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, designated D1-W3T, was isolated from tidal flat sediment of the South Sea, South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain D1-W3T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2 % (w/v) NaCl. Neighbour-joining phylogenetic analyses based on 16S rRNA gene sequences revealed that strain D1-W3T fell within the clade comprising species of the genus Loktanella , clustering with the type strains of Loktanella tamlensis , Loktanella rosea and Loktanella maricola , with which it exhibited the highest 16S rRNA gene sequence similarity values (98.1–98.2 %). The 16S rRNA gene sequence similarity values between strain D1-W3T and the type strains of other species of the genus Loktanella were in the range 93.5–96.5 %. The DNA G+C content of strain D1-W3T was 58.1 mol% and the mean DNA–DNA hybridization values with L. tamlensis KCTC 12722T, L. rosea LMG 22534T and L. maricola DSW-18T were 13–25 %. Strain D1-W3T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, showed that strain D1-W3T could be differentiated from other species of the genus Loktanella . On the basis of the data presented, strain D1-W3T represents a novel species of the genus Loktanella , for which the name Loktanella sediminilitoris sp. nov. is proposed. The type strain is D1-W3T ( = KCTC 32383T = CECT 8284T).

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