Reclassification of Streptomyces hygroscopicus subsp. glebosus and Streptomyces libani subsp. rufus as later heterotypic synonyms of Streptomyces platensis

Komaki, Hisayuki; Tamura, Tomohiko

doi:10.1099/ijsem.0.004279

“…Conventionally, 16S rRNA gene sequence analysis has been employed for bacterial classification; however, owing to the high similarities among Streptomyces species, their classification is considerably complicated and still needs to be extensively studied [1][2][3][4][5][6][7][8][9]. Previous studies have often reported that species of the genus Streptomyces are overclassified [10][11][12][13][14][15][16]. DNA-DNA relatedness is presently used as the ultimate means to define bacterial species [17,18].…”

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confidence: 99%

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

Komaki

¹

2021

International Journal of Systematic and Evolutionary Microbiology

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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 .

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“…Average nucleotide identities were calculated by ANI Calculator [15]. Evolutionary distance in MLSA using atpD , gyrB , recA , rpoB and trpB genes was calculated as reported previously [2–4]. Accession numbers of these genes were as follows: atpD , JOAK01000005 and BNDV01000002; gyrB , JOAK01000001 and BNDV01000016; recA , JOAK01000010 and BNDV01000002; rpoB , JOAK01000021 and BNDV01000002; trpB .…”

Section: Full-textmentioning

confidence: 99%

“…Recently, although 16S rRNA gene sequence analysis has been conventionally employed, the classifications are still complicated due to high sequence similarities among the members in addition to the phenotypic diversities. It has been revealed that many species of the genus Streptomyces had been indeed overclassified in the past and should be reclassified as synonyms [1][2][3][4][5][6][7]. DNA-DNA relatedness is an ultimate means to define bacterial species [8] and recent availability of whole genome sequences enables us to calculate the accurate relatedness digitally [9,10], which makes bacterial identification clearer than before.…”

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confidence: 99%

Reclassification of Streptomyces cinnamonensis as a later heterotypic synonym of Streptomyces virginiae

Komaki

¹

,

Tamura

²

2021

International Journal of Systematic and Evolutionary Microbiology

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We studied the taxonomic relationship between Streptomyces cinnamonensis and Streptomyces virginiae . These type strains shared the same 16S rRNA gene sequence. Phylogenomic analysis supported them being closely related. Digital DNA–DNA relatedness and average nucleotide identity using whole genome sequences indicated that the two species represent the same genomospecies. They shared similar phenotypic characteristics and harboured the same set of secondary metabolite-biosynthetic gene clusters for polyketides and nonribosomal peptides in the genomes. Therefore, according to Rule 24b of the Bacteriological Code, S. cinnamonensis Okami 1952, 572AL (Approved Lists 1980) should be reclassified as a later heterotypic synonym of S. virginiae Grundy et al. 1952, 399AL (Approved Lists 1980) emend. Nouioui et al. 2018. Although 16S rRNA gene sequences were identical among type strains of Streptomyces xanthophaeus , Streptomyces spororaveus and Streptomyces nojiriensis and between those of Streptomyces vinaceus and Streptomyces cirratus , respectively, digital DNA–DNA relatedness indicated that these species are not synonymous.

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“…But their morphologies and products are so diverse that they seem to be overclassified. It is often reported that distinct species sharing the same 16S rRNA gene sequence should be reclassified as synonyms [1–9]. Nowadays, in addition to 16S rRNA gene sequence analysis, molecular-based classification such as multilocus sequence analysis (MLSA) and digital DNA–DNA hybridization using whole genome sequences can be commonly employed for classification of bacterial species [10–13], which makes the bacterial identification clearer than before [14, 15].…”

Section: Full-textmentioning

confidence: 99%

“…It is well known that resolution of 16S rRNA gene sequence similarities are not enough to identify species [16]. We have examined whether Streptomyces species sharing the same 16S rRNA gene sequence are synonyms in recent years [1–7]. Through the studies, results of strains showing 99.93 % similarities (differing in one nucleotide sequence) have been also accumulated as summarized in .…”

Section: Full-textmentioning

confidence: 99%

Reclassification of 15 Streptomyces species as synonyms of Streptomyces albogriseolus, Streptomyces althioticus, Streptomyces anthocyanicus, Streptomyces calvus, Streptomyces griseoincarnatus, Streptomyces mutabilis, Streptomyces pilosus or Streptomyces rochei

Komaki

¹

2019

International Journal of Systematic and Evolutionary Microbiology

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Taxonomic relationships in eight sets of Streptomyces species, (1a) Streptomyces enissocaesilis, Streptomyces plicatus, Streptomyces rochei and Streptomyces vinaceusdrappus , (1b) Streptomyces geysiriensis, (2) Streptomyces luteus and Streptomyces mutabilis, (3) Streptomyces flavoviridis and Streptomyces pilosus, (4) Streptomyces asterosporus and Streptomyces calvus, (5) Streptomyces erythrogriseus, Streptomyces griseoincarnatus, Streptomyces labedae and Streptomyces variabilis , (6a) Streptomyces griseorubens, (6b) Streptomyces matensis, (6c) Streptomyces althioticus, (7) Streptomyces albogriseolus and Streptomyces viridodiastaticus , (8a) Streptomyces humiferus and Streptomyces violaceolatus, (8b) Streptomyces anthocyanicus, Streptomyces coelescens and Streptomyces violaceoruber, were investigated. Type strains within each subset of 1a to 8b shared completely identical 16S rRNA gene sequences. In MLSA, subsets 1a and 1b, 6a to 6c, and 8a and 8b formed an independent clade, respectively, but the evolutionary distances between S. violaceoruber and the other members in set 8 and between S. griseorubens and those in set 6 were 0.022–0.023 and 0.0064–0.0076, respectively. Members in each of the other sets, except for S. labedae , formed an independent clade. In each clade, evolutionary distances between/among the members were <0.007 except for that between S. griseorubens and S. matensis in set 6, suggesting the same species. Digital DNA–DNA relatedness using whole genome sequences and phenotypic similarities supported the synonymies of sets 1 to 3, set 4 except for S. labedae , sets 5 to 7, and set 8 except for S. violaceoruber , respectively. Therefore, S. enissocaesilis, S. geysiriensis, S. plicatus and S. vinaceusdrappus were considered as later heterotypic synonyms of S. rochei; S. luteus as that of S. mutabilis; S. flavoviridis as that of S. pilosus; S. asterosporus as that of S. calvus; S. erythrogriseus and S. variabilis as those of S. griseoincarnatus; S. griseorubens and S. matensis as that of S. althioticus; S. viridodiastaticus as that of S. albogriseolus; S. coelescens, S. humiferus and S. violaceolatus as those of S. anthocyanicus .

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Reclassification of Streptomyces hygroscopicus subsp. glebosus and Streptomyces libani subsp. rufus as later heterotypic synonyms of Streptomyces platensis

Abstract: We investigated the taxonomic relationships among Streptomyces hygroscopicus subsp. … Show more

Cited by 17 publications

References 33 publications

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

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

Reclassification of Streptomyces cinnamonensis as a later heterotypic synonym of Streptomyces virginiae

Reclassification of 15 Streptomyces species as synonyms of Streptomyces albogriseolus, Streptomyces althioticus, Streptomyces anthocyanicus, Streptomyces calvus, Streptomyces griseoincarnatus, Streptomyces mutabilis, Streptomyces pilosus or Streptomyces rochei

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