Strain identifier

BacDive ID: 15005

Type strain: Yes

Species: Streptomyces atroolivaceus

Strain history: CIP <- 2004, CCUG <- 1981, M. Ridell, Göteborg Univ., Göteborg, Sweden <- S.T. Williams

NCBI tax ID(s): 66869 (species)

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General

@ref: 9339

BacDive-ID: 15005

DSM-Number: 40137

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped

description: Streptomyces atroolivaceus DSM 40137 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 66869
  • Matching level: species

strain history

@refhistory
9339<- E.B. Shirling, ISP <- T.P. Preobrazhenskaya, INA
67770KCC S-0345 <-- IFO 12741 <-- SAJ <-- ISP 5137 <-- INA 4776.
116541CIP <- 2004, CCUG <- 1981, M. Ridell, Göteborg Univ., Göteborg, Sweden <- S.T. Williams

doi: 10.13145/bacdive15005.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kitasatosporales
  • family: Streptomycetaceae
  • genus: Streptomyces
  • species: Streptomyces atroolivaceus
  • full scientific name: Streptomyces atroolivaceus (Preobrazhenskaya et al. 1957) Pridham et al. 1958 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Streptomyces olivoviridis
    20215Actinomyces atroolivaceus
    20215Actinomyces olivoviridis

@ref: 9339

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces atroolivaceus

full scientific name: Streptomyces atroolivaceus (Preobrazhenskaya et al. 1957) Pridham et al. 1958 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
116541positiverod-shapedno
125438positive91.363

colony morphology

  • @ref: 116541
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9339GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
36711MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
116541CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperature
18542positiveoptimum28
9339positivegrowth28
36711positivegrowth25
67770positivegrowth28
116541positivegrowth10-37
116541nogrowth41
116541nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
116541obligate aerobe
125438aerobe91.888

spore formation

  • @ref: 125438
  • spore formation: yes
  • confidence: 93.468

halophily

@refsaltgrowthtested relationconcentration
116541NaClpositivegrowth0-6 %
116541NaClnogrowth8 %
116541NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1854217234glucose+
1854222599arabinose+/-
1854217992sucrose-
1854218222xylose-
1854217268myo-inositol-
1854229864mannitol-
1854228757fructose-
1854226546rhamnose+
1854216634raffinose-
1854262968cellulose-
11654116947citrate-carbon source
1165414853esculin+hydrolysis
116541606565hippurate+hydrolysis
11654117632nitrate-reduction
11654116301nitrite-reduction
11654117632nitrate-respiration
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

antibiotic resistance

  • @ref: 116541
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
11654135581indoleno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11654115688acetoin-
11654117234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
116541oxidase-
116541beta-galactosidase+3.2.1.23
116541alcohol dehydrogenase-1.1.1.1
116541gelatinase+/-
116541amylase+
116541DNase-
116541caseinase-3.4.21.50
116541catalase+1.11.1.6
116541tween esterase+
116541gamma-glutamyltransferase+2.3.2.2
116541lecithinase+
116541lipase-
116541lysine decarboxylase-4.1.1.18
116541ornithine decarboxylase-4.1.1.17
116541phenylalanine ammonia-lyase-4.3.1.24
116541tryptophan deaminase-
116541urease+3.5.1.5
68368urease+3.5.1.5
68382alpha-glucosidase+3.2.1.20
68368gelatinase+
68368tryptophan deaminase+4.1.99.1
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116541-++++++++-++-+-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18542+++++-++-++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116541+++++----++++--++-+++--++------+-+---------+-----+---------++-++-+-----++-++---++--------++-----++-

Isolation, sampling and environmental information

isolation

@refsample typecountrycontinent
9339soilUSSRAsia
67770Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_135.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_120;99_135&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AJ781320
  • Sequence Identity:
  • Total samples: 4030
  • soil counts: 2441
  • aquatic counts: 286
  • animal counts: 1009
  • plant counts: 294

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
93391Risk group (German classification)
185421German classification
1165411Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces atroolivaceus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4345D44064120nuccore66869
20218Streptomyces atroolivaceus strain KCTC 9017 16S ribosomal RNA gene, partial sequenceAY9998321420nuccore66869
20218Streptomyces atroolivaceus 16S rRNA gene, type strain LMG 19306AJ7813201478nuccore66869
20218Streptomyces atroolivaceus gene for 16S rRNA, partial sequence, strain: NBRC 12741AB1841131473nuccore66869

Genome sequences

  • @ref: 67770
  • description: Streptomyces atroolivaceus NRRL ISP-5137
  • accession: GCA_000717025
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 66869

GC content

  • @ref: 67770
  • GC-content: 70.7
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes91.363no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.894yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes91.888yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes93.468no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.5no
125438motile2+flagellatedAbility to perform flagellated movementno88.5no

External links

@ref: 9339

culture collection no.: DSM 40137, ATCC 19725, CBS 464.68, IFO 12741, INA 4776/54, ISP 5137, NBRC 12741, RIA 1006, CCUG 11112, CIP 108257, JCM 4345, BCRC 12073, CECT 3316, CGMCC 4.1405, IMET 43088, INA 4776, LMG 19306, NRRL ISP-5137, VKM Ac-970, VTT E-052933, CBS 464-68, IPV 1612

straininfo link

  • @ref: 84113
  • straininfo: 13329

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism27137499Biosynthetic Genes for the Tetrodecamycin Antibiotics.Gverzdys T, Nodwell JRJ Bacteriol10.1128/JB.00140-162016Anti-Bacterial Agents/*biosynthesis/chemistry, Bacterial Proteins/*genetics/metabolism, Biosynthetic Pathways, Furans/chemistry/metabolism, Multigene Family, Streptomyces/chemistry/genetics/*metabolism
Phylogeny34889725Streptomyces silvae sp. nov., isolated from forest soil.Besaury L, Martinet L, Muhle E, Clermont D, Remond CInt J Syst Evol Microbiol10.1099/ijsem.0.0051472021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, France, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Streptomyces/classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9339Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40137)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40137
18542Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40137.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
36711Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5859
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
84113Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13329.1StrainInfo: A central database for resolving microbial strain identifiers
116541Curators of the CIPCollection of Institut Pasteur (CIP 108257)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108257
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets