Strain identifier

BacDive ID: 16167

Type strain: Yes

Species: Streptomyces netropsis

Strain Designation: 4779

Strain history: CIP <- 2003, JCM <- 1983, KCC <- IFO <- SAJ <- ISP <- J. Routien: strain 4779

NCBI tax ID(s): 55404 (species)

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General

@ref: 9413

BacDive-ID: 16167

DSM-Number: 40259

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

description: Streptomyces netropsis 4779 is an aerobe, spore-forming, mesophilic bacterium that was isolated from Soil.

NCBI tax id

  • NCBI tax id: 55404
  • Matching level: species

strain history

@refhistory
9413<- E.B. Shirling, ISP <- J. Routien, Chas. Pfizer and Co., Inc. F. D. 4779
67770KCC S-0063 <-- H. Yonehara <-- NRRL 2268 <-- Chas. Pfizer & Co.; 2937 (J. Routien 4779).
121277CIP <- 2003, JCM <- 1983, KCC <- IFO <- SAJ <- ISP <- J. Routien: strain 4779

doi: 10.13145/bacdive16167.20250331.9.3

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 netropsis
  • full scientific name: Streptomyces netropsis (Finlay et al. 1951) Witt and Stackebrandt 1991

  • synonyms

    @refsynonym
    20215Streptomyces flavopersicus
    20215Streptomyces kentuckensis
    20215Streptoverticillium syringium
    20215Streptomyces syringium
    20215Streptomyces colombiensis
    20215Streptomyces distallicus
    20215Streptoverticillium flavopersicum
    20215Streptoverticillium kentuckense
    20215Streptoverticillium distallicum
    20215Streptomyces netropsis
    20215Streptoverticillium netropsis
    20215Streptomyces syringius

@ref: 9413

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces netropsis

full scientific name: Streptomyces netropsis (Finlay et al. 1951) Witt and Stackebrandt 1991

strain designation: 4779

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
125439positive99.6
125438positive90.026
121277positivefilament-shapedno

colony morphology

  • @ref: 121277
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9413GYM 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
33206MEDIUM 56 - for Micromonospora purpureayesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (10.000g);Yeast extract (5.000 g);Starch maize (20.000 g);Calcium carbonate (1.000 g);Casamino acids (5.000 g)
9413ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf
121277CIP Medium 56yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=56

culture temp

@refgrowthtypetemperature
9413positivegrowth28
33206positivegrowth30
67770positivegrowth28
121277positivegrowth25-37
121277nogrowth10
121277nogrowth41
121277nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
121277obligate aerobe
125438aerobe91.099
125439obligate aerobe97.2

spore formation

  • @ref: 125438
  • spore formation: yes
  • confidence: 92.547

compound production

@refcompound
9413netropsin
20216Netropsin

halophily

@refsaltgrowthtested relationconcentration
121277NaClpositivegrowth0-4 %
121277NaClnogrowth6 %
121277NaClnogrowth8 %
121277NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H8), MK-9(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12127716947citrate-carbon source
1212774853esculin-hydrolysis
121277606565hippurate+hydrolysis
12127717632nitrate-reduction
12127716301nitrite-reduction
12127717632nitrate-respiration

antibiotic resistance

  • @ref: 121277
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refmetaboliteproductionChebi-ID
67770netropsinyes
121277indoleno35581

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12127715688acetoin-
12127717234glucose-

enzymes

@refvalueactivityec
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382acid phosphatase+3.1.3.2
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121277oxidase-
121277beta-galactosidase+3.2.1.23
121277alcohol dehydrogenase-1.1.1.1
121277gelatinase+
121277amylase+
121277DNase+
121277caseinase+3.4.21.50
121277catalase+1.11.1.6
121277tween esterase+
121277gamma-glutamyltransferase+2.3.2.2
121277lecithinase+
121277lipase-
121277lysine decarboxylase-4.1.1.18
121277ornithine decarboxylase-4.1.1.17
121277phenylalanine ammonia-lyase-4.3.1.24
121277protease+
121277tryptophan deaminase-
121277urease+3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121277-+++-+++++++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121277++-++----+---------+-----------++----------------++--+-----++-----------++-----++---+-+-++++-++--+-

Isolation, sampling and environmental information

isolation

@refsample type
67770Soil
121277Environment, Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
94131Risk group (German classification)
1212771Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces netropsis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4063D43995120nuccore55404
20218Streptomyces netropsis gene for 16S rRNA, partial sequence, strain: NBRC 12893AB1848481473nuccore55404
20218Streptomyces netropsis gene for 16S rRNA, partial sequence, strain: NBRC 3723AB1847921475nuccore55404
20218Streptomyces netropsis strain NRRL 2268 16S ribosomal RNA gene, partial sequenceAY9999211318nuccore55404

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces netropsis JCM 4063GCA_014648835scaffoldncbi55404
66792Streptomyces netropsis CECT 3265GCA_014203545scaffoldncbi55404
66792Streptomyces netropsis strain CECT 326555404.10wgspatric55404
66792Streptomyces netropsis strain JCM 406355404.11wgspatric55404
66792Streptomyces netropsis CECT 32652863263905draftimg55404

GC content

  • @ref: 67770
  • GC-content: 71.5

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes90.026no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.42yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes91.099yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes92.547no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.5yes
125438motile2+flagellatedAbility to perform flagellated movementno89no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes86.3
125439BacteriaNetmotilityAbility to perform movementno88.8
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.2

External links

@ref: 9413

culture collection no.: DSM 40259, ATCC 23940, CBS 924.68, ETH 15974, IFO 12893, IPV 1720, IPV 880, ISP 5259, JCM 4063, JCM 4655, NBRC 12893, NRRL B-2268, RIA 1184, BCRC 13374, CECT 3265, CIP 108153, HUT 6086, IFM 1035, IFO 3723, LMG 5979, NBRC 3723, NCB 266, NCIMB 9592, NRRL 2268, PCM 2251, RIA 605, VKM Ac-820, CCRC 13374, KCC S-0655

straininfo link

  • @ref: 85232
  • straininfo: 389372

literature

  • topic: Phylogeny
  • Pubmed-ID: 29464542
  • title: Streptomyces tunisialbus sp. nov., a novel Streptomyces species with antimicrobial activity.
  • authors: Ayed A, Slama N, Mankai H, Bachkouel S, ElKahoui S, Tabbene O, Limam F
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-018-1046-4
  • year: 2018
  • mesh: Anti-Infective Agents/isolation & purification/*pharmacology, Bacteria/drug effects, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Fungi/drug effects, Genes, Bacterial/genetics, Genome, Bacterial, Lavandula/*microbiology, Nucleic Acid Hybridization, Phenotype, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Soil Microbiology, Streptomyces/*chemistry/*classification/genetics/physiology, Tunisia, Vitamin K 2/chemistry
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9413Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40259)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40259
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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
33206Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5744
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
85232Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389372.1StrainInfo: A central database for resolving microbial strain identifiers
121277Curators of the CIPCollection of Institut Pasteur (CIP 108153)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108153
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
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1