Strain identifier

BacDive ID: 16172

Type strain: Yes

Species: Streptomyces orinoci

Strain Designation: 1882, FI 1882

Strain history: CIP <- 2003, JCM <- 1983, KCC <- IFO <- SAJ <- ISP <- B. Camerino: strain FI 1882

NCBI tax ID(s): 67339 (species)

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General

@ref: 9652

BacDive-ID: 16172

DSM-Number: 40571

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, antibiotic compound production

description: Streptomyces orinoci 1882 is an obligate aerobe, spore-forming bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

  • NCBI tax id: 67339
  • Matching level: species

strain history

@refhistory
9652<- E.B. Shirling, ISP <- B. Camerino, Farmitalia, 1882 FI
67770KCC S-0546 <-- IPV 1901 <-- Farmitalia FI 1882.
121441CIP <- 2003, JCM <- 1983, KCC <- IFO <- SAJ <- ISP <- B. Camerino: strain FI 1882

doi: 10.13145/bacdive16172.20240916.9.1

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 orinoci
  • full scientific name: Streptomyces orinoci (Cassinelli et al. 1967) Witt and Stackebrandt 1991

  • synonyms

    • @ref: 20215
    • synonym: Streptoverticillium orinoci

@ref: 9652

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces orinoci

full scientific name: Streptomyces orinoci (Cassinelli et al. 1967) Witt and Stackebrandt 1991

strain designation: 1882, FI 1882

type strain: yes

Morphology

cell morphology

  • @ref: 121441
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19477Broom yellow10-14 daysISP 2
19477Yellow10-14 daysISP 3
19477Yellow10-14 daysISP 4
19477Curry10-14 daysISP 5
19477Yellow10-14 daysISP 6
19477Yellow10-14 daysISP 7
121441

multicellular morphology

@refforms multicellular complexmedium name
19477noISP 2
19477noISP 3
19477noISP 4
19477noISP 5
19477noISP 6
19477noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9652GYM 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
19477ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19477ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19477ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19477ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19477ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19477ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
33204MEDIUM 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)
9652ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf
121441CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121441CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperature
9652positivegrowth28
19477positiveoptimum28
33204positivegrowth30
67770positivegrowth28
121441positivegrowth25-45
121441nogrowth10

Physiology and metabolism

tolerance

  • @ref: 19477
  • compound: Lysozyme
  • percentage: 1

oxygen tolerance

  • @ref: 121441
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: yes
  • confidence: 90.41

compound production

@refcompound
9652neoantimycin
9652neoaureothin
9652ochramycin
20216Neoantimycin
20216neoaureothin
20216ochramycin
19477Neoaureothin
19477Neoanthimycin
67770neoaureothricin
67770ochramycin

halophily

@refsaltgrowthtested relationconcentration
19477NaClpositivemaximum2.5 %
121441NaClpositivegrowth0-2 %
121441NaClnogrowth4 %
121441NaClnogrowth6 %
121441NaClnogrowth8 %
121441NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1947762968cellulose+/-
1947716634raffinose+/-
1947726546rhamnose+/-
1947728757fructose+/-
1947729864mannitol+/-
1947717268myo-inositol+/-
1947718222xylose+/-
1947717992sucrose+/-
1947722599arabinose+/-
1947717234glucose+/-
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
12144116947citrate-carbon source
1214414853esculin-hydrolysis
121441606565hippurate+hydrolysis
12144117632nitrate-reduction
12144116301nitrite-reduction
12144117632nitrate-respiration

antibiotic resistance

  • @ref: 121441
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refmetaboliteproductionChebi-ID
67770neoantimycinyes
68368acetoinyes15688
68368indoleno35581
68368hydrogen sulfideyes16136
121441indoleno35581

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12144115688acetoin-
12144117234glucose-

enzymes

@refvalueactivityec
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23
121441oxidase-
121441beta-galactosidase-3.2.1.23
121441alcohol dehydrogenase-1.1.1.1
121441gelatinase-
121441amylase-
121441DNase-
121441caseinase-3.4.21.50
121441catalase+1.11.1.6
121441tween esterase-
121441gamma-glutamyltransferase+2.3.2.2
121441lecithinase-
121441lipase-
121441lysine decarboxylase-4.1.1.18
121441ornithine decarboxylase-4.1.1.17
121441phenylalanine ammonia-lyase-4.3.1.24
121441tryptophan deaminase-
121441urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121441-+-+-+----+---------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19477-+++++---+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121441+/----------+/-----------+/----------+/------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121441+-++-------+-------+-----------+---------------------------++-----------++++--+----------+++-++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountrycontinent
9652soil
67770SoilOrinoco RiverSouth America
121441Environment, SoilOrinoco riverSouth AmericaMiddle and South America

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
96521Risk group (German classification)
194771Risk group (German classification)
1214411Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces orinoci gene for 16S rRNA, partial sequenceAB122735564nuccore67339
20218Streptomyces orinoci gene for 16S ribosomal RNA, partial sequence, strain: JCM 4546D44225120nuccore67339
20218Streptomyces orinoci gene for 16S rRNA, partial sequence, strain: NBRC 13466AB1848661469nuccore67339
20218Streptomyces orinoci strain NRRL B-3379T 16S ribosomal RNA gene, partial sequenceDQ4425361492nuccore67339

Genome sequences

  • @ref: 67770
  • description: Streptomyces orinoci NRRL B-3379
  • accession: GCA_003121295
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 67339

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes87.746no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no92.542yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes87.742yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes90.41no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.5yes
69480flagellatedmotile2+Ability to perform flagellated movementno88no

External links

@ref: 9652

culture collection no.: DSM 40571, ATCC 23202, CBS 767.72, IFO 13466, IPV 1901, ISP 5571, JCM 4546, JCM 4807, NBRC 13466, NRRL B-3379, RIA 1427, BCRC 15173, CECT 3267, CGMCC 4.1989, CIP 108141, IFM 1226, KCTC 9870, VKM Ac-929, KCC S-0807

straininfo link

  • @ref: 85237
  • straininfo: 389361

literature

  • topic: Phylogeny
  • Pubmed-ID: 27405543
  • title: Streptomyces palmae sp. nov., isolated from oil palm (Elaeis guineensis) rhizosphere soil.
  • authors: Sujarit K, Kudo T, Ohkuma M, Pathom-Aree W, Lumyong S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001298
  • year: 2016
  • mesh: Arecaceae/*microbiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Thailand, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9652Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40571)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40571
19477Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40571.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
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
33204Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5731
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
85237Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389361.1StrainInfo: A central database for resolving microbial strain identifiers
121441Curators of the CIPCollection of Institut Pasteur (CIP 108141)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108141