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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 9652

BacDive-ID: 16172

DSM-Number: 40571

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, rod-shaped, antibiotic compound production

description: Streptomyces orinoci 1882 is an obligate aerobe, mesophilic, Gram-positive 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/bacdive16172.20230509.8.1

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

@refgrowthtypetemperaturerange
9652positivegrowth28mesophilic
19477positiveoptimum28mesophilic
33204positivegrowth30mesophilic
67770positivegrowth28mesophilic
121441positivegrowth25-45
121441nogrowth10psychrophilic

Physiology and metabolism

tolerance

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

oxygen tolerance

  • @ref: 121441
  • oxygen tolerance: obligate aerobe

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 sequenceAB122735564ena67339
20218Streptomyces orinoci gene for 16S ribosomal RNA, partial sequence, strain: JCM 4546D44225120ena67339
20218Streptomyces orinoci gene for 16S rRNA, partial sequence, strain: NBRC 13466AB1848661469ena67339
20218Streptomyces orinoci strain NRRL B-3379T 16S ribosomal RNA gene, partial sequenceDQ4425361492ena67339

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

traitpredictionconfidencetraining_data
flagellatedno98.497no
gram-positiveyes89.875no
anaerobicno99.227no
halophileno94.988no
spore-formingyes93.283no
glucose-utilyes89.918no
aerobicyes89.588no
thermophileno96.584yes
motileno93.46no
glucose-fermentno88.639no

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
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