Strain identifier

BacDive ID: 15161

Type strain: Yes

Species: Streptomyces flavofungini

Strain Designation: Medipex SA-IX-3

Strain history: KCC S-0753 <-- IFO 13371 <-- SAJ <-- ISP 5366 <-- CBS 411.59 <-- J. Uri and I. Békési SA-IX-3.

NCBI tax ID(s): 68200 (species)

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General

@ref: 9286

BacDive-ID: 15161

DSM-Number: 40366

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

description: Streptomyces flavofungini Medipex SA-IX-3 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from desert sand.

NCBI tax id

  • NCBI tax id: 68200
  • Matching level: species

strain history

@refhistory
9286<- E.B. Shirling, ISP <- CBS <- Uri, Medipex SA-IX-3
67770KCC S-0753 <-- IFO 13371 <-- SAJ <-- ISP 5366 <-- CBS 411.59 <-- J. Uri and I. Békési SA-IX-3.

doi: 10.13145/bacdive15161.20250331.9.3

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 flavofungini
  • full scientific name: Streptomyces flavofungini (ex Úri and Békési 1958) Szabó and Preobrazhenskaya 1986

@ref: 9286

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces flavofungini

full scientific name: Streptomyces flavofungini (ex Úri and Békési 1958) Szabó and Preobrazhenskaya 1986

strain designation: Medipex SA-IX-3

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
125439positive100
12543994.7no
125438positive91.97

colony morphology

@refcolony colorincubation periodmedium used
19446Yellow10-14 daysISP 2
1944610-14 daysISP 3
19446Yellow10-14 daysISP 4
19446Yellow10-14 daysISP 5
19446Yellow10-14 daysISP 6
19446Yellow10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
19446noISP 2
19446yesISP 3Aerial MyceliumWhite
19446yesISP 4Aerial MyceliumWhite
19446noISP 5
19446noISP 6
19446yesISP 7Aerial MyceliumWhite

multimedia

  • @ref: 9286
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40366.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9286GYM 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
19446ISP 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
19446ISP 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:
19446ISP 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
19446ISP 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
19446ISP 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
19446ISP 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
9286STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium252.pdf

culture temp

@refgrowthtypetemperature
19446positiveoptimum28
9286positivegrowth28
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 99.4

spore formation

@refspore descriptionspore formationconfidence
19446spore chains: very short, spore surface: smoothyes
125439yes96.5
125438yes93.742

compound production

@refcompound
9286flavofungin
20216Flavofungin

halophily

  • @ref: 19446
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1944662968cellulose+
1944616634raffinose-
1944626546rhamnose-
1944628757fructose+/-
1944629864mannitol+
1944617268myo-inositol-
1944618222xylose-
1944617992sucrose-
1944622599arabinose-
1944617234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refmetaboliteproductionChebi-ID
67770flavofunginyes
68368acetoinno15688
68368indoleno35581
68368hydrogen sulfideno16136

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19446++++--+---+

Isolation, sampling and environmental information

isolation

@refsample type
9286desert sand
67770Desert sand

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Desert
#Environmental#Terrestrial#Sandy
#Condition#Xerophilic

taxonmaps

  • @ref: 69479
  • File name: preview.99_4034.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_91;97_287;98_3057;99_4034&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AB184359
  • Sequence Identity:
  • Total samples: 91
  • soil counts: 70
  • aquatic counts: 4
  • animal counts: 16
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
92861Risk group (German classification)
194461Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces flavofungini gene for 16S ribosomal RNA, partial sequence, strain: JCM 4753D44335120nuccore68200
20218Streptomyces flavofungini gene for 16S rRNA, partial sequence, strain: NBRC 13371AB1843591475nuccore68200
20218Streptomyces flavofungini strain NRRL B-12307 16S ribosomal RNA gene, partial sequenceAY9997921078nuccore68200

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces flavofungini JCM 4753GCA_014650815scaffoldncbi68200
66792Streptomyces flavofungini JCM 4753GCA_016411765scaffoldncbi68200
66792Streptomyces flavofungini strain JCM 475368200.3wgspatric68200
66792Streptomyces flavofungini strain JCM 475368200.4wgspatric68200

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes91.97no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.357no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.628no
125438spore-formingspore-formingAbility to form endo- or exosporesyes93.742yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.5yes
125438motile2+flagellatedAbility to perform flagellated movementno87no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes96.5
125439BacteriaNetmotilityAbility to perform movementno94.7
125439BacteriaNetgram_stainReaction to gram-stainingpositive100
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.4

External links

@ref: 9286

culture collection no.: DSM 40366, ATCC 27430, CBS 411.59, CBS 672.72, IFO 13371, ISP 5366, JCM 4753, NBRC 13371, RIA 1332, BCRC 15154, LMG 8598, NRRL B-12307, VKM Ac-1179

straininfo link

  • @ref: 84265
  • straininfo: 45803

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20525816Streptomyces tacrolimicus sp. nov., a low producer of the immunosuppressant tacrolimus (FK506).Martinez-Castro M, Barreiro C, Romero F, Fernandez-Chimeno RI, Martin JFInt J Syst Evol Microbiol10.1099/ijs.0.024273-02010DNA, Bacterial/genetics, Immunosuppressive Agents/*metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Streptomyces/*classification/genetics/*isolation & purification/metabolism, Tacrolimus/*metabolismMetabolism
Phylogeny26449519Streptomyces alfalfae sp. nov. and comparisons with its closest taxa Streptomyces silaceus, Streptomyces flavofungini and Streptomyces intermedius.She W, Sun Z, Yi L, Zhao S, Liang YInt J Syst Evol Microbiol10.1099/ijsem.0.0006712015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Medicago/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny28005517Streptomyces lasiicapitis sp. nov., an actinomycete that produces kanchanamycin, isolated from the head of an ant (Lasius fuliginosus L.).Ye L, Zhao S, Li Y, Jiang S, Zhao Y, Li J, Yan K, Wang X, Xiang W, Liu CInt J Syst Evol Microbiol10.1099/ijsem.0.0017562017Animals, Ants/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classification/genetics/isolation & purificationTranscriptome
Phylogeny28920834Streptomyces xylanilyticus sp. nov., isolated from soil.Moonmangmee D, Kanchanasin P, Phongsopitanun W, Tanasupawat S, Moonmangmee SInt J Syst Evol Microbiol10.1099/ijsem.0.0022822017Bacterial Typing Techniques, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33774760Streptomyces typhae sp. nov., a novel endophytic actinomycete with antifungal activity isolated the root of cattail (Typha angustifolia L.).Peng C, Zhuang X, Gao C, Wang Z, Zhao J, Huang SX, Liu C, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-021-01561-32021*Actinobacteria, Antifungal Agents, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Streptomyces/genetics, *Typhaceae, Vitamin K 2Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9286Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40366)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40366
19446Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40366.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
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
84265Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45803.1StrainInfo: A central database for resolving microbial strain identifiers
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