Strain identifier

BacDive ID: 16128

Type strain: Yes

Species: Streptomyces xanthochromogenes

Strain history: KCC S-0215 <-- Y. Okami (NIHJ 196) <-- Meiji Seika Kaisha, Ltd.; 689.

NCBI tax ID(s): 67384 (species)

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General

@ref: 9322

BacDive-ID: 16128

DSM-Number: 40111

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

description: Streptomyces xanthochromogenes DSM 40111 is a spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 67384
  • Matching level: species

strain history

@refhistory
9322<- E.B. Shirling, ISP <- T. Niida, Meiji Seika Kaisha Ltd., 689
67770KCC S-0215 <-- Y. Okami (NIHJ 196) <-- Meiji Seika Kaisha, Ltd.; 689.

doi: 10.13145/bacdive16128.20230509.8.1

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 xanthochromogenes
  • full scientific name: Streptomyces xanthochromogenes Arishima et al. 1956 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Streptomyces michiganensis

@ref: 9322

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces xanthochromogenes

full scientific name: Streptomyces xanthochromogenes Arishima et al. 1956

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.131
69480100positive

Culture and growth conditions

culture medium

  • @ref: 9322
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
9322positivegrowth28mesophilic
18537positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9322xanthicin (anti-fungal)
67770Xanthicin

halophily

  • @ref: 18537
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1853717234glucose+
1853722599arabinose-
1853717992sucrose-
1853718222xylose+
1853717268myo-inositol-
1853729864mannitol-
1853728757fructose+
1853726546rhamnose-
1853716634raffinose-
1853762968cellulose-
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

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

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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18537---------+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
9322soilJapanJPNAsia
67770SoilJapanJPNAsiaKawaji, Tochigi Pref.

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
93221Risk group (German classification)
185371German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces xanthochromogenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 4612D44264120ena67384
20218Streptomyces xanthochromogenes gene for 16S rRNA, partial sequence, strain: NBRC 12828AB1841761469ena67384
20218Streptomyces xanthochromogenes strain NRRL B-5410T 16S ribosomal RNA gene, partial sequenceDQ4425591473ena67384

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces xanthochromogenes JCM 4612GCA_014650455scaffoldncbi67384
66792Streptomyces xanthochromogenes strain JCM 461267384.3wgspatric67384

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno98.1no
gram-positiveyes87.991no
anaerobicno98.935no
aerobicyes90.051no
halophileno93.351no
spore-formingyes95.589no
glucose-utilyes88.168no
thermophileno99.143yes
motileno93.428no
glucose-fermentno88.843no

External links

@ref: 9322

culture collection no.: DSM 40111, ATCC 19818, CBS 571.68, DSM 2015, IFO 12828, ISP 5111, JCM 4215, JCM 4612, KCC S-0215, NBRC 12828, NIHJ 196, RIA 1098, BCRC 11876, CGMCC 4.1435, KCTC 19954, NRRL B-5410, VKM Ac-1071

straininfo link

  • @ref: 85193
  • straininfo: 13364

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23340665Streptomyces hundungensis sp. nov., a novel actinomycete with antifungal activity and plant growth promoting traits.Nimaichand S, Tamrihao K, Yang LL, Zhu WY, Zhang YG, Li L, Tang SK, Ningthoujam DS, Li WJJ Antibiot (Tokyo)10.1038/ja.2012.1192013Amino Acids/analysis, Antifungal Agents/metabolism/pharmacology, DNA, Bacterial/genetics, Microscopy, Electron, Scanning, Phenotype, Plant Growth Regulators/metabolism/pharmacology, RNA, Ribosomal, 16S/genetics, Streptomyces/chemistry/genetics/isolation & purification/*metabolism/ultrastructureMetabolism
Biotechnology26543270Strain Improvement of Streptomyces xanthochromogenes RIA 1098 for Enhanced Pravastatin Production at High Compactin Concentrations.Dzhavakhiya VV, Voinova TM, Glagoleva EV, Petukhov DV, Ovchinnikov AI, Kartashov MI, Kuznetsov BB, Skryabin KGIndian J Microbiol10.1007/s12088-015-0537-52015
Phylogeny34382928Streptomyces genisteinicus sp. nov., a novel genistein-producing actinomycete isolated from a Chinese medicinal plant and proposal of Streptomyces michiganensis Corbaz et al. 1957 as a later heterotypic synonym of Streptomyces xanthochromogenes Arishima et al. 1956.Hu S, Li K, Wang Y, Guo Y, Zhou M, Tang X, Gao JInt J Syst Evol Microbiol10.1099/ijsem.0.0049542021Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genistein/*metabolism, Nucleic Acid Hybridization, *Phylogeny, Plant Leaves/microbiology, Plants, Medicinal/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Streptomyces/classification/isolation & purification, Xanthium/*microbiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9322Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40111)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40111
18537Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40111.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
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
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
85193Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13364.1StrainInfo: A central database for resolving microbial strain identifiers