Strain identifier

BacDive ID: 16395

Type strain: Yes

Species: Streptomyces sodiiphilus

Strain history: CIP <- 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 80305

NCBI tax ID(s): 226217 (species)

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General

@ref: 10622

BacDive-ID: 16395

DSM-Number: 41839

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

description: Streptomyces sodiiphilus DSM 41839 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 226217
  • Matching level: species

strain history

@refhistory
10622<- W.-J. Li, YIM
331852003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 80305
67770CIP 107975 <-- W.-J. Li YIM 80305.
122648CIP <- 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 80305

doi: 10.13145/bacdive16395.20230509.8.1

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 sodiiphilus
  • full scientific name: Streptomyces sodiiphilus Li et al. 2005

@ref: 10622

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces sodiiphilus

full scientific name: Streptomyces sodiiphilus Li et al. 2005

type strain: yes

Morphology

cell morphology

@refgram stainmotilitycell shape
31389positiveno
122648positivenorod-shaped

colony morphology

  • @ref: 122648

pigmentation

  • @ref: 31389
  • production: yes

multimedia

  • @ref: 10622
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_41839.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10622TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
33185MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
10622STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://mediadive.dsmz.de/medium/252Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water
10622GYM 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
122648CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
10622positivegrowth28mesophilic
31389positiveoptimum28mesophilic
33185positivegrowth30mesophilic
67770positivegrowth28mesophilic
122648positivegrowth25-37mesophilic
122648nogrowth10psychrophilic
122648nogrowth41thermophilic
122648nogrowth45thermophilic

culture pH

@refabilitytypepH
31389positivegrowth7.0-8.0
31389positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31389aerobe
122648obligate aerobe

spore formation

  • @ref: 31389
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
31389NaClpositiveoptimum3 %
122648NaClpositivegrowth0 %
122648NaClnogrowth2 %
122648NaClnogrowth4 %
122648NaClnogrowth6 %
122648NaClnogrowth8 %
122648NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H6), MK-9(H4), MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3138930089acetate+carbon source
3138926546rhamnose+carbon source
3138917632nitrate+reduction
12264816947citrate-carbon source
1226484853esculin+hydrolysis
122648606565hippurate+hydrolysis
12264817632nitrate+reduction
12264816301nitrite-reduction

metabolite production

  • @ref: 122648
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12264815688acetoin-
12264817234glucose-

enzymes

@refvalueactivityec
31389gelatinase+
122648oxidase-
122648alcohol dehydrogenase-1.1.1.1
122648gelatinase+
122648catalase+1.11.1.6
122648gamma-glutamyltransferase-2.3.2.2
122648lysine decarboxylase-4.1.1.18
122648ornithine decarboxylase-4.1.1.17
122648tryptophan deaminase-
122648urease-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
122648-+++++-----+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
10622soilQinghaj ProvinceChinaCHNAsia
67770Muddy saline-alkaline soil near Chaka salt lakeQinghai ProvinceChinaCHNAsia
122648Environment, SoilQinghaiChinaCHNAsia2002

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
106221Risk group (German classification)
1226481Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31389
  • description: Streptomyces sodiiphilus strain YIM 80305 16S ribosomal RNA gene, partial sequence
  • accession: AY236339
  • length: 1489
  • database: nuccore
  • NCBI tax ID: 226217

GC content

@refGC-contentmethod
1062270.5
6777070.5thermal denaturation, midpoint method (Tm)

External links

@ref: 10622

culture collection no.: DSM 41839, CCTCC AA 203015, CIP 107975, YIM 80305, JCM 13581

straininfo link

  • @ref: 85445
  • straininfo: 134257

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15879277Streptomyces sodiiphilus sp. nov., a novel alkaliphilic actinomycete.Li WJ, Zhang YG, Zhang YQ, Tang SK, Xu P, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.63457-02005Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, Bacterial, Genes, rRNA, Geologic Sediments/*microbiology, Growth Inhibitors/pharmacology, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, Pigments, Biological/biosynthesis, Potassium/pharmacology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/pharmacology, Streptomyces/*classification/cytology/*isolation & purification/physiology, *Water MicrobiologyEnzymology
Phylogeny19329599Streptomyces nanshensis sp. nov., isolated from the Nansha Islands in the South China Sea.Tian XP, Zhang YQ, Li QX, Zhi XY, Tang SK, Zhang S, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.003442-02009Bacterial Typing Techniques, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Streptomyces/*classification/genetics/*isolation & purification/physiology, Vitamin K 2/analysisGenetics
Phylogeny21571936Streptomyces panacagri sp. nov., isolated from soil of a ginseng field.Cui Y, Baek SH, Wang L, Lee HG, Cui C, Lee ST, Im WTInt J Syst Evol Microbiol10.1099/ijs.0.029942-02011Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny25269462Streptomyces bohaiensis sp. nov., a novel actinomycete isolated from Scomberomorus niphonius in the Bohai Sea.Pan HQ, Cheng J, Zhang DF, Yu SY, Khieu TN, Son CK, Jiang Z, Hu JC, Li WJJ Antibiot (Tokyo)10.1038/ja.2014.1372014Animals, Base Composition/genetics, Carbohydrates/chemistry, Fatty Acids/chemistry, Lipids/chemistry, Multilocus Sequence Typing, Oceans and Seas, Perciformes/*microbiology, Phylogeny, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, RNA/methods, Streptomyces/*classification/genetics/isolation & purificationTranscriptome
Phylogeny25391353Streptomyces alkalithermotolerans sp. nov., a novel alkaliphilic and thermotolerant actinomycete isolated from a soda lake.Sultanpuram VR, Mothe T, Mohammed FAntonie Van Leeuwenhoek10.1007/s10482-014-0332-z2014Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, India, Lakes/*microbiology, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classification/genetics/*isolation & purification/physiologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
10622Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41839)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41839
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
31389Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2770028776041
33185Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5545
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
85445Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134257.1StrainInfo: A central database for resolving microbial strain identifiers
122648Curators of the CIPCollection of Institut Pasteur (CIP 107975)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107975