Strain identifier

BacDive ID: 16464

Type strain: Yes

Species: Streptomyces xinghaiensis

Strain Designation: S187

Strain history: <- WJ Li, Yunnan Inst. Microbiol., China

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

@ref: 17319

BacDive-ID: 16464

DSM-Number: 42015

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

description: Streptomyces xinghaiensis S187 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from marine sediment sample.

NCBI tax id

NCBI tax idMatching level
1038929strain
1038928species

strain history

@refhistory
17319<- S.-K. Tang, Yunnan Univ., Yunnan Inst. Microbiol. (YIM), Kunming, China; S187 <- X.-Q. Zhao
67770KCTC 19546 <-- X.-Q. Zhao et al. S187.
67771<- WJ Li, Yunnan Inst. Microbiol., China

doi: 10.13145/bacdive16464.20230509.8.1

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 xinghaiensis
  • full scientific name: Streptomyces xinghaiensis Zhao et al. 2009

@ref: 17319

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces xinghaiensis

full scientific name: Streptomyces xinghaiensis Zhao et al. 2009

strain designation: S187

type strain: yes

Morphology

cell morphology

@refgram stainmotility
29266positiveno
67771positive

colony morphology

@refcolony colorincubation periodmedium used
19835Maize yellow10-14 daysISP 2
19835Signal yellow10-14 daysISP 3
19835Oyster white10-14 daysISP 4
19835Ivory10-14 daysISP 5
19835Signal yellow10-14 daysISP 6
19835Oyster white10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19835yesAerial MyceliumMaize yellowISP 2
19835noISP 3
19835noISP 4
19835noISP 5
19835yesAerial MyceliumChrome yellowISP 6
19835noISP 7

pigmentation

  • @ref: 29266
  • production: yes

multimedia

  • @ref: 17319
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_42015.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17319GYM 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
19835ISP 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
19835ISP 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:
19835ISP 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
19835ISP 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
19835ISP 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
19835ISP 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

culture temp

@refgrowthtypetemperaturerange
17319positivegrowth28mesophilic
19835positiveoptimum28mesophilic
29266positivegrowth10-45
29266positiveoptimum28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29266positivegrowth06-09alkaliphile
29266positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29266aerobe
67771aerobe

spore formation

  • @ref: 29266
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
29266NaClpositivegrowth0-9 %
29266NaClpositiveoptimum2.5 %

observation

@refobservation
29266aggregates in chains
67770quinones: MK-9(H6), MK-9(H8), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2926628757fructose+carbon source
2926628260galactose+carbon source
2926617234glucose+carbon source
2926629864mannitol+carbon source
2926637684mannose+carbon source
2926628044phenylalanine+carbon source
2926626546rhamnose+carbon source
2926633942ribose+carbon source
2926617822serine+carbon source
2926617992sucrose+carbon source

enzymes

@refvalueactivityec
29266catalase+1.11.1.6
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

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19835+++-++---++++-+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17319marine sediment sampleDalian, Xinghai BayChinaCHNAsia
67770Marine sediment from Xinghai BayDalian, Liaoning ProvinceChinaCHNAsia
67771From marine sedimentDalianChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

Safety information

risk assessment

  • @ref: 17319
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17319
  • description: Streptomyces sp. S187 16S ribosomal RNA gene, partial sequence
  • accession: EF577247
  • length: 1490
  • database: ena
  • NCBI tax ID: 1038929

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces xinghaiensis S187GCA_000220705completencbi1038929
66792Streptomyces xinghaiensis S1871038929.3wgspatric1038929

GC content

@refGC-contentmethod
1731972.01
6777072.01high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.898yes
motileno92.898yes
flagellatedno97.99yes
flagellatedno97.99yes
gram-positiveyes92.155yes
gram-positiveyes92.155yes
anaerobicno98.32yes
anaerobicno98.32yes
aerobicyes90.339yes
aerobicyes90.339yes
halophileno85.517no
halophileno85.517no
spore-formingyes94.257yes
spore-formingyes94.257yes
glucose-utilyes87.544yes
glucose-utilyes87.544yes
thermophileno96.348yes
thermophileno96.348yes
glucose-fermentno87.889no
glucose-fermentno87.889no

External links

@ref: 17319

culture collection no.: DSM 42015, CCTCC AA 208049, KCTC 19546, NRRL B-24674, JCM 16958

straininfo link

  • @ref: 85500
  • straininfo: 405633

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19628610Streptomyces xinghaiensis sp. nov., isolated from marine sediment.Zhao XQ, Li WJ, Jiao WC, Li Y, Yuan WJ, Zhang YQ, Klenk HP, Suh JW, Bai FWInt J Syst Evol Microbiol10.1099/ijs.0.009878-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Streptomyces/classification/genetics/*isolation & purification/metabolismMetabolism
Phylogeny24814337Streptomyces chumphonensis sp. nov., isolated from marine sediments.Phongsopitanun W, Thawai C, Suwanborirux K, Kudo T, Ohkuma M, Tanasupawat SInt J Syst Evol Microbiol10.1099/ijs.0.062992-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Streptomyces/*classification/genetics/isolation & purification, Thailand, Vitamin K 2/analogs & derivatives/chemistryGenetics
Metabolism24903341Fluoroacetate biosynthesis from the marine-derived bacterium Streptomyces xinghaiensis NRRL B-24674.Huang S, Ma L, Tong MH, Yu Y, O'Hagan D, Deng HOrg Biomol Chem10.1039/c4ob00970c2014Fluoroacetates/*metabolism, Magnetic Resonance Spectroscopy, Streptomyces/*metabolism, Threonine/analogs & derivatives/metabolism, Transaldolase/genetics, *Water Microbiology
Phylogeny27405543Streptomyces palmae sp. nov., isolated from oil palm (Elaeis guineensis) rhizosphere soil.Sujarit K, Kudo T, Ohkuma M, Pathom-Aree W, Lumyong SInt J Syst Evol Microbiol10.1099/ijsem.0.0012982016Arecaceae/*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/chemistryTranscriptome
Genetics30232534Genome mining of Streptomyces xinghaiensis NRRL B-24674(T) for the discovery of the gene cluster involved in anticomplement activities and detection of novel xiamycin analogs.Chen LY, Wang XQ, Wang YM, Geng X, Xu XN, Su C, Yang YL, Tang YJ, Bai FW, Zhao XQAppl Microbiol Biotechnol10.1007/s00253-018-9337-22018Amino Acid Sequence, Bacterial Proteins/*genetics/metabolism, Complement Inactivator Proteins/*biosynthesis/chemistry, *Genome, Bacterial, Molecular Sequence Data, Molecular Structure, *Multigene Family, Phylogeny, Sequence Alignment, Sesquiterpenes/chemistry/*metabolism, Streptomyces/chemistry/classification/*genetics/metabolismMetabolism
Phylogeny30303472Streptomyces durbertensis sp. nov., isolated from saline-alkali soil.Yu Y, Fu Y, Guo X, Yan R, Wang H, Zhao J, Wang X, Zhang J, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0030472018Alkalies, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17319Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 42015)https://www.dsmz.de/collection/catalogue/details/culture/DSM-42015
19835Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM42015.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
29266Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2568428776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68382Automatically annotated from API zym
85500Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405633.1StrainInfo: A central database for resolving microbial strain identifiers