Strain identifier

BacDive ID: 16454

Type strain: Yes

Species: Streptomyces xiamenensis

Strain Designation: 318

Strain history: CGMCC 4.3534 <-- J. Xu MCCC 1A01550.

NCBI tax ID(s): 408015 (species)

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General

@ref: 10658

BacDive-ID: 16454

DSM-Number: 41903

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

description: Streptomyces xiamenensis 318 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from mangrove sediment.

NCBI tax id

  • NCBI tax id: 408015
  • Matching level: species

strain history

@refhistory
10658<- J. Xu; 318
67770CGMCC 4.3534 <-- J. Xu MCCC 1A01550.

doi: 10.13145/bacdive16454.20230509.8.1

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 xiamenensis
  • full scientific name: Streptomyces xiamenensis Xu et al. 2009

@ref: 10658

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces xiamenensis

full scientific name: Streptomyces xiamenensis Xu et al. 2009

strain designation: 318

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
28885positiveno
69480no91.007
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19533Grey brown10-14 daysISP 2
19533Grey brown10-14 daysISP 3
19533Quarts grey10-14 daysISP 4
19533Ivory10-14 daysISP 5
19533Chestnut brown10-14 daysISP 6
19533Ivory10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19533yesAerial MyceliumCreamISP 2
19533yesAerial MyceliumCreamISP 3
19533yesAerial MyceliumISP 4
19533noISP 5
19533noISP 6
19533noISP 7

multimedia

  • @ref: 10658
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_41903.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10658GYM 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
19533ISP 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
19533ISP 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:
19533ISP 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
19533ISP 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
19533ISP 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
19533ISP 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
10658ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
10658STARCH - 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

culture temp

@refgrowthtypetemperaturerange
10658positivegrowth28mesophilic
19533positiveoptimum28mesophilic
28885positivegrowth28-37mesophilic
28885positiveoptimum32.5mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 28885
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
28885yes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
28885NaClpositivegrowth0-5 %
28885NaClpositiveoptimum2.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2888522599arabinose+carbon source
2888529864mannitol+carbon source
2888537684mannose+carbon source
2888526546rhamnose+carbon source
2888533942ribose+carbon source
2888517992sucrose+carbon source
2888517632nitrate+reduction

enzymes

@refvalueactivityec
28885gelatinase+
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
19533++++++---++-+-++-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10658mangrove sedimentFujian Province, XiamenChinaCHNAsia
67770Mangrove sediment from the national mangrove reserveFujian ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Mangrove
#Environmental#Aquatic#Sediment
#Host#Plants#Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_5379.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_2607;97_3192;98_4009;99_5379&stattab=map
  • Last taxonomy: Streptomyces xiamenensis subclade
  • 16S sequence: EF012099
  • Sequence Identity:
  • Total samples: 2367
  • soil counts: 1224
  • aquatic counts: 365
  • animal counts: 473
  • plant counts: 305

Safety information

risk assessment

  • @ref: 10658
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 10658
  • description: Streptomyces xiamenensis strain MCCC 1A01550 16S ribosomal RNA gene, partial sequence
  • accession: EF012099
  • length: 1493
  • database: ena
  • NCBI tax ID: 408015

Genome sequences

  • @ref: 66792
  • description: Streptomyces xiamenensis MCCC 1A01550
  • accession: GCA_000993785
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 408015

GC content

@refGC-contentmethod
1065871.6
6777071.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.431yes
motileno92.431yes
motileno92.431yes
flagellatedno97.278yes
flagellatedno97.278yes
flagellatedno97.278yes
gram-positiveyes90.155yes
gram-positiveyes90.155yes
gram-positiveyes90.155yes
anaerobicno99.235yes
anaerobicno99.235yes
anaerobicno99.235yes
aerobicyes91.651yes
aerobicyes91.651yes
aerobicyes91.651yes
halophileno78.367no
halophileno78.367no
halophileno78.367no
spore-formingyes94.643yes
spore-formingyes94.643yes
spore-formingyes94.643yes
thermophileno94.594no
thermophileno94.594no
thermophileno94.594no
glucose-utilyes89.257no
glucose-utilyes89.257no
glucose-utilyes89.257no
glucose-fermentno87.326no
glucose-fermentno87.326no
glucose-fermentno87.326no

External links

@ref: 10658

culture collection no.: DSM 41903, CGMCC 4.3534, MCCC 1A01550, JCM 16123

straininfo link

  • @ref: 85491
  • straininfo: 396830

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19244424Streptomyces xiamenensis sp. nov., isolated from mangrove sediment.Xu J, Wang Y, Xie SJ, Xu J, Xiao J, Ruan JSInt J Syst Evol Microbiol10.1099/ijs.0.000497-02009Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal Spacer/analysis, Genes, rRNA, *Geologic Sediments, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, *Rhizophoraceae, Sequence Analysis, DNA, Spores, Bacterial/physiology, Streptomyces/classification/genetics/isolation & purification/physiologyGenetics
Phylogeny23584286Streptomyces harbinensis sp. nov., an endophytic, ikarugamycin-producing actinomycete isolated from soybean root [Glycine max (L.) Merr].Liu C, Wang X, Zhao J, Liu Q, Wang L, Guan X, He H, Xiang WInt J Syst Evol Microbiol10.1099/ijs.0.050088-02013Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Lactams/*metabolism, Likelihood Functions, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soybeans/*microbiology, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
10658Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41903)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41903
19533Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM41903.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
28885Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2532528776041
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/
68382Automatically annotated from API zym
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
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
85491Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396830.1StrainInfo: A central database for resolving microbial strain identifiers