Strain identifier

BacDive ID: 13431

Type strain: Yes

Species: Saccharomonospora xinjiangensis

Strain Designation: XJ-54

Strain history: DSM 44391 <-- C.-L. Jiang XJ-54.

NCBI tax ID(s): 882086 (strain), 75294 (species)

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General

@ref: 11512

BacDive-ID: 13431

DSM-Number: 44391

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Saccharomonospora xinjiangensis XJ-54 is a mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
882086strain
75294species

strain history

@refhistory
11512<- C.-L. Jiang; XJ-54
67770DSM 44391 <-- C.-L. Jiang XJ-54.

doi: 10.13145/bacdive13431.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Saccharomonospora
  • species: Saccharomonospora xinjiangensis
  • full scientific name: Saccharomonospora xinjiangensis Jin et al. 1998

@ref: 11512

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Saccharomonospora

species: Saccharomonospora xinjiangensis

full scientific name: Saccharomonospora xinjiangensis Jin et al. 1998 emend. Nouioui et al. 2018

strain designation: XJ-54

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
19661Beige10-14 daysISP 2
19661Beige10-14 daysISP 3
19661Beige10-14 daysISP 4
19661Beige10-14 daysISP 5
19661Beige10-14 daysISP 6
19661Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19661yesAerial MyceliumWhiteISP 2
19661yesAerial MyceliumWhiteISP 3
19661noISP 4
19661yesAerial MyceliumWhiteISP 5
19661yesAerial MyceliumISP 6
19661noISP 7

multimedia

  • @ref: 11512
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44391.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11512CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://mediadive.dsmz.de/medium/83Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water
11512GYM 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
19661ISP 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
19661ISP 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:
19661ISP 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
19661ISP 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
19661ISP 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
19661ISP 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
11512positivegrowth28mesophilic
19661positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2), MK-9(H4), MK-7(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1966117234glucose+
1966122599arabinose-
1966117992sucrose-
1966118222xylose-
1966117268myo-inositol-
1966129864mannitol+
1966128757fructose+
1966126546rhamnose-
1966116634raffinose-
1966162968cellulose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
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
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
19661+++++++++++-+++++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19661-++++-----+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11512soilXinjiangChinaCHNAsia
67770SoilXinjiangChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4969.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_466;97_2158;98_2648;99_4969&stattab=map
  • Last taxonomy: Saccharomonospora xinjiangensis
  • 16S sequence: AJ306300
  • Sequence Identity:
  • Total samples: 274
  • soil counts: 150
  • aquatic counts: 11
  • animal counts: 77
  • plant counts: 36

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115121Risk group (German classification)
196611Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Saccharomonospora xinjiangensis 16S rRNA gene, strain DSM 44391TAJ3063001490ena882086
67770Saccharomonospora xinjiangensis 16S ribosomal RNA gene, partial sequenceAF0567101557ena882086

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharomonospora xinjiangensis XJ-54882086.3wgspatric882086
66792Saccharomonospora xinjiangensis XJ-542509276054draftimg882086
67770Saccharomonospora xinjiangensis XJ-54GCA_000258175scaffoldncbi882086

GC content

  • @ref: 67770
  • GC-content: 68.9
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.031no
flagellatedno96.777no
gram-positiveyes93.66no
anaerobicno98.693no
halophileyes55.745no
spore-formingyes73.683no
thermophileno84.58yes
glucose-utilyes86.682yes
aerobicyes88.322no
glucose-fermentno93.736no

External links

@ref: 11512

culture collection no.: DSM 44391, CCTCC AA 97021, JCM 11270, CGMCC 4.2111

straininfo link

  • @ref: 82624
  • straininfo: 50609

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9828411Description of Saccharomonospora xinjiangensis sp. nov. based on chemical and molecular classification.Jin X, Xu LH, Mao PH, Hseu TH, Jiang CLInt J Syst Bacteriol10.1099/00207713-48-4-10951998Actinomycetales/*classification/isolation & purification/physiology/ultrastructure, Culture Media, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Spores, Bacterial, Terminology as TopicCultivation
Phylogeny18319456Saccharomonospora saliphila sp. nov., a halophilic actinomycete from an Indian soil.Syed DG, Tang SK, Cai M, Zhi XY, Agasar D, Lee JC, Kim CJ, Jiang CL, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.65449-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, *Soil Microbiology, Species SpecificityGenetics
Phylogeny19767358Saccharomonospora marina sp. nov., isolated from an ocean sediment of the East China Sea.Liu Z, Li Y, Zheng LQ, Huang YJ, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.017038-02009Actinomycetales/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11512Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44391)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44391
19661Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44391.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)
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
82624Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50609.1StrainInfo: A central database for resolving microbial strain identifiers