Strain identifier

BacDive ID: 13467

Type strain: Yes

Species: Saccharopolyspora antimicrobica

Strain Designation: 05-74, I05-00074

Strain history: <- YQ Zhang, Inst. Med. Biotechnol, China

NCBI tax ID(s): 455193 (species)

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General

@ref: 12358

BacDive-ID: 13467

DSM-Number: 45119

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

description: Saccharopolyspora antimicrobica 05-74 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 455193
  • Matching level: species

strain history

@refhistory
12358<- Y.-Q. Zhang; 05-74 <- L.-Y. Yu et al.
67770CCM 7463 <-- Y.-Q. Zhang I05-00074.
67771<- YQ Zhang, Inst. Med. Biotechnol, China

doi: 10.13145/bacdive13467.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Saccharopolyspora
  • species: Saccharopolyspora antimicrobica
  • full scientific name: Saccharopolyspora antimicrobica Yuan et al. 2008

@ref: 12358

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Saccharopolyspora

species: Saccharopolyspora antimicrobica

full scientific name: Saccharopolyspora antimicrobica Yuan et al. 2008 emend. Nouioui et al. 2018

strain designation: 05-74, I05-00074

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
32466positiveno
67771positive
69480positive90.789

colony morphology

@refcolony colorincubation periodmedium used
20166Beige (1001)10-14 daysISP 2
20166Beige (1001)10-14 daysISP 3
20166Beige (1001)10-14 daysISP 4
20166Ochre brown (8001)10-14 daysISP 5
20166Ochre brown (8001)10-14 daysISP 6
20166Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20166noISP 2
20166noISP 3
20166noISP 4
20166noISP 5
20166noISP 6
20166noIPS 7

pigmentation

  • @ref: 32466
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12358GYM 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
12358GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
20166ISP 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
20166ISP 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:
20166ISP 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
20166ISP 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
20166ISP 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
20166ISP 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

@refgrowthtypetemperature
12358positivegrowth28
20166positiveoptimum28
32466positivegrowth20-45
32466positiveoptimum32.5
67770positivegrowth28
67771positivegrowth28-37

culture pH

@refabilitytypepHPH range
32466positivegrowth6-8.5alkaliphile
32466positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32466aerobe
67771aerobe

spore formation

@refspore formationconfidence
32466yes
69480yes90.549

halophily

  • @ref: 32466
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-7 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3246630089acetate+carbon source
3246615963ribitol+carbon source
3246622599arabinose+carbon source
3246617057cellobiose+carbon source
3246616947citrate+carbon source
3246628757fructose+carbon source
3246628260galactose+carbon source
324665417glucosamine+carbon source
3246617234glucose+carbon source
3246617716lactose+carbon source
3246615792malonate+carbon source
3246617306maltose+carbon source
3246629864mannitol+carbon source
3246637684mannose+carbon source
3246628053melibiose+carbon source
3246628044phenylalanine+carbon source
3246616634raffinose+carbon source
3246626546rhamnose+carbon source
3246633942ribose+carbon source
3246617814salicin+carbon source
3246630911sorbitol+carbon source
3246617992sucrose+carbon source
3246618222xylose+carbon source
324664853esculin+hydrolysis
3246617632nitrate+reduction

enzymes

@refvalueactivityec
32466acid phosphatase+3.1.3.2
32466alkaline phosphatase+3.1.3.1
32466alpha-galactosidase+3.2.1.22
32466gelatinase+
32466urease+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

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20166+++++++++++-+-++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12358forest soilTemple of Heaven, BeijingChinaCHNAsia
67770Soil from the Temple of HeavenBeijingChinaCHNAsia
67771From forest soilHebei ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
123581Risk group (German classification)
201661German classification

Sequence information

16S sequences

  • @ref: 12358
  • description: Saccharopolyspora antimicrobica strain I05-00074 16S ribosomal RNA gene, partial sequence
  • accession: EF693956
  • length: 1449
  • database: nuccore
  • NCBI tax ID: 455193

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharopolyspora antimicrobica strain DSM 45119455193.5wgspatric455193
66792Saccharopolyspora antimicrobica DSM 451192627854288draftimg455193
67770Saccharopolyspora antimicrobica DSM 45119GCA_003635025contigncbi455193

GC content

@refGC-contentmethod
1235869.3
6777070.4genome sequence analysis
6777069.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes90.789yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.809no
69480spore-formingspore-formingAbility to form endo- or exosporesyes90.549yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.296yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.75no
69480flagellatedmotile2+Ability to perform flagellated movementno88.194yes

External links

@ref: 12358

culture collection no.: DSM 45119, CCM 7463, KCTC 19303, JCM 16610, CPCC 201024

straininfo link

  • @ref: 82659
  • straininfo: 396626

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18450710Saccharopolyspora antimicrobica sp. nov., an actinomycete from soil.Yuan LJ, Zhang YQ, Guan Y, Wei YZ, Li QP, Yu LY, Li WJ, Zhang YQInt J Syst Evol Microbiol10.1099/ijs.0.65532-02008Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/*classification/genetics/isolation & purification/physiology, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny24510974Saccharopolyspora indica sp. nov., an actinomycete isolated from the rhizosphere of Callistemon citrinus (Curtis).Vaddavalli R, Peddi S, Kothagauni SY, Begum Z, Gaddam B, Periketi M, Linga VRInt J Syst Evol Microbiol10.1099/ijs.0.057539-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, India, Molecular Sequence Data, Myrtaceae/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Saccharopolyspora/*chemistry/genetics/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny30058993Saccharopolyspora maritima sp. nov., an actinomycete isolated from mangrove sediment.Suksaard P, Srisuk N, Duangmal KInt J Syst Evol Microbiol10.1099/ijsem.0.0029412018Avicennia/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Humans, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Thailand, Vitamin K 2/analogs & derivatives/chemistryPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
12358Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45119)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45119
20166Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45119.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
32466Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2868728776041
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
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)
82659Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396626.1StrainInfo: A central database for resolving microbial strain identifiers