Strain identifier

BacDive ID: 16999

Type strain: Yes

Species: Actinomadura flavalba

Strain history: DSM 45200 <-- S.-K. Tang <-- S. Qin et al. YIM 61435.

NCBI tax ID(s): 561175 (strain), 1120938 (species)

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General

@ref: 15712

BacDive-ID: 16999

DSM-Number: 45200

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

description: Actinomadura flavalba DSM 45200 is an aerobe, spore-forming, mesophilic bacterium that was isolated from surface-sterilized leaves of Maytenus austroyunnanensis from tropical rainforest.

NCBI tax id

NCBI tax idMatching level
561175strain
1120938species

strain history

@refhistory
15712<- S.-K. Tang, YIM; YIM 61435 <- S. Qin and et al.
67770DSM 45200 <-- S.-K. Tang <-- S. Qin et al. YIM 61435.

doi: 10.13145/bacdive16999.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Thermomonosporaceae
  • genus: Actinomadura
  • species: Actinomadura flavalba
  • full scientific name: Actinomadura flavalba Qin et al. 2009

@ref: 15712

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura flavalba

full scientific name: Actinomadura flavalba Qin et al. 2009 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29310positive5 µm0.6 µmrod-shapedno
69480no94.474
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
20179Signal yellow (1003)10-14 daysISP 2
20179Light ivory (1015)10-14 daysISP 3
20179Light ivory (1015)10-14 daysISP 4
20179Daffodil yellow (1007)/Oyster white (1013)10-14 daysISP 5
20179Ivory (1014)10-14 daysISP 6
20179Light ivory (1015)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20179noISP 2
20179noISP 3
20179noISP 4
20179noISP 5
20179noISP 6
20179noISP 7

pigmentation

  • @ref: 29310
  • production: no

multimedia

  • @ref: 15712
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45200.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15712GPHF-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
20179ISP 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
20179ISP 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:
20179ISP 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
20179ISP 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
20179ISP 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
20179ISP 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
15712N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
15712TRYPTICASE 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

culture temp

@refgrowthtypetemperaturerange
15712positivegrowth28mesophilic
20179positiveoptimum28mesophilic
29310positivegrowth15-37
29310positiveoptimum28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
29310positivegrowth6.0-8.0
29310positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29310
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29310yes
69481yes100
69480yes100

halophily

  • @ref: 29310
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

@refobservation
29310aggregates in chains
67770quinones: MK-9(H4), MK-9(H6), MK-9(H2), MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2017917234glucose+
2017922599arabinose-
2017917992sucrose-
2017918222xylose-
2017917268myo-inositol-
2017929864mannitol-
2017928757fructose-
2017926546rhamnose-
2017916634raffinose-
2017962968cellulose-
2931028757fructose+carbon source
2931028260galactose+carbon source
293105291gelatin+carbon source
2931017234glucose+carbon source
2931017596inosine+carbon source
2931017716lactose+carbon source
2931017306maltose+carbon source
2931026546rhamnose+carbon source
2931033942ribose+carbon source
2931030911sorbitol+carbon source
2931017992sucrose+carbon source
2931027082trehalose+carbon source
293104853esculin+hydrolysis

enzymes

@refvalueactivityec
29310alkaline phosphatase+3.1.3.1
29310gelatinase+
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
20179++++++++-++-+-++---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
15712surface-sterilized leaves of Maytenus austroyunnanensis from tropical rainforestMaytenus austroyunnanensisXishuangbanna, Yunnan ProvinceChinaCHNAsia
67770Surface-sterilized leaves of Maytenus austroyunnanensis from a tropical rainforestMaytenus austroyunnanensisXishuangbanna, Yunnan Province, south-west ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Leaf (Phyllosphere)
#Host Body-Site#Plant#Sterilized plant part
#Climate#Hot#Tropical

Safety information

risk assessment

  • @ref: 15712
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15712
  • description: Actinomadura flavalba DSM 45200 strain YIM 61435 16S ribosomal RNA gene, partial sequence
  • accession: FJ157185
  • length: 1451
  • database: ena
  • NCBI tax ID: 561175

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura flavalba DSM 45200561175.3wgspatric561175
66792Actinomadura flavalba DSM 452002518645623draftimg561175
67770Actinomadura flavalba DSM 45200GCA_000374305scaffoldncbi561175

GC content

@refGC-contentmethod
1571271.1high performance liquid chromatography (HPLC)
2931071.1
6777073.3genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes91.26yes
anaerobicno98.332yes
halophileno87.31no
spore-formingyes91.46no
glucose-utilyes86.796no
thermophileno97.569yes
aerobicyes90.691yes
motileno94.854no
flagellatedno98.385yes
glucose-fermentno90.307no

External links

@ref: 15712

culture collection no.: DSM 45200, CCTCC AA 208017, JCM 16896, YIM 61435

straininfo link

  • @ref: 86001
  • straininfo: 404791

literature

  • topic: Phylogeny
  • Pubmed-ID: 19622664
  • title: Actinomadura flavalba sp. nov., an endophytic actinomycete isolated from leaves of Maytenus austroyunnanensis.
  • authors: Qin S, Zhao GZ, Li J, Zhu WY, Xu LH, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.010652-0
  • year: 2009
  • mesh: Actinomycetales/classification/cytology/genetics/*isolation & purification, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Maytenus/*microbiology, Molecular Sequence Data, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Spores, Bacterial/cytology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15712Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45200)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45200
20179Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45200.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
29310Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2572328776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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)
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
86001Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404791.1StrainInfo: A central database for resolving microbial strain identifiers