Strain identifier

BacDive ID: 13397

Type strain: Yes

Species: Pseudonocardia endophytica

Strain history: <- S-K Tang, Yunnan Inst. Microbiol, China

NCBI tax ID(s): 401976 (species)

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General

@ref: 12128

BacDive-ID: 13397

DSM-Number: 44969

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

description: Pseudonocardia endophytica DSM 44969 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from pharmaceutical plant Lobelia clavata.

NCBI tax id

  • NCBI tax id: 401976
  • Matching level: species

strain history

@refhistory
12128<- W.-J. Li, YIM <- H.-H. Chen
67770KCTC 19150 <-- S.-K. Tang YIM 56035 <-- H.-H. Chen.
67771<- S-K Tang, Yunnan Inst. Microbiol, China

doi: 10.13145/bacdive13397.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Pseudonocardia
  • species: Pseudonocardia endophytica
  • full scientific name: Pseudonocardia endophytica Chen et al. 2009

@ref: 12128

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia endophytica

full scientific name: Pseudonocardia endophytica Chen et al. 2009

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
31973positive
67771positive
69480no92.274
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19713Gold yellow10-14 daysISP 2
19713Oyster white10-14 daysISP 3
19713Oyster white10-14 daysISP 4
19713Gold yellow10-14 daysISP 5
19713Gold yellow10-14 daysISP 6
19713Oyster white10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19713yesAerial MyceliumCreamISP 2
19713yesAerial MyceliumCreamISP 3
19713yesAerial MyceliumCreamISP 4
19713yesAerial MyceliumCreamISP 5
19713yesAerial MyceliumCreamISP 6
19713yesAerial MyceliumCreamISP 7

pigmentation

  • @ref: 31973
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12128GYM 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
19713ISP 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
19713ISP 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:
19713ISP 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
19713ISP 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
19713ISP 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
19713ISP 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
12128positivegrowth28mesophilic
19713positiveoptimum28mesophilic
31973positivegrowth15-37
31973positiveoptimum26mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepH
31973positivegrowth6.0-8.0
31973positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31973aerobe
67771aerobe

spore formation

@refspore formationconfidence
31973yes
69481yes100

halophily

@refsaltgrowthtested relationconcentration
31973NaClpositivegrowth0-5 %
31973NaClpositiveoptimum2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3197322653asparagine+carbon source
3197328757fructose+carbon source
3197328260galactose+carbon source
3197317234glucose+carbon source
3197329987glutamate+carbon source
3197317754glycerol+carbon source
3197317306maltose+carbon source
3197317272propionate+carbon source
3197333942ribose+carbon source
3197317814salicin+carbon source
3197330911sorbitol+carbon source
3197317992sucrose+carbon source
3197327082trehalose+carbon source

enzymes

@refvalueactivityec
31973catalase+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
19713+++-++---+--+-++---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
12128pharmaceutical plant Lobelia clavataLobelia clavataYunnan Province, XishuangbannaChinaCHNAsia
67771From plantYunnan ProvinceChinaCHNAsia
67770Healthy inner tissue of the traditional Chinese medicinal plant Lobelia clavataLobelia clavataXishuangbanna, Yunnan Province, south-west ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Plant (Factory)
#Infection#Medical product

Safety information

risk assessment

  • @ref: 12128
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12128
  • description: Pseudonocardia endophytica strain YIM 56035 16S ribosomal RNA gene, partial sequence
  • accession: DQ887489
  • length: 1452
  • database: ena
  • NCBI tax ID: 401976

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia endophytica strain DSM 44969401976.4wgspatric401976
66792Pseudonocardia endophytica DSM 449692806310577draftimg401976
67770Pseudonocardia endophytica DSM 44969GCA_004339565contigncbi401976

GC content

@refGC-contentmethod
1212870.3
6777070.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes84.456no
anaerobicno99.043no
halophileno92.877no
spore-formingyes86.754yes
glucose-utilyes88.203yes
aerobicyes94.223yes
thermophileno99.09yes
motileno95.239no
flagellatedno98.393no
glucose-fermentno93.897no

External links

@ref: 12128

culture collection no.: DSM 44969, CCTCC AA 206026, KCTC 19150, YIM 56035, JCM 16220, BCRC 16906

straininfo link

  • @ref: 82594
  • straininfo: 294145

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19244441Pseudonocardia endophytica sp. nov., isolated from the pharmaceutical plant Lobelia clavata.Chen HH, Qin S, Li J, Zhang YQ, Xu LH, Jiang CL, Kim CJ, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.64740-02009Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis/isolation & purification, DNA, Ribosomal/analysis, Genes, rRNA, Lobelia/*microbiology, Medicine, Chinese Traditional, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plants, Medicinal/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityEnzymology
Phylogeny22733061Pseudonocardia nantongensis sp. nov., a novel endophytic actinomycete isolated from the coastal halophyte Tamarix chinensis Lour.Xing K, Qin S, Bian GK, Zhang YJ, Zhang WD, Dai CC, Liu CH, Li WJ, Jiang JHAntonie Van Leeuwenhoek10.1007/s10482-012-9764-52012Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Endophytes/*classification/genetics/*isolation & purification/physiology, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/microbiology, Sequence Analysis, DNA, Tamaricaceae/*microbiology, Ubiquinone/analysisEnzymology
Phylogeny29485391Pseudonocardia soli sp. nov., isolated from mountain soil.Thawai CInt J Syst Evol Microbiol10.1099/ijsem.0.0026722018Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33230720Pseudonocardia cytotoxica sp. nov., a novel actinomycete isolated from an Arctic fjord with potential to produce cytotoxic compound.Dhaneesha M, Umar M, Merlin TS, Krishnan KP, Sukumaran V, Sinha RK, Anas A, Fu P, MacMillan JB, Sajeevan TPAntonie Van Leeuwenhoek10.1007/s10482-020-01490-72020*Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Estuaries, Fatty Acids/analysis, Nucleic Acid Hybridization, Phylogeny, Pseudonocardia, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
12128Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44969)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44969
19713Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44969.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
31973Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2822828776041
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)
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
82594Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID294145.1StrainInfo: A central database for resolving microbial strain identifiers