Strain identifier

BacDive ID: 16786

Type strain: Yes

Species: Desmospora activa

Strain history: <- A. F. Yassin; IMMIB L-1269

NCBI tax ID(s): 1121389 (strain), 500615 (species)

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General

@ref: 15478

BacDive-ID: 16786

DSM-Number: 45169

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

description: Desmospora activa DSM 45169 is an aerobe, spore-forming, mesophilic human pathogen that was isolated from sputa from a patient with suspected pulmonary tuberculosis.

NCBI tax id

NCBI tax idMatching level
500615species
1121389strain

strain history

  • @ref: 15478
  • history: <- A. F. Yassin; IMMIB L-1269

doi: 10.13145/bacdive16786.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Thermoactinomycetaceae
  • genus: Desmospora
  • species: Desmospora activa
  • full scientific name: Desmospora activa Yassin et al. 2009

@ref: 15478

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Thermoactinomycetaceae

genus: Desmospora

species: Desmospora activa

full scientific name: Desmospora activa Yassin et al. 2009

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
28910positive
69480positive100

colony morphology

  • @ref: 60792
  • incubation period: 3 days

pigmentation

  • @ref: 28910
  • production: no

multimedia

  • @ref: 15478
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45169.jpg
  • caption: Medium 535a 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15478COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
15478TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a)yeshttps://mediadive.dsmz.de/medium/535aName: TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a) Composition: None 50.0 g/l Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
15478ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
15478CZAPEK 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
15478TRYPTICASE 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
15478positivegrowth37mesophilic
28910positivegrowth30-50
28910positiveoptimum40thermophilic
60792positivegrowth42thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
28910aerobe
60792microaerophile

spore formation

@refspore formationconfidence
28910yes
69481yes100
69480yes100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2891030089acetate+carbon source
2891016449alanine+carbon source
2891029016arginine+carbon source
2891016947citrate+carbon source
2891028260galactose+carbon source
289105291gelatin+carbon source
2891024265gluconate+carbon source
2891017234glucose+carbon source
2891024996lactate+carbon source
2891017716lactose+carbon source
2891026271proline+carbon source
2891017822serine+carbon source
2891030911sorbitol+carbon source
2891017992sucrose+carbon source
2891027082trehalose+carbon source
2891016199urea+carbon source
2891018222xylose+carbon source
289104853esculin+hydrolysis

enzymes

@refvalueactivityec
28910catalase+1.11.1.6
28910urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
15478sputa from a patient with suspected pulmonary tuberculosisGermanyDEUEurope
60792Human sputumGermanyDEUEurope1995Bonn

isolation source categories

Cat1Cat2Cat3
#Infection#Disease#Tuberculosis
#Infection#Patient
#Host Body Product#Fluids#Sputum

Safety information

risk assessment

  • @ref: 15478
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15478
  • description: Desmospora activa partial 16S rRNA gene, type strain IMMIB L-1269T
  • accession: AM940019
  • length: 1522
  • database: ena
  • NCBI tax ID: 500615

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Desmospora activa DSM 45169GCA_003046315contigncbi1121389
66792Desmospora activa DSM 451691121389.3wgspatric1121389
66792Desmospora activa DSM 451692784132155draftimg1121389
66792Desmospora activa DSM 451692737471615draftimg1121389

GC content

  • @ref: 15478
  • GC-content: 49.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno79.79no
flagellatedno89.763no
gram-positiveyes87.354yes
anaerobicno98.805no
aerobicyes94.493no
halophileno55.42no
spore-formingyes94.019yes
thermophileyes86.114no
glucose-utilyes87.537yes
glucose-fermentno91.573no

External links

@ref: 15478

culture collection no.: DSM 45169, CCUG 55916, IMMIB L-1269

straininfo link

  • @ref: 85802
  • straininfo: 404189

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19244421Desmospora activa gen. nov., sp. nov., a thermoactinomycete isolated from sputum of a patient with suspected pulmonary tuberculosis, and emended description of the family Thermoactinomycetaceae Matsuo et al. 2006.Yassin AF, Hupfer H, Klenk HP, Siering CInt J Syst Evol Microbiol10.1099/ijs.0.001362-02009Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Gram-Positive Bacterial Infections/*microbiology, Gram-Positive Endospore-Forming Bacteria/*classification/genetics/*isolation & purification/physiology, Humans, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Sputum/*microbiologyPathogenicity
Phylogeny25249565Salinithrix halophila gen. nov., sp. nov., a halophilic bacterium in the family Thermoactinomycetaceae.Zarparvar P, Amoozegar MA, Nikou MM, Schumann P, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.064766-02014Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Iran, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, WetlandsGenetics
Phylogeny27671055Paludifilum halophilum gen. nov., sp. nov., a thermoactinomycete isolated from superficial sediment of a solar saltern.Frikha-Dammak D, Fardeau ML, Cayol JL, Ben Fguira-Fourati L, Najeh S, Ollivier B, Maalej SInt J Syst Evol Microbiol10.1099/ijsem.0.0015232016Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Tunisia, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15478Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45169)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45169
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
28910Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2534928776041
60792Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55916)https://www.ccug.se/strain?id=55916
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
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
85802Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404189.1StrainInfo: A central database for resolving microbial strain identifiers