Strain identifier

BacDive ID: 5813

Type strain: Yes

Species: Blastococcus saxobsidens

Strain history: DSM 44509 <-- C. Urzì BC444.

NCBI tax ID(s): 138336 (species)

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General

@ref: 11833

BacDive-ID: 5813

DSM-Number: 44509

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped, pigmented

description: Blastococcus saxobsidens CCUG 61911 is an aerobe, mesophilic, Gram-positive bacterium that has a pink to orange pigmentation and was isolated from calcarenite MA12.

NCBI tax id

  • NCBI tax id: 138336
  • Matching level: species

strain history

@refhistory
11833<- C. Urzi, Univ. Messina; BC444
67770DSM 44509 <-- C. Urzì BC444.

doi: 10.13145/bacdive5813.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Geodermatophilales
  • family: Geodermatophilaceae
  • genus: Blastococcus
  • species: Blastococcus saxobsidens
  • full scientific name: Blastococcus saxobsidens Urzì et al. 2004

@ref: 11833

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Geodermatophilaceae

genus: Blastococcus

species: Blastococcus saxobsidens

full scientific name: Blastococcus saxobsidens Urzì et al. 2004 emend. Hezbri et al. 2016

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapeconfidence
29959positive1.35 µmcoccus-shaped
69480positive100

colony morphology

  • @ref: 24981
  • colony color: pink to orange

pigmentation

@refproductioncolor
24981yespink to orange
29959yes

multimedia

  • @ref: 11833
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44509.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11833GYM 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
11833LUEDEMANN MEDIUM (LUEDEMANN; 1968) (DSMZ Medium 877)yeshttps://mediadive.dsmz.de/medium/877Name: LUEDEMANN MEDIUM (LUEDEMANN; 1968) (DSMZ Medium 877) Composition: Malt extract broth 15.0 g/l Agar 15.0 g/l Glucose 10.0 g/l Starch 10.0 g/l NaCl 5.0 g/l Yeast extract 5.0 g/l CaCO3 2.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
11833positivegrowth28mesophilic
29959positivegrowth20-37
29959positiveoptimum32mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29959positivegrowth5-8.6alkaliphile
29959positiveoptimum6.8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29959aerobe
62732aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.883

observation

@refobservation
29959aggregates in clumps
67770quinones: MK-9(H4), MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
24981167632-oxobutanoate-oxidation
2498129990D-aspartate-oxidation
2498118024D-galacturonic acid-oxidation
2498116899D-mannitol-oxidation
2498117924D-sorbitol-oxidation
2498123652dextrin-oxidation
2498116537galactarate-oxidation
249815291gelatin-oxidation
2498116977L-alanine-oxidation
2498116467L-arginine-oxidation
2498117309pectin-oxidation
24981370543-hydroxybutyrate+oxidation
2498130612D-glucarate+oxidation
249818391D-gluconate+oxidation
2498128066gentiobiose+oxidation
2498117814salicin+oxidation
2498175229sodium bromate+oxidation
2498117968butyrate+/-oxidation
2498129991L-aspartate+/-oxidation
2498137657methyl D-glucoside+/-oxidation
24981506227N-acetylglucosamine+/-oxidation
2498135418n-acetylneuraminate+/-oxidation
2995917128adipate+carbon source
2995922599arabinose+carbon source
2995923652dextrin+carbon source
2995928757fructose+carbon source
2995924265gluconate+carbon source
2995917234glucose+carbon source
2995917596inosine+carbon source
2995917716lactose+carbon source
2995925115malate+carbon source
2995937684mannose+carbon source
2995917268myo-inositol+carbon source
2995933942ribose+carbon source

enzymes

@refvalueactivityec
24981catalase-1.11.1.6
24981cytochrome oxidase+1.9.3.1
29959alkaline phosphatase+3.1.3.1
29959catalase+1.11.1.6
29959cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
11833calcarenite MA12MaltaMLTEurope
62732Globigerine limestone (calcarenite MA12 in DSMZ)MaltaMLTEuropeSiggiewi
67770LimestoneMaltaMLTEuropeSiggiewi

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3416.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_1096;97_2139;98_2620;99_3416&stattab=map
  • Last taxonomy: Blastococcus
  • 16S sequence: AJ316571
  • Sequence Identity:
  • Total samples: 6625
  • soil counts: 3945
  • aquatic counts: 440
  • animal counts: 1429
  • plant counts: 811

Safety information

risk assessment

  • @ref: 11833
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Blastococcus saxobsidens 16S rRNA gene, type strain DSM 44509TFN6006411510ena138336
11833Blastococcus sp. BC448 16S rRNA geneAJ3165711483ena138336

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Blastococcus saxobsidens strain DSM 44509138336.4wgspatric138336
66792Blastococcus saxobsidens strain DSM 44509138336.5wgspatric138336
66792Blastococcus saxobsidens DSM 445092837591487draftimg138336
66792Blastococcus saxobsidens DSM 445092816332115draftimg138336
67770Blastococcus saxobsidens DSM 44509GCA_002938435contigncbi138336
67770Blastococcus saxobsidens DSM 44509GCA_004217455contigncbi138336

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno60no
motileyes74.892no
gram-positiveyes92.304yes
anaerobicno97.689yes
halophileno78.627no
spore-formingno75.626no
glucose-utilyes88.415no
thermophileno97.451no
aerobicyes89.812yes
flagellatedno91.913no
glucose-fermentno90.85no

External links

@ref: 11833

culture collection no.: CCUG 61911, DSM 44509, JCM 13239, NRRL B-24246, BC 444

straininfo link

@refstraininfo
75293113666
75294410466

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14742489Blastococcus saxobsidens sp. nov., and emended descriptions of the genus Blastococcus Ahrens and Moll 1970 and Blastococcus aggregatus Ahrens and Moll 1970.Urzi C, Salamone P, Schumann P, Rohde M, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.02745-02004Actinomycetales/*classification/genetics/isolation & purification/ultrastructure, Calcium Carbonate, DNA, Bacterial/genetics, Fatty Acids/metabolism, Genotype, Italy, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Terminology as TopicGenetics
Phylogeny17012568Blastococcus jejuensis sp. nov., an actinomycete from beach sediment, and emended description of the genus Blastococcus Ahrens and Moll 1970.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.64268-02006Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, Genotype, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Silicon DioxideGenetics
Phylogeny23475341Blastococcus endophyticus sp. nov., an actinobacterium isolated from Camptotheca acuminata.Zhu WY, Zhang JL, Qin YL, Xiong ZJ, Zhang DF, Klenk HP, Zhao LX, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.049239-02013Actinomycetales/*classification/genetics/isolation & purification, Base Composition, Camptotheca/*microbiology, DNA, Bacterial/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Plant Leaves/microbiology, Plants, Medicinal/microbiology, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny28809149Cumulibacter manganitolerans gen. nov., sp. nov., isolated from sludge of a manganese mine.Huang J, Li J, Cao M, Liao S, Wang GInt J Syst Evol Microbiol10.1099/ijsem.0.0020042017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Manganese, *Mining, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29458502Blastococcus xanthinilyticus sp. nov., isolated from monument.Hezbri K, Nouioui I, Rohde M, Sproer C, Schumann P, Gtari M, Klenk HP, Montero-Calasanz MDC, Ghodhbane-Gtari FInt J Syst Evol Microbiol10.1099/ijsem.0.0026462018Actinomycetales/*classification/genetics/isolation & purification, Architecture, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tunisia, Vitamin K 2/chemistryTranscriptome
Phylogeny29969090Blastococcus atacamensis sp. nov., a novel strain adapted to life in the Yungay core region of the Atacama Desert.Castro JF, Nouioui I, Sangal V, Choi S, Yang SJ, Kim BY, Trujillo ME, Riesco R, Montero-Calasanz MDC, Rahmani TPD, Bull AT, Sutcliffe IC, Asenjo JA, Andrews B, Goodfellow MInt J Syst Evol Microbiol10.1099/ijsem.0.0028282018Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Chile, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
11833Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44509)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44509
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
24981K. L. Hezbri, Moussa,Nouioui, Imen,Gtari, Maher,Rohde, Manfred,Spröer, Cathrin,Schumann, Peter,Klenk, Hans-Peter,Ghodhbane-Gtari, Faten,Montero-Calasanz, Maria del Carmen10.1099/ijsem.0.001443Blastococcus capsensis sp. nov., isolated from an archaeological Roman pool and emended description of the genus Blastococcus, B. aggregatus, B. saxobsidens, B. jejuensis and B. endophyticusIJSEM 66: 4864-4872 201627553620
29959Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126328
62732Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 61911)https://www.ccug.se/strain?id=61911
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/
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
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)
75293Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID113666.1StrainInfo: A central database for resolving microbial strain identifiers
75294Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID410466.1StrainInfo: A central database for resolving microbial strain identifiers