Strain identifier

BacDive ID: 23260

Type strain: No

Species: Sphingobacterium spiritivorum

Strain Designation: D7529, F8081

Strain history: CIP <- 1989, NCTC: strain F8081 <- CDC: strain D7529

NCBI tax ID(s): 258 (species)

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General

@ref: 18918

BacDive-ID: 23260

DSM-Number: 11687

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, Gram-negative

description: Sphingobacterium spiritivorum D7529 is an obligate aerobe, Gram-negative bacterium that was isolated from sputum.

NCBI tax id

  • NCBI tax id: 258
  • Matching level: species

strain history

@refhistory
18918<- IFO <- NCTC <- CDC
67770IAM 14314 <-- IFO 14975 <-- NCTC 12113 <-- CDC D7529.
123266CIP <- 1989, NCTC: strain F8081 <- CDC: strain D7529

doi: 10.13145/bacdive23260.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Sphingobacterium
  • species: Sphingobacterium spiritivorum
  • full scientific name: Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983

  • synonyms

    @refsynonym
    20215Flavobacterium spiritivorum
    20215Flavobacterium yabuuchiae

@ref: 18918

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Sphingobacterium

species: Sphingobacterium spiritivorum

full scientific name: Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983 emend. Lai et al. 2016

strain designation: D7529, F8081

type strain: no

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
123266negativerod-shapedno
69480negative99.604

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18918NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
35537MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123266CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
123266CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
18918positivegrowth28
35537positivegrowth30
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

  • @ref: 123266
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12326617632nitrate-reduction
12326616301nitrite-reduction

metabolite production

  • @ref: 123266
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
123266oxidase+
123266catalase+1.11.1.6
123266urease+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

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123266-+++-++-+-+++--+++-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
18918sputumUSAUSANorth America
48559Human sputumUSAUSANorth America
123266Human, SputumUnited States of AmericaUSANorth AmericaMaine

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_3331.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15366;96_1738;97_2079;98_2555;99_3331&stattab=map
  • Last taxonomy: Sphingobacterium spiritivorum subclade
  • 16S sequence: AB680729
  • Sequence Identity:
  • Total samples: 7762
  • soil counts: 926
  • aquatic counts: 1560
  • animal counts: 4723
  • plant counts: 553

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
189182Risk group (German classification)
1232661Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingobacterium spiritivorum gene for 16S rRNA, partial sequence, strain: NBRC 14975AB6807291448nuccore258
20218Flavobacterium yabuuchiae 16S ribosomal RNAD140211272nuccore258

Genome sequences

  • @ref: 66792
  • description: Sphingobacterium spiritivorum strain FDAARGOS_1145
  • accession: 258.10
  • assembly level: complete
  • database: patric
  • NCBI tax ID: 258

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno99.604no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.644no
69480spore-formingspore-formingAbility to form endo- or exosporesno85.812no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.269yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.981yes
69480flagellatedmotile2+Ability to perform flagellated movementno85.5no

External links

@ref: 18918

culture collection no.: DSM 11687, CDC D7529, IFO 14975, NBRC 14975, NCTC 12113, CCUG 26765, LMG 11523, JCM 21154, IAM 14314, CIP 103339

straininfo link

  • @ref: 87483
  • straininfo: 13932

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
18918Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11687)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11687
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
35537Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15126
48559Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 26765)https://www.ccug.se/strain?id=26765
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
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)
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
87483Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13932.1StrainInfo: A central database for resolving microbial strain identifiers
123266Curators of the CIPCollection of Institut Pasteur (CIP 103339)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103339