Strain identifier

BacDive ID: 1734

Type strain: Yes

Species: Bifidobacterium scardovii

Strain history: CCUG 13008 A <-- Blood Dept., PHL, Göteborg SBL 0071/83.

NCBI tax ID(s): 1150461 (strain), 158787 (species)

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General

@ref: 5133

BacDive-ID: 1734

DSM-Number: 13734

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, human pathogen

description: Bifidobacterium scardovii DSM 13734 is an anaerobe, mesophilic human pathogen that was isolated from human blood.

NCBI tax id

NCBI tax idMatching level
1150461strain
158787species

strain history

@refhistory
5133<- CCUG <- Blood Dept., PHL, Göteborg; SBL 0071/83
67770CCUG 13008 A <-- Blood Dept., PHL, Göteborg SBL 0071/83.

doi: 10.13145/bacdive1734.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Bifidobacteriales
  • family: Bifidobacteriaceae
  • genus: Bifidobacterium
  • species: Bifidobacterium scardovii
  • full scientific name: Bifidobacterium scardovii Hoyles et al. 2002

@ref: 5133

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium scardovii

full scientific name: Bifidobacterium scardovii Hoyles et al. 2002 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no92.261
69480100positive

Culture and growth conditions

culture medium

  • @ref: 5133
  • name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/58
  • composition: Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water

culture temp

@refgrowthtypetemperaturerange
5133positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
5133anaerobe
69480anaerobe99.998

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.996

murein

  • @ref: 5133
  • murein short key: A11.20
  • type: A3alpha L-Lys-L-Ser-L-Ala2

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose+builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch+builds acid from28017
68371raffinose+builds acid from16634
68371melezitose+builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    45872C10:04.210
    45872C12:03.812
    45872C14:024.814
    45872C16:029.416
    45872C18:02.218
    45872C13:0 3OH/C15:1 i I/H214.469
    45872C16:1 ω9c3.615.774
    45872C17:1 ω9c0.616.773
    45872C18:1 ω9c8.417.769
    45872C18:1 ω9c DMA3.418.226
    45872C18:2 ω6,9c/C18:0 ANTE6.717.724
    45872C19:0 CYCLO ω9c9.218.87
    45872Unidentified0.818.187
    45872Unidentified0.919.329
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
5133----+++---++++---------++++++++++-+++--+++-----+-+/-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
5133human bloodSwedenSWEEurope
45872Human blood,50-yr-old womanSwedenSWEEurope1982-11-22Göteborg
67770Human bloodSwedenSWEEurope

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Blood

taxonmaps

  • @ref: 69479
  • File name: preview.99_1077.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_625;97_728;98_847;99_1077&stattab=map
  • Last taxonomy: Bifidobacterium scardovii subclade
  • 16S sequence: LC383820
  • Sequence Identity:
  • Total samples: 16961
  • soil counts: 172
  • aquatic counts: 130
  • animal counts: 16622
  • plant counts: 37

Safety information

risk assessment

  • @ref: 5133
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium scardovii partial 16S rRNA gene, strain CCUG 13008AJ3070051380ena1150461
20218Bifidobacterium scardovii gene for 16S rRNA, partial sequence, strain: JCM 12489AB507155642ena1150461
67770Bifidobacterium scardovii gene for 16S ribosomal RNA, partial sequenceAB4373631506ena158787
67770Bifidobacterium scardovii JCM 12489 = DSM 13734 gene for 16S ribosomal RNA, partial sequenceLC3838201472ena1150461

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium scardovii JCM 12489 = DSM 13734GCA_001042635completencbi1150461
66792Bifidobacterium scardovii JCM 12489 = DSM 137341150461.4wgspatric1150461
66792Bifidobacterium scardovii JCM 12489 = DSM 137341150461.5completepatric1150461
66792Bifidobacterium scardovii JCM 12489 = DSM 137341150461.3wgspatric1150461
66792Bifidobacterium scardovii DSM 137342651869654draftimg1150461
66792Bifidobacterium scardovii JCM 124892700989372draftimg1150461
67770Bifidobacterium scardovii JCM 12489 = DSM 13734GCA_000770985contigncbi1150461
67770Bifidobacterium scardovii LMG 21589GCA_000741405contigncbi158787
67770Bifidobacterium scardovii JCM 12489 = DSM 13734GCA_001005065contigncbi1150461

GC content

  • @ref: 67770
  • GC-content: 60.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno87no
motileno95.18no
flagellatedno97.093no
gram-positiveyes92.417no
anaerobicyes94.058no
aerobicno94.588yes
halophileno75.324no
spore-formingno94.215no
thermophileno98.7no
glucose-utilyes88.471no
glucose-fermentyes85.778no

External links

@ref: 5133

culture collection no.: DSM 13734, CCUG 13008 A, ATCC BAA 773, JCM 12489, CCM 7209, KCTC 5849

straininfo link

  • @ref: 71381
  • straininfo: 51923

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12054269Bifidobacterium scardovii sp. nov., from human sources.Hoyles L, Inganas E, Falsen E, Drancourt M, Weiss N, McCartney AL, Collins MDInt J Syst Evol Microbiol10.1099/00207713-52-3-9952002Adult, Aged, Aged, 80 and over, Bacterial Typing Techniques, Bifidobacterium/*classification/*genetics, Blood/*microbiology, DNA, Ribosomal/analysis, Female, Hip/*microbiology, Humans, Middle Aged, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Urine/*microbiologyPathogenicity
Phylogeny24867172Bifidobacterium aesculapii sp. nov., from the faeces of the baby common marmoset (Callithrix jacchus).Modesto M, Michelini S, Stefanini I, Ferrara A, Tacconi S, Biavati B, Mattarelli PInt J Syst Evol Microbiol10.1099/ijs.0.056937-02014Aldehyde-Lyases/chemistry, Animals, Bacterial Typing Techniques, Base Composition, Bifidobacterium/*classification/genetics/isolation & purification, Callithrix/*microbiology, DNA, Bacterial/genetics, Feces/*microbiology, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Genetics25858848Complete Genome Sequence of Bifidobacterium scardovii Strain JCM 12489T, Isolated from Human Blood.Toh H, Oshima K, Nakano A, Yamashita N, Iioka E, Kurokawa R, Morita H, Hattori MGenome Announc10.1128/genomeA.00285-152015Phylogeny
Phylogeny27236565Bifidobacterium aerophilum sp. nov., Bifidobacterium avesanii sp. nov. and Bifidobacterium ramosum sp. nov.: Three novel taxa from the faeces of cotton-top tamarin (Saguinus oedipus L.).Michelini S, Modesto M, Filippini G, Spiezio C, Sandri C, Biavati B, Pisi A, Mattarelli PSyst Appl Microbiol10.1016/j.syapm.2016.04.0052016Aldehyde-Lyases/genetics, Animals, Base Composition, Base Sequence, *Bifidobacterium/classification/genetics/isolation & purification, Chaperonin 60/genetics, DNA Primase/genetics, DNA, Bacterial/genetics, DNA-Directed RNA Polymerases/genetics, Feces/microbiology, HSP40 Heat-Shock Proteins/genetics, *Multilocus Sequence Typing, Peptidoglycan/classification/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Saguinus/*microbiology, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5133Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13734)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13734
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
45872Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 13008 A)https://www.ccug.se/strain?id=13008
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/
68371Automatically annotated from API 50CH acid
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)
71381Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID51923.1StrainInfo: A central database for resolving microbial strain identifiers