Strain identifier

BacDive ID: 1700

Type strain: No

Species: Bifidobacterium indicum

Strain Designation: C-215

Strain history: ATCC 25911 <-- V. Scardovi C-215 (Bifidobacterium indicum).

NCBI tax ID(s): 1687 (species)

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General

@ref: 8610

BacDive-ID: 1700

DSM-Number: 20216

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

description: Bifidobacterium indicum C-215 is an anaerobe, mesophilic bacterium that was isolated from hindgut of honeybee.

NCBI tax id

  • NCBI tax id: 1687
  • Matching level: species

strain history

@refhistory
8610<- V. Scardovi, C-215
67770ATCC 25911 <-- V. Scardovi C-215 (Bifidobacterium indicum).

doi: 10.13145/bacdive1700.20230509.8.1

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 indicum
  • full scientific name: Bifidobacterium indicum Scardovi and Trovatelli 1969 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bifidobacterium coryneforme

@ref: 8610

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium indicum

full scientific name: Bifidobacterium indicum Scardovi and Trovatelli 1969 emend. Nouioui et al. 2018

strain designation: C-215

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no90.972
69480100positive

Culture and growth conditions

culture medium

  • @ref: 8610
  • 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
8610positivegrowth37mesophilic
52435positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8610anaerobe
52435anaerobe
69480anaerobe99.119

spore formation

@refspore formationconfidence
69481no100
69480no99.999

murein

  • @ref: 8610
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
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
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
68371melibiose+builds acid from28053
68371esculin+builds acid from4853
68371N-acetylglucosamine-builds acid from59640
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
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
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
    52435C14:02.414
    52435C16:028.416
    52435C18:011.318
    52435C16:1 ω7c2.215.819
    52435C17:0 anteiso1.716.722
    52435C18:1 ω6c1.617.858
    52435C18:1 ω9c18.317.769
    52435C18:2 ω6,9c/C18:0 ANTE22.417.724
    52435C19:0 CYCLO ω9c4.218.87
    52435Unidentified4.818.184
    52435Unidentified2.719.33
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8610----+-----+/-++-----------+/-++/----++/----+---+/-----------
8610----+++---+++--------+-+++++++++---+---++------+-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinenthost species
8610hindgut of honeybee
52435Honeybee hindgut,Apis mellifica caucasicaNorwayNOREurope
67770Hindgut of honeybee Apis mellifica caucasicaApis mellifica caucasica

isolation source categories

Cat1Cat2Cat3
#Host#Arthropoda#Insecta
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_3998.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_1481;97_1767;98_2161;99_3998&stattab=map
  • Last taxonomy: Bifidobacterium
  • 16S sequence: LC071833
  • Sequence Identity:
  • Total samples: 15599
  • soil counts: 246
  • aquatic counts: 210
  • animal counts: 15035
  • plant counts: 108

Safety information

risk assessment

  • @ref: 8610
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium coryneforme strain ATCC 25911 16S ribosomal RNA gene, partial sequenceM587331473ena1687
20218Bifidobacterium coryneforme ATCC25911 16S-23S intergenic spacerU09523459ena1687
20218Bifidobacterium coryneforme strain CCUG 34986 16S ribosomal RNA gene, partial sequenceEF1872381370ena1687
20218Bifidobacterium coryneforme gene for 16S rRNA, partial sequence, strain: JCM 5819AB116297475ena1687
20218Bifidobacterium coryneforme gene for 16S rRNA, partial sequence, strain: JCM 5819AB507093668ena1687
67770Bifidobacterium coryneforme gene for 16S ribosomal RNA, partial sequenceAB4373581507ena1687
67770Bifidobacterium coryneforme gene for 16S ribosomal RNA, partial sequence, strain: JCM 5819LC0718331452ena1687

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium coryneforme LMG18911GCA_000737865completencbi1687
66792Bifidobacterium coryneforme DSM 202161437599.3wgspatric1437599
66792Bifidobacterium coryneforme strain LMG 189111687.3completepatric1687
66792Bifidobacterium coryneforme DSM 202162693429521draftimg1437599
66792Bifidobacterium coryneforme LMG 189112597490194completeimg1687
67770Bifidobacterium coryneforme DSM 20216GCA_000771345contigncbi1437599

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.727no
flagellatedno97.527no
gram-positiveyes92.893no
anaerobicyes97.105yes
aerobicno96.394no
halophileno60.404no
spore-formingno94.743no
thermophileno95.614no
glucose-utilyes85.222no
glucose-fermentyes75.501no

External links

@ref: 8610

culture collection no.: CCUG 34986, LMG 18911, DSM 20216, ATCC 25911, JCM 5819, BCRC 14675, CGMCC 1.2279, KCTC 3233, LMG 11584

straininfo link

  • @ref: 71347
  • straininfo: 9632

literature

  • topic: Cultivation
  • Pubmed-ID: 11068673
  • title: Bile salt toxicity to some bifidobacteria strains: role of conjugated bile salt hydrolase and pH.
  • authors: Grill JP, Perrin S, Schneider F
  • journal: Can J Microbiol
  • DOI: 10.1139/w00-066
  • year: 2000
  • mesh: Amidohydrolases/*metabolism, Bifidobacterium/*drug effects/enzymology/growth & development, Culture Media, Glycodeoxycholic Acid/*pharmacology, Hydrogen-Ion Concentration, Taurodeoxycholic Acid/*pharmacology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8610Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20216)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20216
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
52435Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34986)https://www.ccug.se/strain?id=34986
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/
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)
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
71347Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9632.1StrainInfo: A central database for resolving microbial strain identifiers