Strain identifier

BacDive ID: 1707

Type strain: Yes

Species: Bifidobacterium indicum

Strain Designation: C 410

Strain history: ATCC 25912 <-- V. Scardovi C410.

NCBI tax ID(s): 1341694 (strain), 1691 (species)

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General

@ref: 8483

BacDive-ID: 1707

DSM-Number: 20214

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive

description: Bifidobacterium indicum C 410 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from hindgut of honeybee.

NCBI tax id

NCBI tax idMatching level
1341694strain
1691species

strain history

@refhistory
8483<- V. Scardovi, C 410
67770ATCC 25912 <-- V. Scardovi C410.

doi: 10.13145/bacdive1707.20230509.8.1

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: 8483

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 410

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

Culture and growth conditions

culture medium

  • @ref: 8483
  • 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
8483positivegrowth37mesophilic
52434positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8483anaerobe
52434anaerobe
69480anaerobe99.189

spore formation

@refspore formationconfidence
69481no100
69480no99.999

murein

  • @ref: 8483
  • 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
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
68371lactose-builds acid from17716
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
    52434C12:00.512
    52434C14:02.914
    52434C16:024.416
    52434C17:00.717
    52434C18:011.218
    52434C16:1 ω7c315.819
    52434C16:1 ω9c0.515.774
    52434C17:0 anteiso1.116.722
    52434C17:0 CYCLO0.816.888
    52434C17:0 iso 3OH3.218.161
    52434C17:1 ω8c0.816.792
    52434C18:1 ω9c26.217.769
    52434C18:2 ω6,9c/C18:0 ANTE16.717.724
    52434C19:0 CYCLO ω9c6.918.87
    52434Unidentified1.219.315
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8483----+++---+++--------+-++++++-++---+---++---------
8483----+++---+++--------+-+++++---+---+---++--------+/-

Isolation, sampling and environmental information

isolation

@refsample type
8483hindgut of honeybee
52434Honeybee hindgut
67770Hindgut of honeybee

isolation source categories

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

Safety information

risk assessment

  • @ref: 8483
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium indicum 16S ribosomal RNAM587371477ena1691
20218Bifidobacterium indicum ATCC 25912 16S-23S intergenic spacer, partial sequenceU09791471ena1691
20218Bifidobacterium indicum gene for 16S rRNA, partial sequence, strain: JCM 1302AB116303475ena1691
20218Bifidobacterium indicum gene for 16S rRNA, partial sequence, strain: JCM 1302AB507099663ena1691
20218Bifidobacterium indicum gene for 16S rRNA, partial sequence, strain: JCM 1302D861881514ena1691
20218Bifidobacterium indicum strain KCTC 3230 16S ribosomal RNA gene, partial sequenceGU3618221477ena1691
67770Bifidobacterium indicum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1302LC0718071423ena1691

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium indicum LMG 11587 = DSM 20214GCA_000706765completencbi1341694
66792Bifidobacterium indicum LMG 11587 = DSM 202141341694.4completepatric1341694
66792Bifidobacterium indicum LMG 11587 = DSM 202141341694.3wgspatric1341694
66792Bifidobacterium indicum DSM 202142660238275draftimg1341694
66792Bifidobacterium indicum DSM 202142802429577completeimg1341694
67770Bifidobacterium indicum LMG 11587 = DSM 20214GCA_000771325contigncbi1341694

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.625no
flagellatedno97.462no
gram-positiveyes93.38no
anaerobicyes97.134yes
halophileno61.127no
spore-formingno94.682no
thermophileno96.138yes
glucose-utilyes85.065no
aerobicno96.337no
glucose-fermentyes75.502no

External links

@ref: 8483

culture collection no.: DSM 20214, ATCC 25912, CCUG 34985, JCM 1302, BCRC 14674, CGMCC 1.2275, KCTC 3230, LMG 11587

straininfo link

  • @ref: 71354
  • straininfo: 9639

literature

  • topic: Phylogeny
  • Pubmed-ID: 20950979
  • title: Bombiscardovia coagulans gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of bumblebees.
  • authors: Killer J, Kopecny J, Mrazek J, Havlik J, Koppova I, Benada O, Rada V, Kofronova O
  • journal: Syst Appl Microbiol
  • DOI: 10.1016/j.syapm.2010.08.002
  • year: 2010
  • mesh: *Actinobacteria/classification/genetics/isolation & purification, Aldehyde-Lyases/metabolism, Animals, *Bacterial Typing Techniques, Base Composition/genetics, Base Sequence, Bees/*microbiology, Chaperonin 60/genetics, Cold Temperature, DNA, Bacterial/analysis/genetics, Fatty Acids/analysis/chemistry, Gastrointestinal Tract/microbiology, Lipids/chemistry, Molecular Sequence Data, Peptidoglycan/genetics, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8483Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20214)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20214
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
52434Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34985)https://www.ccug.se/strain?id=34985
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
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
71354Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9639.1StrainInfo: A central database for resolving microbial strain identifiers