Strain identifier

BacDive ID: 1750

Type strain: Yes

Species: Bifidobacterium bohemicum

Strain Designation: JEMLUCVIII-4

Strain history: CCM 7729 <-- J. Killer JEMLUCVIII-4.

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 16506

BacDive-ID: 1750

DSM-Number: 22767

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

description: Bifidobacterium bohemicum JEMLUCVIII-4 is an anaerobe, mesophilic bacterium that was isolated from bumblebee digestive tract.

NCBI tax id

NCBI tax idMatching level
1437606strain
638617species

strain history

@refhistory
16506<- J. Killer, Inst. Animal Physiology and Genetics, Academy Sci. of the Czech Republic, Prague; JEMLUCVIII-4
67770CCM 7729 <-- J. Killer JEMLUCVIII-4.

doi: 10.13145/bacdive1750.20230509.8.1

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 bohemicum
  • full scientific name: Bifidobacterium bohemicum Killer et al. 2011

@ref: 16506

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium bohemicum

full scientific name: Bifidobacterium bohemicum Killer et al. 2011 emend. Nouioui et al. 2018

strain designation: JEMLUCVIII-4

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no90.874
69480100positive

Culture and growth conditions

culture medium

  • @ref: 16506
  • 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
16506positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
16506anaerobe
69480anaerobe99.503

spore formation

@refspore formationconfidence
69481no100
69480no99.997

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
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
68371erythritol-builds acid from17113

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
16506-+/--+/-+++--++++++------++++++---+----+---+---------+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
16506bumblebee (Bombus lucorum) digestive tractBombus lucorumSouth Bohemian RegionCzech RepublicCZEEurope
67770Digestive tract contents of a bumblebee (Bombus lucorum) from South BohemiaBombus lucorumCzech RepublicCZEEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1596.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_906;97_1056;98_1261;99_1596&stattab=map
  • Last taxonomy: Bifidobacterium bohemicum subclade
  • 16S sequence: LC521981
  • Sequence Identity:
  • Total samples: 4171
  • soil counts: 102
  • aquatic counts: 62
  • animal counts: 3988
  • plant counts: 19

Safety information

risk assessment

  • @ref: 16506
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
16506Bifidobacterium bohemicum DSM 22767 16S ribosomal RNA gene, partial sequenceFJ8587361228ena1437606
67770Bifidobacterium bohemicum JCM 18049 gene for 16S rRNA, partial sequenceLC5219811461ena638617

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium bohemicum DSM 227671437606.5wgspatric1437606
66792Bifidobacterium bohemicum DSM 227671437606.3wgspatric1437606
66792Bifidobacterium bohemicum DSM 227672657244953draftimg1437606
66792Bifidobacterium bohemicum DSM 227672597490239draftimg1437606
67770Bifidobacterium bohemicum DSM 22767GCA_000771605contigncbi1437606
67770Bifidobacterium bohemicum DSM 22767GCA_000741525contigncbi1437606

GC content

  • @ref: 16506
  • GC-content: 51.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.2no
gram-positiveyes94.533no
anaerobicyes93.287no
halophileno52.383no
spore-formingno95.39no
glucose-utilyes87.196no
aerobicno97.575yes
flagellatedno96.866no
glucose-fermentyes84.106no
thermophileno93.62yes

External links

@ref: 16506

culture collection no.: DSM 22767, CCM 7729, JCM 18049, KCTC 15184

straininfo link

  • @ref: 71397
  • straininfo: 377596

literature

  • topic: Phylogeny
  • Pubmed-ID: 20656822
  • title: Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract.
  • authors: Killer J, Kopecny J, Mrazek J, Koppova I, Havlik J, Benada O, Kott T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.022525-0
  • year: 2010
  • mesh: Aldehyde-Lyases/metabolism, Animals, Bees/*microbiology, Bifidobacterium/*classification/genetics/*isolation & purification, Chaperonin 60/genetics, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Gastrointestinal Tract/microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16506Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22767)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22767
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
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)
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
71397Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID377596.1StrainInfo: A central database for resolving microbial strain identifiers