Strain identifier

BacDive ID: 1739

Type strain: Yes

Species: Bifidobacterium bombi

Strain Designation: BluCI/TP

Strain history: <- DSM <- J Kopecny, Inst Animal Physiol and Genetics, Czech Acad. Sci, Prague <- J Killer; BluCI/TP

NCBI tax ID(s): 1341695 (strain), 471511 (species)

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General

@ref: 8255

BacDive-ID: 1739

DSM-Number: 19703

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

description: Bifidobacterium bombi BluCI/TP is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from digestive tract content of the bumblebee Bombus lucorum.

NCBI tax id

NCBI tax idMatching level
1341695strain
471511species

strain history

@refhistory
8255<- J. Kopecny, Inst. Animal Physiol. and Genetics, Czech Acad. Sci., Prague <- J. Killer; BluCI/TP
67771<- DSM <- J Kopecny, Inst Animal Physiol and Genetics, Czech Acad. Sci, Prague <- J Killer; BluCI/TP

doi: 10.13145/bacdive1739.20230509.8.1

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 bombi
  • full scientific name: Bifidobacterium bombi Killer et al. 2009

@ref: 8255

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium bombi

full scientific name: Bifidobacterium bombi Killer et al. 2009 emend. Nouioui et al. 2018

strain designation: BluCI/TP

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28974positive1 µm0.45 µmrod-shapedno
67771rod-shapedno
67771positive
69480positive100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8255BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)yeshttps://mediadive.dsmz.de/medium/58Name: 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
8255MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8255positivegrowth30mesophilic
28974positivegrowth10-37
28974positiveoptimum30mesophilic
67771positivegrowth30mesophilic

culture pH

  • @ref: 28974
  • ability: positive
  • type: growth
  • pH: >4.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8255anaerobe
28974anaerobe
67771anaerobe
69480anaerobe99.291

spore formation

@refspore formationconfidence
28974no
67771no
69481no100
69480no99.996

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2897437684mannose+carbon source
2897428053melibiose+carbon source
2897417814salicin+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose+builds acid from
6837117716lactose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8255-----+----++-----------++++---+----+---+----------
8255----++----++++---------++++-+/--+----+---++/----------
8255----++----++++---------++++---+----+---+----------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
8255digestive tract content of the bumblebee Bombus lucorumBombus lucorumCentral BohemiaCzech RepublicCZEEurope
67771From digestive tract content of the bumblebee `Bombus lucorum`Central BohemiaCzech RepublicCZEEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5879.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_2815;97_3458;98_4372;99_5879&stattab=map
  • Last taxonomy: Bifidobacterium bombi subclade
  • 16S sequence: HE582780
  • Sequence Identity:
  • Total samples: 19565
  • soil counts: 196
  • aquatic counts: 307
  • animal counts: 19033
  • plant counts: 29

Safety information

risk assessment

  • @ref: 8255
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
8255Bifidobacterium bombi strain BlucI/TP 16S ribosomal RNA gene, partial sequenceEU1275491287ena471511
67771Bifidobacterium bombi partial 16S rRNA gene, type strain DSM 19703THE5827801514ena1341695

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium bombi DSM 19703GCA_000771085contigncbi1341695
66792Bifidobacterium bombi DSM 19703GCA_000737845contigncbi1341695
66792Bifidobacterium bombi DSM 197031341695.4wgspatric1341695
66792Bifidobacterium bombi DSM 197031341695.3wgspatric1341695
66792Bifidobacterium bombi DSM 197032600255079draftimg1341695
66792Bifidobacterium bombi DSM 197032663763384draftimg1341695

GC content

@refGC-contentmethod
825547.3high performance liquid chromatography (HPLC)
2897447

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.375yes
gram-positiveyes91.064yes
anaerobicyes93.134no
halophileno50no
spore-formingno96.657yes
thermophileno95.676yes
glucose-utilyes83.806no
aerobicno96.902no
flagellatedno96.373yes
glucose-fermentyes81.858no

External links

@ref: 8255

culture collection no.: DSM 19703, ATCC BAA 1567, KCTC 15159

straininfo link

  • @ref: 71386
  • straininfo: 364117

literature

  • topic: Phylogeny
  • Pubmed-ID: 19567560
  • title: Bifidobacterium bombi sp. nov., from the bumblebee digestive tract.
  • authors: Killer J, Kopecny J, Mrazek J, Rada V, Benada O, Koppova I, Havlik J, Straka J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.002915-0
  • year: 2009
  • mesh: Acetates/metabolism, Aldehyde-Lyases/metabolism, Anaerobiosis, Animals, Bacterial Typing Techniques, Base Composition, Bees/*microbiology, Bifidobacterium/*classification/genetics/*isolation & purification/physiology, Carbohydrate Metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Gastrointestinal Tract/*microbiology, Lactic Acid/metabolism, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial/cytology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8255Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19703)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19703
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
28974Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2541028776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
71386Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID364117.1StrainInfo: A central database for resolving microbial strain identifiers