Strain identifier

BacDive ID: 1749

Type strain: Yes

Species: Bifidobacterium actinocoloniiforme

Strain Designation: LISLUCIII-P2

Strain history: CCM 7728 <-- J. Killer LISLUCIII-P2.

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

@ref: 16505

BacDive-ID: 1749

DSM-Number: 22766

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

description: Bifidobacterium actinocoloniiforme LISLUCIII-P2 is an anaerobe, mesophilic bacterium that was isolated from bumblebee digestive tract.

NCBI tax id

NCBI tax idMatching level
1437605strain
638619species

strain history

@refhistory
16505<- J. Killer, Inst. Animal Physiology and Genetics, Academy Sci. of the Czech Republic, Prague; LISLUCIII-P2
67770CCM 7728 <-- J. Killer LISLUCIII-P2.

doi: 10.13145/bacdive1749.20230509.8.1

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

@ref: 16505

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium actinocoloniiforme

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

strain designation: LISLUCIII-P2

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no90.837
69480100positive

Culture and growth conditions

culture medium

  • @ref: 16505
  • 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
16505positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
16505anaerobe
69480anaerobe99.607

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.998

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
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

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
16505----+++---++---------+-+++++--++/--------+----------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
16505bumblebee (Bombus lucorum) digestive tractBombus lucorumCentral BohemiaCzech RepublicCZEEurope
67770Digestive tract contents of a bumblebee (Bombus lucorum) from Central BohemiaBombus lucorumCzech RepublicCZEEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4508.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_2256;97_2731;98_3389;99_4508&stattab=map
  • Last taxonomy: Bifidobacterium actinocoloniiforme subclade
  • 16S sequence: LC521980
  • Sequence Identity:
  • Total samples: 21382
  • soil counts: 217
  • aquatic counts: 377
  • animal counts: 20713
  • plant counts: 75

Safety information

risk assessment

  • @ref: 16505
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
16505Bifidobacterium actinocoloniiforme DSM 22766 16S ribosomal RNA gene, partial sequenceFJ8587311262ena1437605
67770Bifidobacterium actinocoloniiforme JCM 18048 gene for 16S rRNA, partial sequenceLC5219801464ena638619

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium actinocoloniiforme DSM 22766GCA_001263395completencbi1437605
66792Bifidobacterium actinocoloniiforme DSM 227661437605.3wgspatric1437605
66792Bifidobacterium actinocoloniiforme DSM 227661437605.7completepatric1437605
66792Bifidobacterium actinocoloniiforme DSM 227661437605.6wgspatric1437605
66792Bifidobacterium actinocoloniiforme DSM 227662645727657completeimg1437605
66792Bifidobacterium actinocoloniiforme LISLUCIII-P22600254971draftimg1437605
67770Bifidobacterium actinocoloniiforme DSM 22766GCA_000771585contigncbi1437605
67770Bifidobacterium actinocoloniiforme DSM 22766GCA_000741095contigncbi1437605

GC content

  • @ref: 16505
  • GC-content: 52.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno64no
motileno94.053no
flagellatedno97.138no
gram-positiveyes93.319no
anaerobicyes97.166yes
aerobicno97.772yes
halophileno54.977no
spore-formingno95.233no
thermophileno91.859yes
glucose-utilyes88.96no
glucose-fermentyes77.597no

External links

@ref: 16505

culture collection no.: DSM 22766, CCM 7728, JCM 18048, KCTC 15183

straininfo link

  • @ref: 71396
  • straininfo: 400411

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20656822Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract.Killer J, Kopecny J, Mrazek J, Koppova I, Havlik J, Benada O, Kott TInt J Syst Evol Microbiol10.1099/ijs.0.022525-02010Aldehyde-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, DNAGenetics
Genetics26404606Complete Genome Sequence of Bifidobacterium actinocoloniiforme Type Strain DSM 22766T, Isolated from Bumblebee Digestive Tracts.Chen X, E Z, Gu D, Lv L, Li YGenome Announc10.1128/genomeA.01084-152015Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16505Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22766)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22766
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)
71396Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400411.1StrainInfo: A central database for resolving microbial strain identifiers