Strain identifier

BacDive ID: 1749

Type strain: Yes

Species: Bifidobacterium actinocoloniiforme

Strain Designation: LISLUCIII-P2

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

NCBI tax ID(s): 1437605 (strain), 638619 (species)

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General

@ref: 16505

BacDive-ID: 1749

DSM-Number: 22766

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

description: Bifidobacterium actinocoloniiforme LISLUCIII-P2 is an anaerobe, Gram-positive 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/bacdive1749.20240916.9.1

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

  • @ref: 69480
  • motility: no
  • confidence: 94.5

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

@refgrowthtypetemperature
16505positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 16505
  • oxygen tolerance: anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 90.484

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 sequenceFJ8587311262nuccore1437605
67770Bifidobacterium actinocoloniiforme JCM 18048 gene for 16S rRNA, partial sequenceLC5219801464nuccore638619

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

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno64no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes82.426no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes64.67no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no94.975yes
69480spore-formingspore-formingAbility to form endo- or exosporesno90.484no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno93.988yes
69480flagellatedmotile2+Ability to perform flagellated movementno94.5no

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)
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
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