Strain identifier

BacDive ID: 1758

Type strain: Yes

Species: Alloscardovia criceti

Strain Designation: OMB105

Strain history: M. Okamoto OMB 105.

NCBI tax ID(s): 1122228 (strain), 356828 (species)

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General

@ref: 7178

BacDive-ID: 1758

DSM-Number: 17774

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

description: Alloscardovia criceti OMB105 is an anaerobe, mesophilic bacterium that was isolated from dental plaque, golden hamster.

NCBI tax id

NCBI tax idMatching level
1122228strain
356828species

strain history

@refhistory
7178<- Masaaki Okamoto, OMB105
67770M. Okamoto OMB 105.

doi: 10.13145/bacdive1758.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Bifidobacteriales
  • family: Bifidobacteriaceae
  • genus: Alloscardovia
  • species: Alloscardovia criceti
  • full scientific name: Alloscardovia criceti (Okamoto et al. 2007) Killer et al. 2013

  • synonyms

    • @ref: 20215
    • synonym: Metascardovia criceti

@ref: 7178

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Alloscardovia

species: Alloscardovia criceti

full scientific name: Alloscardovia criceti (Okamoto et al. 2007) Killer et al. 2013 emend. Nouioui et al. 2018

strain designation: OMB105

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no90.272
69480100positive

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_17774_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17774_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17774_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17774_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17774_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 7178
  • 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
7178positivegrowth37mesophilic
67770positivegrowth35mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7178anaerobe
69480anaerobe96.767

spore formation

@refspore formationconfidence
69481no100
69480no100

murein

  • @ref: 7178
  • murein short key: A11.20
  • type: A3alpha L-Lys-L-Ser-L-Ala2

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
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
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
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
7178------------------------+/-+----+/----------+/----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7178dental plaque, golden hamsterJapanJPNAsia
67770Dental plaque of golden hamster fed with a high-carbohydrate diet

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Rodentia (Other)
#Host Body-Site#Oral cavity and airways#Plaque
#Host Body-Site#Oral cavity and airways#Tooth

taxonmaps

  • @ref: 69479
  • File name: preview.99_5773.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_476;97_544;98_4300;99_5773&stattab=map
  • Last taxonomy: Alloscardovia criceti subclade
  • 16S sequence: NR_041347
  • Sequence Identity:
  • Total samples: 1609
  • soil counts: 23
  • aquatic counts: 20
  • animal counts: 1560
  • plant counts: 6

Safety information

risk assessment

  • @ref: 7178
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7178Alloscardovia criceti DSM 17774 strain OMB105 16S ribosomal RNA, partial sequenceNR_0413471455nuccore1122228
67770Metascardovia criceti gene for 16S ribosomal RNA, partial sequence, strain: OMB105AB2411051455ena1122228
67770Alloscardovia criceti gene for 16S ribosomal RNA, partial sequence, strain: JCM 13493LC2581471477ena356828

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Metascardovia criceti DSM 177741122228.3wgspatric1122228
66792Alloscardovia criceti DSM 177742519103191draftimg1122228
67770Alloscardovia criceti DSM 17774GCA_000376885contigncbi1122228

GC content

@refGC-contentmethod
717853
6777053high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.931no
flagellatedno97.248no
gram-positiveyes90.439no
anaerobicyes93.533yes
aerobicno97.664yes
halophileno55.653no
spore-formingno96.691no
thermophileno95.767yes
glucose-utilyes85.584no
glucose-fermentyes82.265no

External links

@ref: 7178

culture collection no.: DSM 17774, JCM 13493, LMG 24385

straininfo link

  • @ref: 71405
  • straininfo: 319381

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17704637Metascardovia criceti Gen. Nov., Sp. Nov., from hamster dental plaque.Okamoto M, Benno Y, Leung KP, Maeda NMicrobiol Immunol10.1111/j.1348-0421.2007.tb03964.x2007Animals, Base Sequence, Bifidobacteriales Infections/*microbiology, Bifidobacterium/*classification/genetics/isolation & purification, Chaperonin 60/genetics, Cricetinae, Dental Plaque/*microbiology, Phylogeny, RNA, Ribosomal, 16S/geneticsEnzymology
Phylogeny23907220Alloscardovia macacae sp. nov., isolated from the milk of a macaque (Macaca mulatta), emended description of the genus Alloscardovia and proposal of Alloscardovia criceti comb. nov.Killer J, Rockova S, Vlkova E, Rada V, Havlik J, Kopecny J, Bunesova V, Benada O, Kofronova O, Pechar R, Profousova IInt J Syst Evol Microbiol10.1099/ijs.0.051326-02013Actinobacteria/*classification/genetics/isolation & purification, Aldehyde-Lyases/metabolism, Animals, Bacterial Typing Techniques, Base Composition, Carbohydrates/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Female, Genes, Bacterial, Macaca mulatta/*microbiology, Milk/*microbiology, Molecular Sequence Data, Multilocus Sequence Typing, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny28820091Alloscardovia venturai sp. nov., a fructose 6-phosphate phosphoketolase-positive species isolated from the oral cavity of a guinea-pig (Cavia aperea f. porcellus).Sechovcova H, Killer J, Pechar R, Geigerova M, Svejstil R, Salmonova H, Mekadim C, Rada V, Vlkova E, Kofronova O, Benada OInt J Syst Evol Microbiol10.1099/ijsem.0.0020312017Actinobacteria/*classification/genetics/isolation & purification, Aldehyde-Lyases/*metabolism, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fructose, Genes, Bacterial, Guinea Pigs/*microbiology, Mouth/*microbiology, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7178Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17774)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17774
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
71405Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID319381.1StrainInfo: A central database for resolving microbial strain identifiers