Strain identifier

BacDive ID: 1763

Type strain: Yes

Species: Scardovia inopinata

Strain Designation: B3109

Strain history: AS 1.2187 <-- DSM 10107 <-- B. Biavati <-- F. Crociani B3109.

NCBI tax ID(s): 1150468 (strain), 78259 (species)

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General

@ref: 3800

BacDive-ID: 1763

DSM-Number: 10107

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

description: Scardovia inopinata B3109 is an anaerobe, mesophilic bacterium that was isolated from human dental caries.

NCBI tax id

NCBI tax idMatching level
1150468strain
78259species

strain history

@refhistory
3800<- B. Biavati <- F. Crociani, B3109
67770AS 1.2187 <-- DSM 10107 <-- B. Biavati <-- F. Crociani B3109.

doi: 10.13145/bacdive1763.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Bifidobacteriales
  • family: Bifidobacteriaceae
  • genus: Scardovia
  • species: Scardovia inopinata
  • full scientific name: Scardovia inopinata (Crociani et al. 1996) Jian and Dong 2002

  • synonyms

    • @ref: 20215
    • synonym: Bifidobacterium inopinatum

@ref: 3800

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Scardovia

species: Scardovia inopinata

full scientific name: Scardovia inopinata (Crociani et al. 1996) Jian and Dong 2002 emend. Downes et al. 2011 emend. Nouioui et al. 2018

strain designation: B3109

type strain: yes

Morphology

cell morphology

  • @ref: 125438
  • motility: no
  • confidence: 95.5

Culture and growth conditions

culture medium

  • @ref: 3800
  • 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
3800positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 3800
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
125439no98.3
125438no91.543

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371methyl alpha-D-glucopyranoside-builds acid from320061
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-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
3800-----++----++----------++++-+-++---+++-++---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3800human dental cariesBolognaItalyITAEurope
67770Human dental caries

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Oral cavity and airways#Tooth
#Host Body-Site#Other#Wound

Safety information

risk assessment

  • @ref: 3800
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bifidobacterium inopinatum gene for 16S rRNAAB0290871557nuccore1150468
3800Scardovia inopinata gene for 16S rRNA, partial sequence, strain: DSM 10107D893321532nuccore1150468
67770Scardovia inopinata JCM 12537 gene for 16S ribosomal RNA, partial sequenceLC3838341480nuccore1150468

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Scardovia inopinata JCM 12537GCA_001042695completencbi1150468
66792Scardovia inopinata NCTC12937GCA_900445765contigncbi78259
66792Parascardovia denticolens strain NCTC1293778258.9wgspatric78258
66792Scardovia inopinata F0304641146.3wgspatric641146
66792Scardovia inopinata JCM 125371150468.4completepatric1150468
66792Parascardovia denticolens NCTC 129372811995288draftimg78258

GC content

@refGC-contentmethod
380054high performance liquid chromatography (HPLC)
380045thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthmicroaerophile80.3
125439BacteriaNetgram_stainReaction to gram-stainingpositive59.5
125439BacteriaNetmotilityAbility to perform movementno86.9
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.3
125438gram-positivegram-positivePositive reaction to Gram-stainingyes83.284no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes69.418no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no94.12yes
125438spore-formingspore-formingAbility to form endo- or exosporesno91.543no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.981yes
125438motile2+flagellatedAbility to perform flagellated movementno95.5no

External links

@ref: 3800

culture collection no.: DSM 10107, JCM 12537, CCUG 35729, CGMCC 1.2187, LMG 17242, LMG 18313, NCTC 12937, VTT E-991435

straininfo link

  • @ref: 71410
  • straininfo: 9642

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8934909Bifidobacterium inopinatum sp. nov. and Bifidobacterium denticolens sp. nov., two new species isolated from human dental caries.Crociani F, Biavati B, Alessandrini A, Chiarini C, Scardovi VInt J Syst Bacteriol10.1099/00207713-46-2-5641996Bacterial Proteins/analysis, Bifidobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, Dental Caries/*microbiology, Dextrans/metabolism, Electrophoresis, Polyacrylamide Gel, Fermentation, Phenotype, Plasmids, SolubilityEnzymology
Phylogeny17625172Alloscardovia omnicolens gen. nov., sp. nov., from human clinical samples.Huys G, Vancanneyt M, D'Haene K, Falsen E, Wauters G, Vandamme PInt J Syst Evol Microbiol10.1099/ijs.0.64812-02007Actinobacteria/*classification/genetics/*isolation & purification/metabolism, Aerobiosis, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, Belgium, Chaperonin 60/genetics, Cluster Analysis, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fermentation, Genes, rRNA, Genotype, Gram-Positive Bacterial Infections/*microbiology, Humans, Molecular Sequence Data, Norway, Nucleic Acid Hybridization, Phylogeny, Polymerase Chain Reaction, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, SwedenGenetics
Phylogeny20139283Scardovia wiggsiae sp. nov., isolated from the human oral cavity and clinical material, and emended descriptions of the genus Scardovia and Scardovia inopinata.Downes J, Mantzourani M, Beighton D, Hooper S, Wilson MJ, Nicholson A, Wade WGInt J Syst Evol Microbiol10.1099/ijs.0.019752-02010Acetic Acid/metabolism, Actinobacteria/*classification/genetics/*isolation & purification/physiology, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fermentation, Gram-Positive Bacterial Infections/*microbiology, Humans, Lactic Acid/metabolism, Molecular Sequence Data, Mouth/*microbiology, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Genetics25977411Complete Genome Sequence of Scardovia inopinata JCM 12537T, Isolated from Human Dental Caries.Oshima K, Hayashi J, Toh H, Nakano A, Omori E, Hattori Y, Morita H, Honda K, Hattori MGenome Announc10.1128/genomeA.00481-152015Phylogeny
Cultivation27660160Acidogenicity of dual-species biofilms of bifidobacteria and Streptococcus mutans.de Matos BM, Brighenti FL, Do T, Beighton D, Koga-Ito CYClin Oral Investig10.1007/s00784-016-1958-12016Animals, Bifidobacterium/*growth & development, Biofilms/*growth & development, Cell Culture Techniques, Culture Media, Hydrogen-Ion Concentration, Lactobacillus acidophilus, Streptococcus mutans/*growth & development

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3800Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10107)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10107
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
71410Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9642.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1