Strain identifier

BacDive ID: 1761

Type strain: Yes

Species: Parascardovia denticolens

Strain Designation: B3028

Strain history: AS 1.2280 <-- DSM 10105 <-- B. Biavati <-- F. Crociani B3028.

NCBI tax ID(s): 864564 (strain), 78258 (species)

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General

@ref: 3798

BacDive-ID: 1761

DSM-Number: 10105

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

description: Parascardovia denticolens B3028 is an anaerobe, mesophilic, Gram-positive human pathogen that was isolated from human dental caries.

NCBI tax id

NCBI tax idMatching level
864564strain
78258species

strain history

@refhistory
3798<- B. Biavati <- F. Crociani, B3028
67770AS 1.2280 <-- DSM 10105 <-- B. Biavati <-- F. Crociani B3028.

doi: 10.13145/bacdive1761.20230509.8.1

Name and taxonomic classification

LPSN

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

  • synonyms

    • @ref: 20215
    • synonym: Bifidobacterium denticolens

@ref: 3798

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Parascardovia

species: Parascardovia denticolens

full scientific name: Parascardovia denticolens (Crociani et al. 1996) Jian and Dong 2002 emend. Nouioui et al. 2018

strain designation: B3028

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 99.719

Culture and growth conditions

culture medium

  • @ref: 3798
  • 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
3798positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
3798anaerobe
69480anaerobe99.271

spore formation

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

murein

  • @ref: 3798
  • murein short key: A11.32
  • type: A4alpha L-Lys(L-Orn)-D-Asp

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
68371melibiose+builds acid from28053
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
3798----++----+++-----------+/-+++++/-++-+-+++--+/----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3798human dental cariesBolognaItalyITAEurope
67770Human dental caries

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2994.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_1573;97_1879;98_2307;99_2994&stattab=map
  • Last taxonomy: Parascardovia denticolens subclade
  • 16S sequence: LC383835
  • Sequence Identity:
  • Total samples: 19537
  • soil counts: 132
  • aquatic counts: 417
  • animal counts: 18923
  • plant counts: 65

Safety information

risk assessment

  • @ref: 3798
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Parascardovia denticolens gene for 16S rRNA, partial sequence, strain: DSM 10105D893311518ena864564
67770Parascardovia denticolens JCM 12538 gene for 16S ribosomal RNA, partial sequenceLC3838351466ena864564

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parascardovia denticolens DSM 10105 = JCM 12538GCA_001042675completencbi864564
66792Parascardovia denticolens DSM 10105 = JCM 12538GCA_000191785chromosomencbi864564
66792Parascardovia denticolens DSM 10105 = JCM 12538864564.3wgspatric864564
66792Parascardovia denticolens DSM 10105 = JCM 12538864564.6completepatric864564
66792Parascardovia denticolens F0305641144.3wgspatric641144
66792Parascardovia denticolens JCM 125382811994997completeimg864564
66792Parascardovia denticolens DSM 10105649989980draftimg864564

GC content

  • @ref: 3798
  • GC-content: 55
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno79no
motileno95.143no
flagellatedno97.748no
gram-positiveyes90.288no
anaerobicyes94.81yes
aerobicno98.399yes
halophileno59.301no
spore-formingno96.757no
thermophileno95.415yes
glucose-utilyes89.453no
glucose-fermentyes80.922no

External links

@ref: 3798

culture collection no.: DSM 10105, JCM 12538, CCUG 35728, CCUG 36886, CGMCC 1.2280, KCTC 5846, LMG 17241, LMG 18312, NCTC 12936, VTT E-991434

straininfo link

  • @ref: 71408
  • straininfo: 9633

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
Genetics25977413Complete Genome Sequence of Parascardovia denticolens JCM 12538T, Isolated from Human Dental Caries.Oshima K, Hayashi J, Toh H, Nakano A, Shindo C, Komiya K, Morita H, Honda K, Hattori MGenome Announc10.1128/genomeA.00485-152015Phylogeny
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
3798Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10105)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10105
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)
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)
71408Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9633.1StrainInfo: A central database for resolving microbial strain identifiers