Strain identifier

BacDive ID: 155

Type strain: Yes

Species: Schaalia odontolytica

Strain Designation: 2A.10, X363

Strain history: CIP <- 1984, ATCC <- 1956, CDC: strain X363 <- NCTC <- I. Batty: strain 2A.10

NCBI tax ID(s): 1660 (species)

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General

@ref: 7919

BacDive-ID: 155

DSM-Number: 19120

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

description: Schaalia odontolytica 2A.10 is an anaerobe, mesophilic, Gram-positive human pathogen that was isolated from dental caries, deep carious lesions around teeth.

NCBI tax id

  • NCBI tax id: 1660
  • Matching level: species

strain history

@refhistory
7919<- CCUG; CCUG 20536 <- NCTC; NCTC 9935 <- I. Batty;
67770DSM 19120 <-- CCUG 20536 <-- NCTC 9935 <-- I. Batty 2A.10.
121388CIP <- 1984, ATCC <- 1956, CDC: strain X363 <- NCTC <- I. Batty: strain 2A.10

doi: 10.13145/bacdive155.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Actinomycetales
  • family: Actinomycetaceae
  • genus: Schaalia
  • species: Schaalia odontolytica
  • full scientific name: Schaalia odontolytica (Batty 1958) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Actinomyces odontolyticus

@ref: 7919

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Schaalia

species: Schaalia odontolytica

full scientific name: Schaalia odontolytica (Batty 1958) Nouioui et al. 2018

strain designation: 2A.10, X363

type strain: yes

Morphology

cell morphology

  • @ref: 121388
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7919COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf
40306MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
7919BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
121388CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
40306positivegrowth37mesophilic
7919positivegrowth37mesophilic
67770positivegrowth37mesophilic
121388positivegrowth25-41
121388nogrowth10psychrophilic
121388nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7919anaerobe
7919microaerophile
121388facultative anaerobe

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
121388citrate-carbon source16947
121388esculin-hydrolysis4853
121388hippurate-hydrolysis606565
121388nitrate+reduction17632
121388nitrite-reduction16301
68379nitrate+reduction17632
68379esculin-hydrolysis4853
68379urea-hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose+fermentation17634
68379D-mannitol-fermentation16899
68379maltose+fermentation17306
68379lactose+fermentation17716
68379sucrose+fermentation17992
68379glycogen-fermentation28087
68377D-glucose+builds acid from17634
68377D-fructose+builds acid from15824
68377maltose+builds acid from17306
68377sucrose-builds acid from17992
68377ornithine-degradation18257
68377urea-hydrolysis16199
68377tryptophan-energy source27897
68380urea-hydrolysis16199
68380D-mannose-fermentation16024
68380nitrate+reduction17632
68380tryptophan-energy source27897

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
12138835581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6838035581indole-
6837735581indole-
12138815688acetoin-
12138817234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68380glutamyl-glutamate arylamidase-
68380glycin arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380proline-arylamidase+3.4.11.5
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380urease-3.5.1.5
68377tryptophan deaminase-4.1.99.1
68377gamma-glutamyltransferase-2.3.2.2
68377proline-arylamidase+3.4.11.5
68377beta-galactosidase+3.2.1.23
68377alkaline phosphatase-3.1.3.1
68377lipase-
68377urease-3.5.1.5
68377ornithine decarboxylase-4.1.1.17
68377beta-lactamase-3.5.2.6
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase+3.5.1.B15
121388oxidase-
121388beta-galactosidase+3.2.1.23
121388alcohol dehydrogenase-1.1.1.1
121388gelatinase-
121388DNase-
121388catalase-1.11.1.6
121388tween esterase-
121388gamma-glutamyltransferase-2.3.2.2
121388lecithinase-
121388lipase-
121388lysine decarboxylase-4.1.1.18
121388ornithine decarboxylase-4.1.1.17
121388phenylalanine ammonia-lyase-4.3.1.24
121388tryptophan deaminase-
121388urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
7919++---+------+---+++-+
65633++---++-----++-+++--

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121388--++-+-------+-+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121388---------+++---------------++-+/-----++--+---------

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
65633-+++-----++--

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
7919---+-+-----+-++--+++++-++++-+
7919---+----------+--+/-++/-+/-+/--+/-+/-++/--+/-
7919-+-+-+-------++--+++++-++++-+
65633---+-+------+-+--+++++-++++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
7919dental caries, deep carious lesions around teethBirminghamUnited KingdomGBREurope52.4862-1.8904
67770Deep carious lesions around teeth
121388Human, Deep carious lesions

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1414.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_224;96_819;97_953;98_1120;99_1414&stattab=map
  • Last taxonomy: Schaalia odontolytica subclade
  • 16S sequence: X80504
  • Sequence Identity:
  • Total samples: 64020
  • soil counts: 654
  • aquatic counts: 1146
  • animal counts: 61736
  • plant counts: 484

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
7919yesyes2Risk group (German classification)
1213882Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomyces odontolyticus gene for 16S ribosomal RNA, partial sequence, strain: JCM 14871AB8189501501ena1660
20218Actinomyces odontolyticus 16S ribosomal RNA gene, partial sequenceAF058053269ena1660
20218Actinomyces odontolyticus 16S rRNA gene, strain CCUG 20536TAJ2340401412ena1660
7919A.odontolyticus 16S rDNAX805041394ena1660

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Schaalia odontolytica NCTC9935GCA_900445025contigncbi1660
66792Actinomyces odontolyticus strain NCTC99351660.24wgspatric1660
66792Schaalia odontolytica NCTC 99352811995233draftimg1660

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno95.425no
gram-positiveyes93.693no
anaerobicno72.554no
aerobicno96.134no
halophileno87.822no
spore-formingno93.516no
thermophileno87.584no
glucose-utilyes89.448no
flagellatedno97.747no
glucose-fermentyes81.576yes

External links

@ref: 7919

culture collection no.: DSM 19120, ATCC 17929, CCUG 20536, DSM 43760, JCM 14871, NCTC 9935, CCM 4740, CIP 101124, LMG 18080

straininfo link

  • @ref: 69837
  • straininfo: 10615

literature

  • topic: Pathogenicity
  • Pubmed-ID: 10530260
  • title: An evaluation of the action of different root canal irrigants on facultative aerobic-anaerobic, obligate anaerobic, and microaerophilic bacteria.
  • authors: D'Arcangelo C, Varvara G, De Fazio P
  • journal: J Endod
  • DOI: 10.1016/S0099-2399(06)81170-2
  • year: 1999
  • mesh: Anti-Infective Agents, Local/administration & dosage/*pharmacology, Bacteria, Anaerobic/*drug effects, Cetrimonium, Cetrimonium Compounds/administration & dosage/pharmacology, Chlorhexidine/administration & dosage/pharmacology, Colony Count, Microbial, Dose-Response Relationship, Drug, Edetic Acid/administration & dosage/pharmacology, Root Canal Irrigants/administration & dosage/*pharmacology, Sodium Hypochlorite/administration & dosage/pharmacology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7919Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19120)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19120
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
40306Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/12665
65633Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 20536)https://www.ccug.se/strain?id=20536
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
68377Automatically annotated from API NH
68379Automatically annotated from API Coryne
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
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
69837Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10615.1StrainInfo: A central database for resolving microbial strain identifiers
121388Curators of the CIPCollection of Institut Pasteur (CIP 101124)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20101124