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, Gram-positive, human pathogen

description: Schaalia odontolytica 2A.10 is an anaerobe, 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/bacdive155.20240916.9.1

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

@refgram staincell shapemotilityconfidence
121388positiverod-shapedno
69480no96.875

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

@refgrowthtypetemperature
40306positivegrowth37
7919positivegrowth37
67770positivegrowth37
121388positivegrowth25-41
121388nogrowth10
121388nogrowth45

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 14871AB8189501501nuccore1660
20218Actinomyces odontolyticus 16S ribosomal RNA gene, partial sequenceAF058053269nuccore1660
20218Actinomyces odontolyticus 16S rRNA gene, strain CCUG 20536TAJ2340401412nuccore1660
7919A.odontolyticus 16S rDNAX805041394nuccore1660
124043Schaalia odontolytica JCM 14871 gene for 16S rRNA, partial sequence.LC752402580nuccore1660
124043Schaalia odontolytica strain NCTC 9935 16S ribosomal RNA gene, partial sequence.OR1337581548nuccore1660

Genome sequences

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

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes89.903no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no70.984no
69480spore-formingspore-formingAbility to form endo- or exosporesno84.09no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno93.142yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no75.979yes
69480flagellatedmotile2+Ability to perform flagellated movementno96.875no

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
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)
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
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy