Strain identifier

BacDive ID: 176

Type strain: Yes

Species: Actinomyces radicidentis

Strain Designation: AO 96-06841

Strain history: CIP <- 1999, CCUG <- 1996,T. Monsen, PHLS, Umea, Sweden: strain AO 96-06841

NCBI tax ID(s): 111015 (species)

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General

@ref: 5818

BacDive-ID: 176

DSM-Number: 15433

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

description: Actinomyces radicidentis AO 96-06841 is a microaerophile, mesophilic bacterium that was isolated from infected human tooth root.

NCBI tax id

  • NCBI tax id: 111015
  • Matching level: species

strain history

@refhistory
5818<- CCUG <- T. Monsen, PHLS, Umea; AO 96-06841
122114CIP <- 1999, CCUG <- 1996,T. Monsen, PHLS, Umea, Sweden: strain AO 96-06841

doi: 10.13145/bacdive176.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Actinomycetales
  • family: Actinomycetaceae
  • genus: Actinomyces
  • species: Actinomyces radicidentis
  • full scientific name: Actinomyces radicidentis Collins et al. 2001

@ref: 5818

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Actinomyces

species: Actinomyces radicidentis

full scientific name: Actinomyces radicidentis Collins et al. 2001 emend. Nouioui et al. 2018

strain designation: AO 96-06841

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.004
69480100positive
122114nopositivecoccus-shaped

colony morphology

  • @ref: 122114
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5818TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
5818COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
42163MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
122114CIP Medium 6-Boites-Bioradyeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6-Boites-Biorad
122114CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
5818positivegrowth37mesophilic
42163positivegrowth37mesophilic
122114positivegrowth25-45
122114nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
5818microaerophile
122114facultative anaerobe

spore formation

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

halophily

  • @ref: 122114
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1221144853esculin+hydrolysis
122114606565hippurate-hydrolysis
12211417632nitrate-reduction
12211416301nitrite+reduction
12211417632nitrate+respiration
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose+fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol+fermentation
6837917306maltose+fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation
6837516199urea-hydrolysis
6837529016arginine-hydrolysis
6837518257ornithine-degradation
683754853esculin-hydrolysis
6837517634D-glucose+fermentation
6837515824D-fructose+fermentation
6837516024D-mannose+fermentation
6837517306maltose+fermentation
6837517716lactose+fermentation
6837527082trehalose+fermentation
6837516899D-mannitol+fermentation
6837516634raffinose+fermentation
6837516988D-ribose+fermentation
6837517057cellobiose-fermentation
6837517632nitrate-reduction
6837517992sucrose+fermentation
6837559640N-acetylglucosamine+fermentation
6837532528turanose+fermentation
6837522599arabinose-fermentation

antibiotic resistance

  • @ref: 68375
  • ChEBI: 28368
  • metabolite: novobiocin
  • is antibiotic: yes
  • is sensitive: yes
  • sensitivity conc.: 1.8 µg

metabolite production

@refChebi-IDmetaboliteproduction
6837515688acetoinno
12211435581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
6837515688acetoin-
12211415688acetoin-
12211417234glucose+

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
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 (C 4)+
68382alkaline phosphatase-3.1.3.1
68375beta-glucuronidase-3.2.1.31
68375pyrrolidonyl arylamidase-3.4.19.3
68375alkaline phosphatase-3.1.3.1
68375L-arginine arylamidase-
68375beta-galactosidase+3.2.1.23
68375beta-glucosidase-3.2.1.21
68375ornithine decarboxylase-4.1.1.17
68375arginine dihydrolase-3.5.3.6
68375urease-3.5.1.5
68379catalase+1.11.1.6
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
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
122114oxidase-
122114beta-galactosidase-3.2.1.23
122114alcohol dehydrogenase-1.1.1.1
122114gelatinase+/-
122114amylase+
122114DNase-
122114caseinase+3.4.21.50
122114catalase+1.11.1.6
122114tween esterase+
122114gamma-glutamyltransferase-2.3.2.2
122114lecithinase-
122114lipase-
122114lysine decarboxylase-4.1.1.18
122114ornithine decarboxylase-4.1.1.17
122114phenylalanine ammonia-lyase-4.3.1.24
122114protease-
122114tryptophan deaminase-
122114urease-3.5.1.5

fatty acid profile

  • @reffatty acidpercentageECL
    53356C10:01.110
    53356C12:01.412
    53356C14:02.614
    53356C16:045.216
    53356C18:01.518
    53356C16:1 ω9c2.915.774
    53356C18:1 ω9c41.817.769
    53356C18:2 ω6,9c/C18:0 ANTE2.617.724
    53356Unidentified0.818.221
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG
  • @reffatty acidpercentageECL
    53356C10:01.710
    53356C12:00.912
    53356C14:02.914
    53356C16:047.516
    53356C18:0118
    53356C16:0 3OH0.617.52
    53356C16:1 ω9c3.615.774
    53356C18:1 ω9c38.417.769
    53356C18:2 ω6,9c/C18:0 ANTE2.117.724
    53356Unidentified1.218.225
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
53356-++--++-+-+-++-++++-+
5818-++--++-+---++-++++-+

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
53356--+--+----+-++-++---
122114--++-+----++++-++---

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
53356----+++++++++---+----+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
5818infected human tooth rootUmeaSwedenSWEEurope
53356Human tooth root infectionUmeåSwedenSWEEurope1996-09-01
122114Human, Tooth root infectionUmeaSwedenSWEEurope

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Human
#Host Body-Site#Oral cavity and airways#Tooth

taxonmaps

  • @ref: 69479
  • File name: preview.99_3560.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_124;96_1853;97_2223;98_2729;99_3560&stattab=map
  • Last taxonomy: Actinomyces radicidentis subclade
  • 16S sequence: AJ251986
  • Sequence Identity:
  • Total samples: 5330
  • soil counts: 59
  • aquatic counts: 168
  • animal counts: 5074
  • plant counts: 29

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
58182Risk group (German classification)
1221142Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5818
  • description: Actinomyces radicidentis partial 16S rRNA gene
  • accession: AJ251986
  • length: 1401
  • database: ena
  • NCBI tax ID: 111015

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomyces radicidentis CCUG 36733GCA_001553565completencbi111015
66792Actinomyces radicidentis strain CCUG 36733111015.3completepatric111015
66792Actinomyces radicidentis CCUG 367332687453525completeimg111015

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno60no
flagellatedno97.25no
gram-positiveyes93.465no
anaerobicno95.917yes
aerobicno84.336no
halophileno87.104no
spore-formingno96.432no
thermophileno97.396yes
glucose-utilyes87.803no
motileno92.12no
glucose-fermentyes79.3yes

External links

@ref: 5818

culture collection no.: DSM 15433, CCUG 36733, CIP 106352

straininfo link

  • @ref: 69858
  • straininfo: 53001

literature

  • topic: Phylogeny
  • Pubmed-ID: 10970390
  • title: Characterization of Actinomyces isolates from infected root canals of teeth: description of Actinomyces radicidentis sp. nov.
  • authors: Collins MD, Hoyles L, Kalfas S, Sundquist G, Monsen T, Nikolaitchouk N, Falsen E
  • journal: J Clin Microbiol
  • DOI: 10.1128/JCM.38.9.3399-3403.2000
  • year: 2000
  • mesh: Actinomyces/*classification/genetics/*isolation & purification/metabolism, Actinomycosis/*microbiology, Adult, Aged, Aged, 80 and over, Dental Pulp Cavity/*microbiology, Female, Genes, Bacterial, Genes, rRNA, Humans, Male, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitle
5818Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15433)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15433
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
42163Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18473
53356Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 36733)https://www.ccug.se/strain?id=36733
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)
68375Automatically annotated from API ID32STA
68379Automatically annotated from API Coryne
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)
69858Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID53001.1StrainInfo: A central database for resolving microbial strain identifiers
122114Curators of the CIPCollection of Institut Pasteur (CIP 106352)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106352