Strain identifier

BacDive ID: 187

Type strain: Yes

Species: Actinomyces oricola

Strain Designation: R5292

Strain history: CIP <- 2002, CCUG <- V. Hall, PHLS, Cardiff, UK: strain R5292

NCBI tax ID(s): 206043 (species)

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General

@ref: 6830

BacDive-ID: 187

DSM-Number: 17234

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

description: Actinomyces oricola R5292 is an anaerobe, mesophilic, Gram-positive human pathogen that was isolated from human, dental abscess.

NCBI tax id

  • NCBI tax id: 206043
  • Matching level: species

strain history

@refhistory
6830<- CCUG <- V.Hall, PHLS, R5292
67770CCUG 46090 <-- V. Hall R5292.
67771<- CCUG <- V Hall, PHLS, R5292
121434CIP <- 2002, CCUG <- V. Hall, PHLS, Cardiff, UK: strain R5292

doi: 10.13145/bacdive187.20230509.8.1

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 oricola
  • full scientific name: Actinomyces oricola Hall et al. 2003

@ref: 6830

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Actinomyces

species: Actinomyces oricola

full scientific name: Actinomyces oricola Hall et al. 2003

strain designation: R5292

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
23121positiverod-shapedno
67771rod-shapedno
67771positive
121434positiverod-shapedno

colony morphology

@reftype of hemolysiscolony colorincubation periodmedium used
23121gammawhite2 daysFastidious Anaerobe Agar with 5 % horse blood
121434

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6830PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
6830COLUMBIA 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
23121Fastidious Anaerobe Agar with 5 % horse bloodyes
38219MEDIUM 10 - Chocolate medium for Actinobacillus pleuropneumoniae, Capnocytophaga cynodegmi, Haemophilus and NeisseriayesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml);PolyVitex mischung (10.000 ml)
121434CIP Medium 10yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=10

culture temp

@refgrowthtypetemperaturerange
6830positivegrowth37mesophilic
38219positivegrowth37mesophilic
57053positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic
121434positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6830anaerobe
23121facultative anaerobe
57053anaerobe
67771anaerobe

spore formation

@refspore formation
23121no
67771no

halophily

@refsaltgrowthtested relationconcentration
121434NaClpositivegrowth0 %
121434NaClnogrowth2 %
121434NaClnogrowth4 %
121434NaClnogrowth6 %
121434NaClnogrowth8 %
121434NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2312123456cyclodextrin-builds acid from
2312118333D-arabitol-builds acid from
2312116988D-ribose-builds acid from
2312165327D-xylose-builds acid from
2312128087glycogen-builds acid from
2312130849L-arabinose-builds acid from
2312117716lactose-builds acid from
2312129864mannitol-builds acid from
231216731melezitose-builds acid from
2312128053melibiose-builds acid from
23121320055methyl beta-D-glucopyranoside-builds acid from
2312127941pullulan-builds acid from
2312130911sorbitol-builds acid from
2312133954tagatose-builds acid from
2312127082trehalose-builds acid from
2312127897tryptophan-energy source
231215291gelatin-hydrolysis
23121606565hippurate-hydrolysis
2312128017starch-hydrolysis
2312117632nitrate-reduction
2312127613amygdalin+builds acid from
2312117057cellobiose+builds acid from
2312128757fructose+builds acid from
2312117234glucose+builds acid from
2312116634raffinose+builds acid from
2312117814salicin+builds acid from
2312117992sucrose+builds acid from
2312127082trehalose+builds acid from
231214853esculin+hydrolysis
2312117306maltose+/-builds acid from
2312116634raffinose+/-builds acid from
2312117992sucrose+/-builds acid from
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
1214344853esculin+hydrolysis
121434606565hippurate+hydrolysis
12143417632nitrate-reduction
12143416301nitrite-reduction
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source
6838129016arginine-hydrolysis
6838116988D-ribose-builds acid from
6838116899D-mannitol-builds acid from
6838130911sorbitol-builds acid from
6838117716lactose-builds acid from
6838127082trehalose-builds acid from
6838116634raffinose-builds acid from
6838117992sucrose-builds acid from
6838130849L-arabinose-builds acid from
6838118333D-arabitol-builds acid from
6838140585alpha-cyclodextrin-builds acid from
68381606565hippurate-hydrolysis
6838128087glycogen-builds acid from
6838127941pullulan-builds acid from
6838117306maltose-builds acid from
6838128053melibiose-builds acid from
683816731melezitose-builds acid from
68381320055methyl beta-D-glucopyranoside-builds acid from
6838116443D-tagatose-builds acid from
6838116199urea-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
2312135581indoleno
2312115688acetoinno
12143435581indoleno
6838035581indoleno
6838115688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
2312115688acetoin-
2312135581indole-
6838115688acetoin-
6838035581indole-
12143415688acetoin-
12143417234glucose-

enzymes

@refvalueactivityec
231216-phospho-beta-galactosidase-3.2.1.85
23121alanine arylamidase+3.4.11.2
23121alkaline phosphatase+/-3.1.3.1
23121alpha-arabinosidase-3.2.1.55
23121alpha-fucosidase-3.2.1.51
23121alpha-galactosidase+3.2.1.22
23121alpha-glucosidase+3.2.1.20
23121arginine dihydrolase-3.5.3.6
23121beta-galactosidase+/-3.2.1.23
23121beta-glucosidase+3.2.1.21
23121beta-glucuronidase-3.2.1.31
23121beta-mannosidase-3.2.1.25
23121catalase-1.11.1.6
23121glutamate decarboxylase-4.1.1.15
23121glutamyl-glutamate arylamidase-
23121glycin arylamidase+
23121glycyl tryptophan arylamidase-
23121histidine arylamidase-
23121L-arginine arylamidase+
23121lecithinase-
23121leucine arylamidase+3.4.11.1
23121leucyl glycin arylamidase+3.4.11.1
23121lipase-
23121N-acetyl-beta-glucosaminidase-3.2.1.52
23121phenylalanine deaminase+4.3.1.5
23121proline-arylamidase+3.4.11.5
23121pyrazinamidase+3.5.1.B15
23121pyroglutamic acid arylamidase-
23121serine arylamidase-
23121tripeptide aminopeptidase+3.4.11.4
23121tryptophan deaminase-4.1.99.1
23121tyrosine arylamidase+
23121urease-3.5.1.5
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
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase-
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase-3.4.19.3
68381beta-galactosidase-3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase-
68381alkaline phosphatase-3.1.3.1
68381alpha-galactosidase+3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase+3.2.1.21
68381arginine dihydrolase-3.5.3.6
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
68380leucyl glycin arylamidase-3.4.11.1
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
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
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
121434oxidase-
121434beta-galactosidase+3.2.1.23
121434alcohol dehydrogenase-1.1.1.1
121434gelatinase-
121434amylase-
121434DNase-
121434caseinase-3.4.21.50
121434catalase-1.11.1.6
121434tween esterase-
121434gamma-glutamyltransferase-2.3.2.2
121434lecithinase-
121434lipase-
121434lysine decarboxylase-4.1.1.18
121434ornithine decarboxylase-4.1.1.17
121434protease-
121434tryptophan deaminase-
121434urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    57053C12:00.512
    57053C14:00.914
    57053C16:038.916
    57053C18:011.718
    57053C16:1 ω7c0.615.819
    57053C16:1 ω9c0.715.774
    57053C17:1 ω5c ISO1.116.461
    57053C18:1 ω9c32.217.769
    57053C18:2 ω6,9c/C18:0 ANTE7.217.724
    57053C19:1 ISO I1.118.473
    57053C20:1 ω9c0.719.77
    57053Unidentified0.616.758
    57053Unidentified0.918.175
    57053Unidentified318.221
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121434--------------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121434----+/-------+---------++-+-+++/-+-------------------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
6830--++-++-----------+/--++-+-+/----

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
6830-+--+---------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
6830human, dental abscessCardiffUnited KingdomGBREurope
23121dental abscess of a male patient
57053Human dental abscess,maleBuryUnited KingdomGBREurope1993
67770Human dental abscess
67771From human dental abscessmale, CardiffUnited KingdomGBREurope
121434Human, Dental abscessUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host#Human
#Host Body-Site#Oral cavity and airways#Tooth
#Host Body-Site#Other#Abscess
#Host#Human#Male

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
6830yes, in single cases1Risk group (German classification)
1214342Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
6830Actinomyces oricola 16S rRNA gene, type strain CCUG 46090TAJ5072951508ena206043
67770Actinomyces oricola gene for 16S ribosomal RNA, partial sequenceAB6266311497ena206043

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomyces oricola R52922867461147draftimg206043
67770Actinomyces oricola R5292GCA_004104015contigncbi206043

External links

@ref: 6830

culture collection no.: KCTC 15234, DSM 17234, CCUG 46090, CIP 107639, Hall R5292, JCM 17565

straininfo link

  • @ref: 69869
  • straininfo: 19447

literature

  • topic: Phylogeny
  • Pubmed-ID: 13130041
  • title: Actinomyces oricola sp. nov., from a human dental abscess.
  • authors: Hall V, Collins MD, Hutson RA, Inganas E, Falsen E, Duerden BI
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02576-0
  • year: 2003
  • mesh: Abscess/*microbiology, Actinomyces/*classification/genetics/*isolation & purification/metabolism, Actinomycosis/microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Humans, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Tooth Diseases/*microbiology
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6830Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17234)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17234
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
23121Val Hall, Matthew D. Collins, Roger A. Hutson, Elisabeth Inganäs, Enevold Falsen, Brian I. Duerden10.1099/ijs.0.02576-0Actinomyces oricola sp. nov., from a human dental abscessIJSEM 53: 1515-1518 200313130041
38219Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5097
57053Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46090)https://www.ccug.se/strain?id=46090
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
68380Automatically annotated from API rID32A
68381Automatically annotated from API rID32STR
68382Automatically annotated from API zym
69869Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID19447.1StrainInfo: A central database for resolving microbial strain identifiers
121434Curators of the CIPCollection of Institut Pasteur (CIP 107639)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107639