Strain identifier

BacDive ID: 149

Type strain: Yes

Species: Actinomyces denticolens

Strain Designation: Sh8/4303

Strain history: CIP <- 1988, NCTC: strain Sh8/4303 <- 1982, R.A.D. Williams, London Hosp.

NCBI tax ID(s): 52767 (species)

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General

@ref: 8993

BacDive-ID: 149

DSM-Number: 20671

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

description: Actinomyces denticolens Sh8/4303 is an anaerobe, mesophilic bacterium that was isolated from dental plaque of dairy cattle.

NCBI tax id

  • NCBI tax id: 52767
  • Matching level: species

strain history

@refhistory
8993<- NCTC <- V.E. Dent, Sh8/4303
118912CIP <- 1988, NCTC: strain Sh8/4303 <- 1982, R.A.D. Williams, London Hosp.

doi: 10.13145/bacdive149.20230509.8.1

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 denticolens
  • full scientific name: Actinomyces denticolens Dent and Williams 1984

@ref: 8993

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Actinomyces

species: Actinomyces denticolens

full scientific name: Actinomyces denticolens Dent and Williams 1984 emend. Nouioui et al. 2018

strain designation: Sh8/4303

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.376
69480100positive
118912nopositiverod-shaped

colony morphology

  • @ref: 118912
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
35491MEDIUM 7 - for ActinomycesyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.200 g);Calcium chloride dihydrate (0.020 g);Agar (15.000 g);Glucose (5.000 g);Yeast extract (5.000 g);Ammonium sulphate (1.000 g);Casitone (4.000 g);Starch maize (1.000 g);Heart i
8993PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yesName: 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 waterhttps://mediadive.dsmz.de/medium/104
118912CIP Medium 7yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=7

culture temp

@refgrowthtypetemperaturerange
35491positivegrowth37mesophilic
8993positivegrowth37mesophilic
51164positivegrowth37mesophilic
118912positivegrowth30-41
118912nogrowth10psychrophilic
118912nogrowth25mesophilic
118912nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8993anaerobe
51164anaerobe
51164microaerophile
118912facultative anaerobe

spore formation

@refspore formationconfidence
69481no98
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
118912NaClpositivegrowth0-2 %
118912NaClnogrowth4 %
118912NaClnogrowth6 %
118912NaClnogrowth8 %
118912NaClnogrowth10 %

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
68371melezitose-builds acid from6731
68371cellobiose-builds acid from17057
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
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
118912citrate-carbon source16947
118912esculin+hydrolysis4853
118912hippurate-hydrolysis606565
118912nitrate+reduction17632
118912nitrite-reduction16301
118912nitrate+respiration17632
68380urea-hydrolysis16199
68380arginine-hydrolysis29016
68380D-mannose-fermentation16024
68380L-glutamate-degradation29985
68380nitrate+reduction17632
68380tryptophan-energy source27897

antibiotic resistance

  • @ref: 118912
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
11891235581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6838035581indole-
11891215688acetoin-
11891217234glucose+

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
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin 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
68380proline-arylamidase+3.4.11.5
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-
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
118912oxidase-
118912beta-galactosidase+3.2.1.23
118912alcohol dehydrogenase-1.1.1.1
118912gelatinase-
118912amylase+
118912DNase-
118912caseinase+3.4.21.50
118912catalase+1.11.1.6
118912tween esterase-
118912gamma-glutamyltransferase-2.3.2.2
118912lecithinase-
118912lysine decarboxylase-4.1.1.18
118912ornithine decarboxylase-4.1.1.17
118912phenylalanine ammonia-lyase-4.3.1.24
118912tryptophan deaminase-
118912urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118912--+++++---+-++-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118912----+/-----+/-+/-+/-+/----+/-+/------+/-+/-+/--+/-+/-+/-+/-+/-+/--+/-+/-+/---+/----------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8993--+/-+/--+-----+/---+---+-++-+-----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
8993dental plaque of dairy cattle
51164Cattle,supragingival plaque of dairy cattleUnited KingdomGBREurope
118912Animal, Cow, dental plaqueUnited KingdomGBREuropeEngland

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body-Site#Oral cavity and airways#Plaque
#Host Body-Site#Oral cavity and airways#Tooth

taxonmaps

  • @ref: 69479
  • File name: preview.99_2112.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_124;96_1160;97_1363;98_1652;99_2112&stattab=map
  • Last taxonomy: Actinomyces denticolens subclade
  • 16S sequence: X80412
  • Sequence Identity:
  • Total samples: 9520
  • soil counts: 337
  • aquatic counts: 126
  • animal counts: 9004
  • plant counts: 53

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
89931Risk group (German classification)
1189122Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: A.denticolens 16S rDNA
  • accession: X80412
  • length: 1422
  • database: ena
  • NCBI tax ID: 52767

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomyces denticolens NCTC11490GCA_900445045contigncbi52767
66792Actinomyces denticolens DSM 20671GCA_001995055contigncbi52767
66792Actinomyces denticolens DSM 20671GCA_002072185scaffoldncbi52767
66792Actinomyces denticolens strain DSM 2067152767.4wgspatric52767
66792Actinomyces denticolens strain DSM 2067152767.5wgspatric52767
66792Actinomyces denticolens strain NCTC1149052767.7wgspatric52767
66792Actinomyces denticolens NCTC 114902808606642draftimg52767

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
flagellatedno97.533no
gram-positiveyes95.672no
anaerobicno87.419no
halophileno87.777no
spore-formingno92.707no
glucose-utilyes87.408no
aerobicno94.908no
thermophileno93.865no
glucose-fermentyes83.075no
motileno92.977no

External links

@ref: 8993

culture collection no.: DSM 20671, ATCC 43322, NCTC 11490, CCUG 32758, CIP 103126

straininfo link

  • @ref: 69831
  • straininfo: 41771

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics28385845Whole-Genome Sequences of Two Closely Related Bacteria, Actinomyces sp. Strain Chiba101 and Actinomyces denticolens DSM 20671(T).Kanesaki Y, Ishige T, Sekigawa Y, Kobayashi T, Torii Y, Yokoyama E, Ishiwata H, Hamada M, Tamura T, Azuma R, Murakami SGenome Announc10.1128/genomeA.00126-172017
Phylogeny30224576Actinomyces denticolens as a causative agent of actinomycosis in animals.Murakami S, Kobayashi T, Sekigawa Y, Torii Y, Kanesaki Y, Ishige T, Yokoyama E, Ishiwata H, Hamada M, Tamura TJ Vet Med Sci10.1292/jvms.18-02072018Actinomyces/*classification/isolation & purification, Actinomycosis/microbiology/pathology/*veterinary, Animals, Horse Diseases/microbiology, Horses, Molecular Typing, Palatine Tonsil/microbiology, RNA, Fungal, RNA, Ribosomal, 16S, Swine, Swine Diseases/*microbiology/pathologyEnzymology
Phylogeny33560201Actinomyces marmotae sp. nov. and Actinomyces procaprae sp. nov. isolated from wild animals and reclassification of Actinomyces liubingyangii and Actinomyces tangfeifanii as Boudabousia liubingyangii comb. nov. and Boudabousia tangfeifanii comb. nov., respectively.Yang C, Bai Y, Dong K, Yang J, Lai XH, Lu S, Zhang G, Cheng Y, Jin D, Zhang S, Lv X, Huang Y, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0046962021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8993Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20671)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20671
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
35491Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14889
51164Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32758)https://www.ccug.se/strain?id=32758
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
68371Automatically annotated from API 50CH acid
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
69831Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41771.1StrainInfo: A central database for resolving microbial strain identifiers
118912Curators of the CIPCollection of Institut Pasteur (CIP 103126)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103126