Strain identifier

BacDive ID: 151

Type strain: Yes

Species: Actinomyces israelii

Strain Designation: Jr 277 (CDC W855)

Strain history: CIP <- 1988, ATCC <- A. Howell: strain Jr 277 (CDC W855)

NCBI tax ID(s): 1120944 (strain), 1659 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 10954

BacDive-ID: 151

DSM-Number: 43320

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

description: Actinomyces israelii Jr 277 is an anaerobe, mesophilic bacterium that was isolated from human brain abscess.

NCBI tax id

NCBI tax idMatching level
1659species
1120944strain

strain history

@refhistory
10954<- M.A. Gerencser, WVU 46 <- ATCC <- A. Howell, NIH, 277
67770DSM 43320 <-- M. A. Gerencser WVU 46 <-- ATCC 12102 <-- A. Howell NIH 277.
120287CIP <- 1988, ATCC <- A. Howell: strain Jr 277 (CDC W855)

doi: 10.13145/bacdive151.20230509.8.1

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 israelii
  • full scientific name: Actinomyces israelii (Kruse 1896) Lachner-Sandoval 1898 (Approved Lists 1980)
  • synonyms

    @refsynonym
    20215Streptothrix israeli
    20215Actinobacterium israeli

@ref: 10954

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Actinomyces

species: Actinomyces israelii

full scientific name: Actinomyces israelii (Kruse 1896) Lachner-Sandoval 1898 emend. Nouioui et al. 2018

strain designation: Jr 277 (CDC W855)

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.876
69480100positive
120287nopositiverod-shaped

colony morphology

@refincubation period
468022-3 days
120287

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
40615MEDIUM 39 - for ActinomycesyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
10954PYG 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
10954COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yesName: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar basehttps://mediadive.dsmz.de/medium/693
120287CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
40615positivegrowth37mesophilic
10954positivegrowth37mesophilic
46802positivegrowth37mesophilic
67770positivegrowth37mesophilic
120287positivegrowth30-37mesophilic
120287nogrowth10psychrophilic
120287nogrowth25mesophilic
120287nogrowth41thermophilic
120287nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
10954anaerobe
46802anaerobe
69480anaerobe94.264
120287facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.989

halophily

@refsaltgrowthtested relationconcentration
120287NaClpositivegrowth0-4 %
120287NaClnogrowth6 %
120287NaClnogrowth8 %
120287NaClnogrowth10 %

murein

  • @ref: 10954
  • murein short key: A11.52
  • type: A5alpha L-Lys-L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12028716947citrate-carbon source
1202874853esculin-hydrolysis
120287606565hippurate-hydrolysis
12028717632nitrate+reduction
12028716301nitrite-reduction
12028717632nitrate-respiration
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation
6837717634D-glucose+builds acid from
6837715824D-fructose+builds acid from
6837717306maltose+builds acid from
6837717992sucrose-builds acid from
6837718257ornithine-degradation
6837716199urea-hydrolysis
6837727897tryptophan-energy source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016634raffinose+fermentation
6838029985L-glutamate-degradation
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
12028735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6838035581indole-
6837735581indole-
12028715688acetoin-
12028717234glucose-

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-
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
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
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
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
68379catalase-1.11.1.6
68379gelatinase-
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
120287oxidase-
120287beta-galactosidase-3.2.1.23
120287alcohol dehydrogenase-1.1.1.1
120287gelatinase-
120287amylase+
120287DNase-
120287caseinase-3.4.21.50
120287catalase+1.11.1.6
120287tween esterase-
120287gamma-glutamyltransferase-2.3.2.2
120287lecithinase-
120287lipase-
120287lysine decarboxylase-4.1.1.18
120287ornithine decarboxylase-4.1.1.17
120287phenylalanine ammonia-lyase-4.3.1.24
120287tryptophan deaminase-
120287urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlRIBXYLMANMALLACSACGLYGCAT
46802-+-+--+----------+--

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120287-----+-------+-++---

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
46802-+++------+--

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
10954---+-+++--+/-+--+---+-++-+-----
10954--+/-+-+++--++------+-++-+-----
10954--+/-+/--+++/---++--+--+/-+-++-++++/--+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10954human brain abscess
46802Human brain abscessMN,RochesterUSAUSANorth America
67770Human brain abscess
120287Human, Brain abscessRochester, MinnesotaUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Organ#Brain
#Host Body-Site#Other#Abscess
#Infection#Patient

taxonmaps

  • @ref: 69479
  • File name: preview.99_14341.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_124;96_7391;97_8869;98_10873;99_14341&stattab=map
  • Last taxonomy: Actinomyces israelii subclade
  • 16S sequence: X82450
  • Sequence Identity:
  • Total samples: 12358
  • soil counts: 91
  • aquatic counts: 282
  • animal counts: 11935
  • plant counts: 50

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
109542Risk group (German classification)
1202872Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomyces israelii strain ATCC 12102 16S ribosomal RNA gene, partial sequenceAF058042280ena1659
20218A.israelii 16S rRNA geneX824501441ena1659
20218Actinomyces israelii gene for 16S ribosomal RNA, partial sequence, strain: JCM 12964AB8491231512ena1659

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomyces israelii DSM 433201120944.3wgspatric1120944
66792Actinomyces israelii strain NCTC129721659.4completepatric1659
66792Actinomyces israelii DSM 433202565956542draftimg1120944
66792Actinomyces israelii NCTC129722843235134completeimg1659
67770Actinomyces israelii DSM 43320GCA_000711965scaffoldncbi1120944
67770Actinomyces israelii NCTC12972GCA_900637225completencbi1659

GC content

  • @ref: 67770
  • GC-content: 70

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno64no
motileno94.713no
gram-positiveyes95.247no
anaerobicno69.865no
aerobicno96.906yes
halophileno90.011no
spore-formingno95.131no
thermophileno97.286yes
glucose-utilyes83.372no
flagellatedno96.741no
glucose-fermentyes77.486no

External links

@ref: 10954

culture collection no.: DSM 43320, ATCC 12102, JCM 12964, CCUG 18307, IMET 10792, CCUG 2271, NIH 277, WVU 46, CIP 103259, KCTC 15377, NCTC 12972

straininfo link

  • @ref: 69833
  • straininfo: 35496

literature

Pubmed-IDtitleauthorsjournalyearmeshtopicDOItopic2
2489354[Transmission electron microscopic studies of fine structure by fast freeze method on Actinomyces israelii ATCC 12102].Watanabe T, Matui T, Suzuki MShigaku1989Actinomycetales/*ultrastructure, Cell Membrane/ultrastructure, Cell Wall/ultrastructure, Cytoplasm/ultrastructure, Freezing
17584471Production of antagonistic substance by Eikenella corrodens isolated from the oral cavity of human beings with and without periodontal disease.Apolonio AC, Carvalho MA, Ribas RN, Sousa-Gaia LG, Santos KV, Lana MA, Nicoli JR, Farias LMJ Appl Microbiol2007Acute Disease, *Antibiosis, Bacteriocins/*biosynthesis, Bacteriological Techniques, Chronic Disease, Culture Media, Eikenella corrodens/*metabolism/physiology, Gingiva/microbiology, Humans, Microbial Sensitivity Tests/methods, Mouth/*microbiology, Periodontitis/*microbiologyCultivation10.1111/j.1365-2672.2006.03211.xPathogenicity
19769270[Initial study on the discrimination of oral common Actinomycetes with metabonomics method].Li MY, Guo Q, Zhou XD, Xiong P, Jia XM, Xiao XR, Li W, Xiao LYHua Xi Kou Qiang Yi Xue Za Zhi2009Actinobacteria, *Actinomyces, Magnetic Resonance Spectroscopy, *Metabolomics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10954Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43320)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43320
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
40615Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15037
46802Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 18307)https://www.ccug.se/strain?id=18307
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/
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)
69833Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID35496.1StrainInfo: A central database for resolving microbial strain identifiers
120287Curators of the CIPCollection of Institut Pasteur (CIP 103259)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103259