Strain identifier

BacDive ID: 144

Type strain: Yes

Species: Actinobaculum suis

Strain history: CIP <- 1997, DSM <- ATCC <- J.G. Wegienek and C.A. Reddy: strain 50052, Corynebacterium suis <- M.A. Soltys

NCBI tax ID(s): 1657 (species)

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General

@ref: 8985

BacDive-ID: 144

DSM-Number: 20639

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, psychrophilic, Gram-positive, rod-shaped, colony-forming, animal pathogen

description: Actinobaculum suis DSM 20639 is an anaerobe, psychrophilic, Gram-positive animal pathogen that forms circular colonies and was isolated from cystitis and pyelonephritis of pig.

NCBI tax id

  • NCBI tax id: 1657
  • Matching level: species

strain history

@refhistory
8985<- ATCC <- M.A. Soltys, 50052 (Corynebacterium suis)
123376CIP <- 1997, DSM <- ATCC <- J.G. Wegienek and C.A. Reddy: strain 50052, Corynebacterium suis <- M.A. Soltys

doi: 10.13145/bacdive144.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Actinomycetales
  • family: Actinomycetaceae
  • genus: Actinobaculum
  • species: Actinobaculum suis
  • full scientific name: Actinobaculum suis (Wegienek and Reddy 1982 ex Soltys and Spratling 1957) Lawson et al. 1997

  • synonyms

    @refsynonym
    20215Actinomyces suis
    20215Eubacterium suis

@ref: 8985

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Actinobaculum

species: Actinobaculum suis

full scientific name: Actinobaculum suis (Wegienek and Reddy 1982) Lawson et al. 1997 emend. Yassin et al. 2015 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23353positive1.0-3.0 µm0.5 µmrod-shapedno
23354positive2.0-3.0 µm0.3-0.5 µmrod-shapedno
69480positive99.999
123376positiverod-shapedno

colony morphology

@reftype of hemolysiscolony sizecolony colorcolony shapeincubation periodmedium used
23354gamma0.3-0.5 mmwhitecircular2 daysColumbia blood agar
23354gamma3.0-5.0 mmgrey and opaque7 daysColumbia blood agar
123376

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
23354Columbia blood agaryes
23353Peptone-yeast extract-starch brothyes
8985CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
33054MEDIUM 243 - for Actinobaculum suisyesDistilled water make up to (1000.000 ml);Maltose (1.000 g);Agar (15.000g);Glucose (4.000 g);Yeast extract (5.000 g);Potassium di-hydrogen phosphate (5.000 g);Resazurin (1.000 mg);Cooked meat medium (125.000 g);Cellobiose (1.000 g);Starch maize (1.000 g);C
123376CIP Medium 243yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=243

culture temp

@refgrowthtypetemperaturerange
23353nogrowth<23psychrophilic
23354positivegrowth30-43
23354nogrowth22-23psychrophilic
23353positivemaximum43thermophilic
23353positiveminimum30mesophilic
23353positiveoptimum37mesophilic
23354positiveoptimum37mesophilic
8985positivegrowth37mesophilic
33054positivegrowth37mesophilic
46981positivegrowth37mesophilic
123376positivegrowth30-41
123376nogrowth10psychrophilic
123376nogrowth25mesophilic
123376nogrowth45thermophilic

culture pH

@refabilitytypepH
23353nogrowth<5.0
23353positiveoptimum7.0-8.0
23354positiveoptimum7.0-8.0
23354nogrowth<5.0

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8985anaerobe
23353anaerobe
23354obligate anaerobe
46981anaerobe
69480anaerobe97.059

spore formation

@refspore formationconfidence
23354no
69481no99
69480no100

halophily

@refsaltgrowthtested relationconcentration
123376NaClpositivegrowth0 %
123376NaClnogrowth2 %
123376NaClnogrowth4 %
123376NaClnogrowth6 %
123376NaClnogrowth8 %
123376NaClnogrowth10 %

murein

@refmurein short keytype
8985A11.53A5alpha L-Lys-L-Ala-L-Lys-D-Glu
23353A5alpha L-Lys-L-Ala-L-Lys-D-Glu

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2335415963ribitol-builds acid from
2335427613amygdalin-builds acid from
2335417057cellobiose-builds acid from
2335417634D-glucose-builds acid from
2335416813galactitol-builds acid from
2335417113erythritol-builds acid from
2335428757fructose-builds acid from
2335428260galactose-builds acid from
2335417754glycerol-builds acid from
2335417268myo-inositol-builds acid from
2335415443inulin-builds acid from
2335430849L-arabinose-builds acid from
2335417716lactose-builds acid from
2335429864mannitol-builds acid from
2335437684mannose-builds acid from
233546731melezitose-builds acid from
2335428053melibiose-builds acid from
2335416634raffinose-builds acid from
2335426546rhamnose-builds acid from
2335417814salicin-builds acid from
2335430911sorbitol-builds acid from
2335417992sucrose-builds acid from
2335426986threonine-builds acid from
2335427082trehalose-builds acid from
2335327897tryptophan-energy source
2335315963ribitol-fermentation
2335327613amygdalin-fermentation
2335322599arabinose-fermentation
2335317057cellobiose-fermentation
2335316813galactitol-fermentation
2335317113erythritol-fermentation
233534853esculin-fermentation
2335328757fructose-fermentation
2335328260galactose-fermentation
2335317234glucose-fermentation
2335317754glycerol-fermentation
2335317268myo-inositol-fermentation
2335315443inulin-fermentation
2335324996lactate-fermentation
2335317716lactose-fermentation
2335329864mannitol-fermentation
2335337684mannose-fermentation
233536731melezitose-fermentation
2335328053melibiose-fermentation
2335315361pyruvate-fermentation
2335316634raffinose-fermentation
2335326546rhamnose-fermentation
2335317814salicin-fermentation
2335330911sorbitol-fermentation
2335317992sucrose-fermentation
2335326986threonine-fermentation
2335327082trehalose-fermentation
233534853esculin-hydrolysis
233535291gelatin-hydrolysis
233544853esculin-hydrolysis
233545291gelatin-hydrolysis
2335317632nitrate-reduction
2335416988D-ribose+builds acid from
2335465327D-xylose+builds acid from
2335428087glycogen+builds acid from
2335417306maltose+builds acid from
2335428017starch+builds acid from
2335328087glycogen+fermentation
2335317306maltose+fermentation
2335328017starch+fermentation
23354606565hippurate+hydrolysis
1233764853esculin-hydrolysis
123376606565hippurate+hydrolysis
12337617632nitrate-reduction
12337616301nitrite-reduction
12337617632nitrate+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
6838016199urea+hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
2335335581indoleno
12337635581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
2335335581indole-
6838035581indole-
12337615688acetoin-
12337617234glucose-

enzymes

@refvalueactivityec
23354acid phosphatase+3.1.3.2
23354alkaline phosphatase+3.1.3.1
23354alpha-chymotrypsin-3.4.21.1
23354alpha-fucosidase-3.2.1.51
23354alpha-galactosidase-3.2.1.22
23354alpha-glucosidase+3.2.1.20
23354alpha-mannosidase+3.2.1.24
23354arginine dihydrolase-3.5.3.6
23354beta-galactosidase-3.2.1.23
23354beta-glucosidase-3.2.1.21
23354beta-glucuronidase+3.2.1.31
23354catalase-1.11.1.6
23354cystine arylamidase-3.4.11.3
23354cytochrome oxidase-1.9.3.1
23354esterase (C 4)-
23354esterase lipase (C 8)+
23354leucine arylamidase+3.4.11.1
23354lipase (C 14)-
23354N-acetyl-beta-glucosaminidase+3.2.1.52
23354naphthol-AS-BI-phosphohydrolase+
23354pyrazinamidase-3.5.1.B15
23354pyrrolidonyl arylamidase+3.4.19.3
23354trypsin-3.4.21.4
23353tryptophan deaminase-4.1.99.1
23353urease+3.5.1.5
23354valine arylamidase-
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
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
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
123376oxidase-
123376beta-galactosidase-3.2.1.23
123376alcohol dehydrogenase-1.1.1.1
123376gelatinase-
123376amylase+
123376DNase-
123376caseinase-3.4.21.50
123376catalase-1.11.1.6
123376tween esterase-
123376gamma-glutamyltransferase-2.3.2.2
123376lecithinase-
123376lipase-
123376lysine decarboxylase-4.1.1.18
123376ornithine decarboxylase-4.1.1.17
123376phenylalanine ammonia-lyase-4.3.1.24
123376protease-
123376tryptophan deaminase+
123376urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlRIBXYLMANMALLACSACGLYGCAT
46981--+++-+--+--++-+--+-

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123376-+++-+-+--++--++----

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8985+----+--+--+/-----+/-+/-+++++++++-+

Isolation, sampling and environmental information

isolation

@refsample type
8985cystitis and pyelonephritis of pig
23354from swine
46981Swine cystitis and pyelonephritis
123376Animal, Swine, cystitis

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host Body-Site#Urogenital tract
#Host#Mammals#Suidae (Pig,Swine)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5893.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_247;96_2820;97_3465;98_4381;99_5893&stattab=map
  • Last taxonomy: Actinobaculum suis subclade
  • 16S sequence: S83623
  • Sequence Identity:
  • Total samples: 442
  • soil counts: 21
  • aquatic counts: 15
  • animal counts: 399
  • plant counts: 7

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
8985yes2Risk group (German classification)
1233761Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8985
  • description: Actinobaculum suis strain DSM 20639 16S ribosomal RNA gene, partial sequence
  • accession: S83623
  • length: 1506
  • database: ena
  • NCBI tax ID: 1657

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinobaculum suis DSM 20639GCA_900102025contigncbi1657
66792Actinobaculum suis strain DSM 206391657.8wgspatric1657
66792Actinobaculum suis DSM 206392675903157draftimg1657

GC content

@refGC-contentmethod
898555.0thermal denaturation, midpoint method (Tm)
2335355.0Thermal denaturation, fluorometry

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno94.003no
gram-positiveyes92.975yes
anaerobicyes69.559yes
aerobicno94.723yes
halophileno71.274no
spore-formingno96.715yes
thermophileno92.786no
glucose-utilyes90.647no
flagellatedno96.987yes
glucose-fermentyes67.286yes

External links

@ref: 8985

culture collection no.: DSM 20639, ATCC 33144, CCUG 19206, CIP 105361, LMG 18291, Soltys 50052

straininfo link

  • @ref: 69827
  • straininfo: 92512

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1371060Phylogenetic evidence for the transfer of Eubacterium suis to the genus Actinomyces as Actinomyces suis comb. nov.Ludwig W, Kirchhof G, Weizenegger M, Weiss NInt J Syst Bacteriol10.1099/00207713-42-1-1611992Actinomyces/*classification/genetics, Base Sequence, Eubacterium/*classification/genetics, Molecular Sequence Data, RNA, Bacterial/*chemistry, RNA, Ribosomal, 16S/*chemistryGenetics
Pathogenicity12688126In vitro sensitivity of Hungarian Actinobaculum suis strains to selected antimicrobials.Biksi I, Major A, Fodor L, Szenci O, Vetesi FActa Vet Hung10.1556/AVet.51.2003.1.52003Actinomycetaceae/*drug effects/*pathogenicity, Actinomycetales Infections/microbiology/*veterinary, Animals, Anti-Bacterial Agents/*pharmacology, *Drug Resistance, Bacterial, Female, Male, Microbial Sensitivity Tests, Swine, Swine Diseases/*microbiology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8985Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20639)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20639
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
23353Paul A. Lawson, Enevold Falsen, Eva Akervall, Peter Vandamme, Matthew D. Collins10.1099/00207713-47-3-899Characterization of Some Actinomyces-Like Isolates from Human Clinical Specimens: Reclassification of Actinomyces suis (Soltys and Spratling) as Actinobaculum suis comb. nov. and Description of Actinobaculum schaalii sp. nov.IJSEM 47: 899-903 19979226926
23354A. F. Yassin, C. Spröer, R. Pukall, M. Sylvester, C. Siering, P. Schumann10.1099/ijs.0.069294-0Dissection of the genus Actinobaculum: Reclassification of Actinobaculum schaalii Lawson et al. 1997 and Actinobaculum urinale Hall et al. 2003 as Actinotignum schaalii gen. nov., comb. nov. and Actinotignum urinale comb. nov., description of Actinotignum sanguinis sp. nov. and emended descriptions of the genus Actinobaculum and Actinobaculum suis; and re-examination of the culture deposited as Actinobaculum massiliense CCUG 47753T (=DSM 19118T), revealing that it does not represent a strain of this speciesIJSEM 65: 615-624 201525406238
33054Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17372
46981Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 19206)https://www.ccug.se/strain?id=19206
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
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)
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
69827Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92512.1StrainInfo: A central database for resolving microbial strain identifiers
123376Curators of the CIPCollection of Institut Pasteur (CIP 105361)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105361