Strain identifier

BacDive ID: 6314

Type strain: Yes

Species: Jonesia denitrificans

Strain Designation: 55134

Strain history: CIP <- 1955, R. Sohier: strain L26, Listeria denitrificans

NCBI tax ID(s): 471856 (strain), 43674 (species)

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General

@ref: 8951

BacDive-ID: 6314

DSM-Number: 20603

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, animal pathogen

description: Jonesia denitrificans 55134 is an anaerobe, mesophilic, Gram-positive animal pathogen that builds an aerial mycelium and was isolated from boiled ox blood.

NCBI tax id

NCBI tax idMatching level
43674species
471856strain

strain history

@refhistory
8951<- F. Fiedler <- ATCC <- A. Prévot, 55134 <- R. Sohier
375981955, R. Sohier: strain L26, Listeria denitrificans
67770CIP 55.134 <-- R. Sohier L26.
118898CIP <- 1955, R. Sohier: strain L26, Listeria denitrificans

doi: 10.13145/bacdive6314.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Jonesiaceae
  • genus: Jonesia
  • species: Jonesia denitrificans
  • full scientific name: Jonesia denitrificans (Prévot 1961) Rocourt et al. 1987

  • synonyms

    • @ref: 20215
    • synonym: Listeria denitrificans

@ref: 8951

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Jonesiaceae

genus: Jonesia

species: Jonesia denitrificans

full scientific name: Jonesia denitrificans (Prévot 1961) Rocourt et al. 1987 emend. Nouioui et al. 2018

strain designation: 55134

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
118898negativerod-shapedyes

colony morphology

@refincubation periodmedium used
1876310-14 daysISP 2
1876310-14 daysISP 3
1876310-14 daysISP 4
1876310-14 daysISP 5

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
18763noISP 2
18763noISP 3
18763noISP 4
18763yesISP 5Aerial MyceliumWhite

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_20603_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8951COLUMBIA 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
8951BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
18763ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18763ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18763ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18763ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
37598MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118898CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
118898CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18763positiveoptimum37mesophilic
8951positivegrowth37mesophilic
37598positivegrowth30mesophilic
46273positivegrowth37mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
46273anaerobe
46273microaerophile
118898facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.988

halophily

  • @ref: 18763
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 7.5 %

murein

  • @ref: 8951
  • murein short key: A11.48
  • type: A4alpha L-Lys-L-Ser-D-Glu

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1876362968cellulose-
1876316634raffinose-
1876326546rhamnose-
1876328757fructose-
1876329864mannitol-
1876317268myo-inositol-
1876318222xylose-
1876317992sucrose-
1876322599arabinose-
1876317234glucose-
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
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
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
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11889817632nitrate+reduction
11889816301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11889835581indoleyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382naphthol-AS-BI-phosphohydrolase-
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
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23
118898oxidase-
118898catalase+1.11.1.6
118898urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    46273C14:04.514
    46273C15:00.715
    46273C16:014.716
    46273C18:00.418
    46273C13:0 ANTEISO212.701
    46273C14:0 ISO3.513.618
    46273C15:0 ANTEISO49.614.711
    46273C15:0 ISO4.614.621
    46273C15:1 ANTEISO A314.526
    46273C16:0 iso8.715.626
    46273C17:0 anteiso4.816.722
    46273C17:0 iso0.416.629
    46273C18:1 ω9c1.317.769
    46273C18:2 ω6,9c/C18:0 ANTE1.817.724
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18763--+-+----+-++-+++--
118898----+---------++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18763+---+------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118898+/---+-+---++++/-----------++++++/--++/----++-++--------+/-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
8951boiled ox blood
46273Boiled ox bloodFranceFRAEurope
67770Boiled ox blood
118898Animal, Boiled ox blood

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body Product#Fluids#Blood

taxonmaps

  • @ref: 69479
  • File name: preview.99_4380.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2193;97_2652;98_3289;99_4380&stattab=map
  • Last taxonomy: Jonesia denitrificans subclade
  • 16S sequence: X83811
  • Sequence Identity:
  • Total samples: 1540
  • soil counts: 236
  • aquatic counts: 156
  • animal counts: 1091
  • plant counts: 57

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
8951yes2Risk group (German classification)
187632Risk group (German classification)
1188981Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Jonesia denitrificans 16S rRNA geneX784201514ena471856
20218J.denitrificans 16S rRNA geneX838111420ena471856

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Jonesia denitrificans NCTC10816GCA_900475835completencbi43674
66792Jonesia denitrificans DSM 20603GCA_000024065completencbi471856
66792Jonesia denitrificans DSM 20603471856.5completepatric471856
66792Jonesia denitrificans strain FDAARGOS 144043674.5completepatric43674
66792Jonesia denitrificans strain NCTC1081643674.4completepatric43674
66792Jonesia denitrificans NCTC 108162808606808completeimg43674
66792Jonesia denitrificans 55134, DSM 20603644736376completeimg471856

GC content

@refGC-contentmethod
895157.0
6777058.42genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno82no
motileyes75.621no
flagellatedno90.439no
gram-positiveyes92.02no
anaerobicno98.778no
aerobicyes53.574yes
halophileno70.487no
spore-formingno90.312no
thermophileno97.589yes
glucose-utilyes84.284yes
glucose-fermentyes54.341no

External links

@ref: 8951

culture collection no.: DSM 20603, ATCC 14870, CIP 55134, NCTC 10816, CCUG 15532, CIP 55.134, JCM 11481, BCRC 15368, CCM 4048, CECT 918, IFM 10529, IFO 15587, IMSNU 21281, NBRC 15587

straininfo link

  • @ref: 75788
  • straininfo: 36187

literature

topicPubmed-IDtitleauthorsjournalDOIyear
Genetics21304666Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134).Pukall R, Gehrich-Schroter G, Lapidus A, Nolan M, Glavina Del Rio T, Lucas S, Chen F, Tice H, Pitluck S, Cheng JF, Copeland A, Saunders E, Brettin T, Detter JC, Bruce D, Goodwin L, Pati A, Ivanova N, Mavromatis K, Ovchinnikova G, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Han CStand Genomic Sci10.4056/sigs.416462009
23194802The Murein Types of Listeria grayi, Listeria murrayi and Listeria denitrificans.Fiedler F, Seger JSyst Appl Microbiol10.1016/S0723-2020(83)80002-21983

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8951Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20603)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20603
18763Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20603.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
37598Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8810
46273Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 15532)https://www.ccug.se/strain?id=15532
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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)
75788Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36187.1StrainInfo: A central database for resolving microbial strain identifiers
118898Curators of the CIPCollection of Institut Pasteur (CIP 55.134)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2055.134