Strain identifier

BacDive ID: 11315

Type strain: Yes

Species: Janthinobacterium agaricidamnosum

Strain Designation: W1R3

Strain history: CIP <- 1999, S.P. Lincoln, Hort. Research Int., Warwickshire, UK: strain W1r3

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General

@ref: 3651

BacDive-ID: 11315

DSM-Number: 9628

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Janthinobacterium agaricidamnosum W1R3 is an aerobe, mesophilic, motile bacterium that was isolated from diseased Agaricoccus bisporus tissue.

NCBI tax id

NCBI tax idMatching level
1349767strain
55508species

strain history

@refhistory
3651<- S. P. Lincoln, Horticultural Reasearch Institute, Wellesbourne, Warwickshire, UK
402891999, S.P. Lincoln, Hort. Research Int., Warwickshire, UK: strain W1r3
67770IAM 14973 <-- DSM 9628 <-- S. P. Lincoln W1R3.
116149CIP <- 1999, S.P. Lincoln, Hort. Research Int., Warwickshire, UK: strain W1r3

doi: 10.13145/bacdive11315.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Janthinobacterium
  • species: Janthinobacterium agaricidamnosum
  • full scientific name: Janthinobacterium agaricidamnosum Lincoln et al. 1999

@ref: 3651

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Janthinobacterium

species: Janthinobacterium agaricidamnosum

full scientific name: Janthinobacterium agaricidamnosum Lincoln et al. 1999

strain designation: W1R3

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.158
6948099.997negative
116149yesnegativerod-shaped

colony morphology

  • @ref: 116149

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3651OXOID NUTRIENT BROTH (DSMZ Medium 948)yeshttps://mediadive.dsmz.de/medium/948Name: OXOID NUTRIENT BROTH (DSMZ Medium 948) Composition: Nutrient broth 13.0 g/l Distilled water
3651NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
3651NUTRIENT AGAR (OXOID CM3) (DSMZ Medium 605)yeshttps://mediadive.dsmz.de/medium/605Name: NUTRIENT AGAR (OXOID CM3) (DSMZ Medium 605) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Yeast extract 2.0 g/l Lab-Lemco beef extract 1.0 g/l Distilled water
40289MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116149CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
3651positivegrowth28mesophilic
40289positivegrowth25mesophilic
55687positivegrowth22psychrophilic
67770positivegrowth25mesophilic
116149positivegrowth5-30
116149nogrowth37mesophilic
116149nogrowth41thermophilic
116149nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
55687aerobe
116149obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
116149NaClpositivegrowth0 %
116149NaClnogrowth4 %
116149NaClnogrowth6 %
116149NaClnogrowth8 %
116149NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11614916947citrate+carbon source
1161494853esculin-hydrolysis
116149606565hippurate+hydrolysis
11614917632nitrate-builds gas from
11614917632nitrate-reduction
11614916301nitrite-builds gas from
11614916301nitrite-reduction
11614915792malonate+assimilation
11614917234glucose+/-degradation
11614917632nitrate-respiration

antibiotic resistance

  • @ref: 116149
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116149
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11614915688acetoin-
11614917234glucose-

enzymes

@refvalueactivityec
116149oxidase+
116149beta-galactosidase+3.2.1.23
116149alcohol dehydrogenase-1.1.1.1
116149gelatinase+/-
116149amylase-
116149DNase-
116149caseinase-3.4.21.50
116149catalase+1.11.1.6
116149tween esterase+
116149gamma-glutamyltransferase+2.3.2.2
116149lecithinase-
116149lipase-
116149lysine decarboxylase-4.1.1.18
116149ornithine decarboxylase-4.1.1.17
116149phenylalanine ammonia-lyase-4.3.1.24
116149protease-
116149tryptophan deaminase-
116149urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116149-+++-+++--++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116149++-++--+--------+--+------+----+++------------++-+++-+--------+----------------++-----+-+-+----+---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
3651diseased Agaricoccus bisporus tissueAgaricoccus bisporusLittlehamptonUnited KingdomGBREurope
55687Diseased Agaricoccus bisporus tissueLittlehamptonUnited KingdomGBREurope
67770Rotting Agaricus bisporusAgaricus bisporusUnited KingdomGBREurope
116149Agaricus bisporusUnited KingdomGBREurope1992

isolation source categories

  • Cat1: #Host
  • Cat2: #Fungi
  • Cat3: #Mushroom

taxonmaps

  • @ref: 69479
  • File name: preview.99_781.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_429;97_540;98_623;99_781&stattab=map
  • Last taxonomy: Janthinobacterium agaricidamnosum
  • 16S sequence: Y08845
  • Sequence Identity:
  • Total samples: 226
  • soil counts: 47
  • aquatic counts: 72
  • animal counts: 29
  • plant counts: 78

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
36511Risk group (German classification)
1161491Risk group (French classification)

Sequence information

16S sequences

  • @ref: 3651
  • description: J.agaricidamnosum 16S rRNA gene
  • accession: Y08845
  • length: 1469
  • database: ena
  • NCBI tax ID: 55508

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Janthinobacterium agaricidamnosum NBRC 102515 = DSM 9628GCA_000723165completencbi1349767
66792Janthinobacterium agaricidamnosum NBRC 102515 = DSM 96281349767.10wgspatric1349767
66792Janthinobacterium agaricidamnosum NBRC 102515 = DSM 96281349767.4completepatric1349767
66792Janthinobacterium agaricidamnosum W1R32731957621draftimg1349767
66792Janthinobacterium agaricidamnosum W1R32585427668completeimg1349767
67770Janthinobacterium agaricidamnosum NBRC 102515 = DSM 9628GCA_001571185contigncbi1349767

GC content

@refGC-contentmethod
365164.2thermal denaturation, midpoint method (Tm)
6777064.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.931no
flagellatedyes83.991no
gram-positiveno98.48no
anaerobicno99.259yes
aerobicyes92.997yes
halophileno93.841no
spore-formingno93.034no
glucose-utilyes88.324no
thermophileno99.52yes
glucose-fermentno86.73no

External links

@ref: 3651

culture collection no.: CCUG 43140, CIP 106332, DSM 9628, NCPPB 3945, JCM 21444, IAM 14973, NBRC 102515

straininfo link

  • @ref: 80548
  • straininfo: 48653

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10555339Janthinobacterium agaricidamnosum sp. nov., a soft rot pathogen of Agaricus bisporus.Lincoln SP, Fermor TR, Tindall BJInt J Syst Bacteriol10.1099/00207713-49-4-15771999*Agaricus/physiology, Bacterial Typing Techniques, Betaproteobacteria/chemistry/*classification/isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Humidity, Molecular Sequence Data, Nucleic Acid Hybridization, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, DNAGenetics
Genetics25883287Genome Sequence of Mushroom Soft-Rot Pathogen Janthinobacterium agaricidamnosum.Graupner K, Lackner G, Hertweck CGenome Announc10.1128/genomeA.00277-152015
Phylogeny32176602Janthinobacterium violaceinigrum sp. nov., Janthinobacterium aquaticum sp. nov. and Janthinobacterium rivuli sp. nov., isolated from a subtropical stream in China.Lu H, Deng T, Cai Z, Liu F, Yang X, Wang Y, Xu MInt J Syst Evol Microbiol10.1099/ijsem.0.0040972020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
36514532Scalable downstream method for the cyclic lipopetide jagaricin.Stein J, Schlosser N, Bardl B, Peschel G, Meyer F, Kloss F, Rosenbaum MA, Regestein LEng Life Sci10.1002/elsc.2021000792021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3651Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9628)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9628
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
40289Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18451
55687Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43140)https://www.ccug.se/strain?id=43140
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
80548Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48653.1StrainInfo: A central database for resolving microbial strain identifiers
116149Curators of the CIPCollection of Institut Pasteur (CIP 106332)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106332