Strain identifier

BacDive ID: 5006

Type strain: Yes

Species: Pantoea dispersa

Strain Designation: 1611

Strain history: CIP <- 1988, LMG <- 1980, F. Gavini, CUEMT, Lille, France , Erwinia herbicola <- ATCC <- Ajinomoto Co. Inc., Japan

NCBI tax ID(s): 59814 (species)

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General

@ref: 9109

BacDive-ID: 5006

DSM-Number: 30073

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped, human pathogen

description: Pantoea dispersa 1611 is an aerobe, mesophilic, Gram-negative human pathogen of the family Erwiniaceae.

NCBI tax id

  • NCBI tax id: 59814
  • Matching level: species

strain history

@refhistory
9109<- ATCC <- Ajinomoto Co., Inc., 1611
118947CIP <- 1988, LMG <- 1980, F. Gavini, CUEMT, Lille, France , Erwinia herbicola <- ATCC <- Ajinomoto Co. Inc., Japan

doi: 10.13145/bacdive5006.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Erwiniaceae
  • genus: Pantoea
  • species: Pantoea dispersa
  • full scientific name: Pantoea dispersa Gavini et al. 1989

@ref: 9109

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Erwiniaceae

genus: Pantoea

species: Pantoea dispersa

full scientific name: Pantoea dispersa Gavini et al. 1989

strain designation: 1611

type strain: yes

Morphology

cell morphology

  • @ref: 118947
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

multimedia

  • @ref: 9109
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_30073.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9109NUTRIENT 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
40611MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118947CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
118947CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
9109positivegrowth28mesophilic
40611positivegrowth30mesophilic
48162positivegrowth24-35
118947positivegrowth30-37mesophilic
118947nogrowth5psychrophilic
118947nogrowth10psychrophilic
118947nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
48162aerobe
118947obligate aerobe

compound production

  • @ref: 9109
  • compound: 5' inosinic acid

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol+builds acid from18333
68371L-fucose-builds acid from18287
68371D-tagatose-builds acid from16443
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371maltose+builds acid from17306
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol+builds acid from17268
68371L-rhamnose+builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68368L-arabinose+fermentation30849
68368amygdalin+fermentation27613
68368melibiose+fermentation28053
68368sucrose+fermentation17992
68368L-rhamnose+fermentation62345
68368sorbitol-fermentation30911
68368myo-inositol+fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate+assimilation16947
68368lysine-degradation25094
118947citrate+carbon source16947
118947glucose-fermentation17234
118947lactose-fermentation17716
118947nitrate-reduction17632
118947nitrite-reduction16301
118947malonate-assimilation15792
118947sodium thiosulfate-builds gas from132112

antibiotic resistance

  • @ref: 118947
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11894735581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11894715688acetoin-
11894717234glucose-

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
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368lysine decarboxylase-4.1.1.18
68368beta-galactosidase+3.2.1.23
118947oxidase-
118947beta-galactosidase+3.2.1.23
118947alcohol dehydrogenase-1.1.1.1
118947gelatinase+
118947catalase+1.11.1.6
118947lysine decarboxylase-4.1.1.18
118947ornithine decarboxylase-4.1.1.17
118947phenylalanine ammonia-lyase-4.3.1.24
118947tryptophan deaminase-
118947urease-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
118947-+++-+----++-+---+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
9109++-++----+-+++-+++++-
9109+---+----+-+++-+++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118947+/-+/-+/-+++---++++-++/-++---++/-+/-+/-+/-+/-++/-+/-++------+-+/--+/--+-+/-+/--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118947+++++--+-++--+-+++++++-+--+----+++-----++--+++-+++++-+++++-++------------+-+--+++-+---+--++++++----

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample type
40611JapanJPNAsia
48162Soil
118947JapanJPNAsiaEnvironment, Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_974.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_651;98_760;99_974&stattab=map
  • Last taxonomy: Pantoea
  • 16S sequence: FJ756349
  • Sequence Identity:
  • Total samples: 13169
  • soil counts: 878
  • aquatic counts: 1633
  • animal counts: 8308
  • plant counts: 2350

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
9109yes, in single cases1Risk group (German classification)
1189471Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pantoea dispersa strain DSM 30073 16S ribosomal RNA gene, partial sequenceFJ7563491506ena59814
20218Pantoea dispersa strain LMG2603 16S ribosomal RNA gene, partial sequenceDQ5043051347ena59814
20218Pantoea dispersa strain LMG 2603 16S ribosomal RNA gene, partial sequenceFJ6118651361ena59814

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pantoea dispersa DSM 30073GCA_014155765scaffoldncbi59814
66792Pantoea dispersa strain DSM 3007359814.155wgspatric59814
66792Pantoea dispersa strain DSM 30073 strain RIT 41359814.23wgspatric59814

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.951no
flagellatedno67.96no
gram-positiveno97.729no
anaerobicno98.798yes
aerobicno53.673yes
halophileno86.966no
spore-formingno93.831no
glucose-utilyes94.749no
thermophileno99.448no
glucose-fermentyes87.573no

External links

@ref: 9109

culture collection no.: DSM 30073, ATCC 14589, CCUG 25232, LMG 2603, CIP 103338

straininfo link

  • @ref: 74501
  • straininfo: 3796

literature

  • topic: Phylogeny
  • Pubmed-ID: 1581180
  • title: Pantoea punctata sp. nov., Pantoea citrea sp. nov., and Pantoea terrea sp. nov. isolated from fruit and soil samples.
  • authors: Kageyama B, Nakae M, Yagi S, Sonoyama T
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-42-2-203
  • year: 1992
  • mesh: Base Composition, Erwinia/classification/*isolation & purification/ultrastructure, Fruit/*microbiology, Gluconates/*metabolism, Microscopy, Electron, Nucleic Acid Hybridization, Phenotype, *Soil Microbiology
  • topic2: Phenotype

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9109Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30073)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30073
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
40611Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15125
48162Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 25232)https://www.ccug.se/strain?id=25232
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)
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
74501Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3796.1StrainInfo: A central database for resolving microbial strain identifiers
118947Curators of the CIPCollection of Institut Pasteur (CIP 103338)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103338