Strain identifier

BacDive ID: 4992

Type strain: Yes

Species: Pantoea agglomerans

Strain Designation: Graham Price, Brice

Strain history: CIP <- 1952, NCTC, Bacterium typhiflavum <- 1956, M.S. Pereira : strain Brice, Chromobacterium typhiflavum

NCBI tax ID(s): 1220570 (strain), 549 (species)

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General

@ref: 1395

BacDive-ID: 4992

DSM-Number: 3493

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

description: Pantoea agglomerans Graham Price is a mesophilic, motile bacterium that was isolated from knee laceration.

NCBI tax id

NCBI tax idMatching level
1220570strain
549species

strain history

@refhistory
1395<- CIP <- NCTC <- M.S. Pereira, strain Graham Price
67770Y. Kosako 83002 <-- R. Sakazaki 236 <-- W. H. Ewing CDC 1461-67 <-- D. Graham <-- NCTC 9381 <-- M. Pereira strain Graham Price (=ICPB 3435).
116156CIP <- 1952, NCTC, Bacterium typhiflavum <- 1956, M.S. Pereira : strain Brice, Chromobacterium typhiflavum

doi: 10.13145/bacdive4992.20230509.8.1

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 agglomerans
  • full scientific name: Pantoea agglomerans (Beijerinck 1888) Gavini et al. 1989

  • synonyms

    @refsynonym
    20215Bacillus milletiae
    20215Bacterium herbicola
    20215Enterobacter agglomerans
    20215Erwinia herbicola
    20215Erwinia milletiae
    20215Bacillus agglomerans

@ref: 1395

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Erwiniaceae

genus: Pantoea

species: Pantoea agglomerans

full scientific name: Pantoea agglomerans (Beijerinck 1888) Gavini et al. 1989

strain designation: Graham Price, Brice

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.924
6948099.964negative
116156yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1395COLUMBIA 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
1395TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
37336MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116156CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1395positivegrowth30mesophilic
37336positivegrowth30mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.915
116156no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11615616947citrate-carbon source
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

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11615635581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837735581indole-
6836815688acetoin+
6836835581indole-
11615615688acetoin+
11615617234glucose-

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
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
68368cytochrome oxidase-1.9.3.1
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
116156oxidase-
116156beta-galactosidase+3.2.1.23
116156alcohol dehydrogenase-1.1.1.1
116156catalase+1.11.1.6
116156lysine decarboxylase-4.1.1.18
116156ornithine decarboxylase-4.1.1.17
116156urease-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
44222-+-+-+----++-----+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
1395+--------+++++/--+++++-
1395+--------++++-++++++-
1395+--------+-++--++-++-

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
44222-++-+---++-+-

Isolation, sampling and environmental information

isolation

@refsample typesampling datecountryorigin.countrycontinentgeographic locationisolation date
1395knee laceration
44222Knee laceration1956ZimbabweZWEAfrica
67770Knee laceration
116156Human, Knee laceration (young man who fell while playing football)United KingdomGBREuropeSalisbury1956-04-03

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Limb#Leg
#Host Body-Site#Other#Wound
#Host Body-Site#Limb#Joint

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
13952Risk group (German classification)
1161561Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pantoea agglomerans strain ATCC 27155 16S ribosomal RNA gene, partial sequenceAF1309531271ena549
20218Pantoea agglomerans strain ATCC 27155 16S ribosomal RNA gene, partial sequenceFJ971873797ena549
20218Pantoea agglomerans partial 16S rRNA gene, isolate OS-21.aAM2373451198ena549
20218Pantoea agglomerans gene for 16S rRNA, partial sequenceAB0046911449ena549
20218Pantoea agglomerans strain LMG 1286 16S ribosomal RNA gene, partial sequenceFJ6118391387ena549
20218Pantoea agglomerans gene for 16S rRNA, partial sequence, strain: NBRC 102470AB6818121466ena549
20218Pantoea agglomerans 16S ribosomal RNA, partial 5' end, strain NCTC 9381 TAJ001239509ena549
20218Pantoea agglomerans 16S ribosomal RNA, partial 3' end, strain NCTC 9381 TAJ001240509ena549
20218Pantoea agglomerans partial 16S rRNA gene, strain NCTC9381TAJ2514661512ena549
1395Pantoea agglomerans 16S rRNA gene (strain DSM 3493)AJ2334231473ena549

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pantoea agglomerans NBRC 1024701220570.3wgspatric1220570
66792Pantoea agglomerans strain FDAARGOS 1447549.416completepatric549
66792Pantoea agglomerans strain NCTC9381549.99wgspatric549
66792Pantoea agglomerans NBRC 1024702731957702draftimg1220570
67770Pantoea agglomerans NBRC 102470GCA_001598475contigncbi1220570
67770Pantoea agglomerans NCTC9381GCA_900454405contigncbi549

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.069no
anaerobicno98.772no
halophileno83.149no
spore-formingno94.849no
glucose-utilyes95.41no
thermophileno99.006yes
aerobicno70.455no
motileyes93.704no
flagellatedno68.478no
glucose-fermentyes91.641no

External links

@ref: 1395

culture collection no.: DSM 3493, ATCC 27155, CIP 57.51, NCTC 9381, WDCM 00170, CCUG 539, LMG 1286, JCM 1236, BCRC 14807, CDC 1461-67, CECT 850, CGMCC 1.2244, HUT 8112, IAM 12659, ICPB 3435, KCTC 2564, NBRC 102470, NCIMB 13953, VTT E-90413, CCTM 899, CCUG 1461-67, USCC 1520

straininfo link

  • @ref: 74487
  • straininfo: 13737

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny319202Taxonomy of the genus Serratia.Grimont PA, Grimont F, De Rosnay HLJ Gen Microbiol10.1099/00221287-98-1-391977Bacteriological Techniques, Enterobacteriaceae/classification, Erwinia/classification, Serratia/*classification
Phylogeny1581180Pantoea punctata sp. nov., Pantoea citrea sp. nov., and Pantoea terrea sp. nov. isolated from fruit and soil samples.Kageyama B, Nakae M, Yagi S, Sonoyama TInt J Syst Bacteriol10.1099/00207713-42-2-2031992Base Composition, Erwinia/classification/*isolation & purification/ultrastructure, Fruit/*microbiology, Gluconates/*metabolism, Microscopy, Electron, Nucleic Acid Hybridization, Phenotype, *Soil MicrobiologyPhenotype
Phylogeny14687210Isolation of endophytic diazotroph Pantoea agglomerans and nondiazotroph Enterobacter asburiae from sweetpotato stem in Japan.Asis CA Jr, Adachi KLett Appl Microbiol10.1046/j.1472-765x.2003.01434.x2004Bacterial Typing Techniques, DNA, Ribosomal/chemistry/isolation & purification, Enterobacter/classification/growth & development/*isolation & purification/metabolism, Ipomoea batatas/*microbiology, Japan, Molecular Sequence Data, Nitrogen Fixation, Oxidation-Reduction, Pantoea/classification/growth & development/*isolation & purification/metabolism, Phenotype, Plant Stems/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, SymbiosisEnzymology
18365722[Study of ectoparasitism of ultramicrobacteria of the genus Kaistia, strains NF1 and NF3 by electron and fluorescence microscopy].Suzina NE, Esikova TZ, Akimov VN, Abashina TN, Dmitriev VV, Polivtseva VN, Duda VI, Boronin AMMikrobiologiia2008Alphaproteobacteria/*physiology/ultrastructure, Bacillus subtilis/physiology/ultrastructure, Bacteriolysis, Comamonadaceae/physiology/ultrastructure, Microscopy, Electron, Microscopy, Fluorescence, *Soil Microbiology
30743637First Report of Leaf Blight Caused by Pantoea agglomerans on Rice in Korea.Lee HB, Hong JP, Kim SBPlant Dis10.1094/PDIS-05-10-03742010
30780539First Report of Pantoea agglomerans Causing Leaf Blight and Vascular Wilt in Maize and Sorghum in Mexico.Morales-Valenzuela G, Silva-Rojas HV, Ochoa-Martinez D, Valadez-Moctezuma E, Alarcon-Zuniga B, Zelaya-Molina LX, Cordova-Tellez L, Mendoza-Onofre L, Vaquera-Huerta H, Carballo-Carballo A, Farfan-Gomez A, Avila-Quezada GPlant Dis10.1094/PDIS-91-10-1365A2007
Metabolism34822536Antifungal Activity of Biocontrol Agents In Vitro and Potential Application to Reduce Mycotoxins (Aflatoxin B1 and Ochratoxin A).Illueca F, Vila-Donat P, Calpe J, Luz C, Meca G, Quiles JMToxins (Basel)10.3390/toxins131107522021Aflatoxin B1/*metabolism, Antifungal Agents/*pharmacology, Bacillus amyloliquefaciens/metabolism, Cell-Free System, Fungicides, Industrial/*pharmacology, In Vitro Techniques, Ochratoxins/*metabolism, Paenibacillus/metabolism, Pantoea/metabolism, *Pest Control, Biological, Poisons/*metabolismBiotechnology
36194731First report of bacterial wilt disease caused by Pantoea agglomerans on the ornamental perennial Oxalis articulata in China.Wang Y, Su P, Zhang P, Zhang YPlant Dis10.1094/PDIS-08-22-1883-PDN2022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1395Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3493)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3493
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
37336Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/9638
44222Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 539)https://www.ccug.se/strain?id=539
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/
68368Automatically annotated from API 20E
68377Automatically annotated from API NH
68382Automatically annotated from API zym
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
74487Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13737.1StrainInfo: A central database for resolving microbial strain identifiers
116156Curators of the CIPCollection of Institut Pasteur (CIP 57.51)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2057.51