Strain identifier

BacDive ID: 5178

Type strain: Yes

Species: Tatumella punctata

Strain Designation: BD 876

Strain history: CIP <- 1998, B. Kageyama, Shionogi and Co., Osaka, Japan: strain SHS 2006

NCBI tax ID(s): 399969 (species)

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General

@ref: 5123

BacDive-ID: 5178

DSM-Number: 13700

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Tatumella punctata BD 876 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from mandarin orange.

NCBI tax id

  • NCBI tax id: 399969
  • Matching level: species

strain history

@refhistory
5123<- ATCC <- Shionogi and Co., Ltd. (Erwinia punctata)
358471998, B. Kageyame, Shionogi & Co., Osaka, Japan: strain SHS 2006
67770B. Kageyama SHS 2006.
122060CIP <- 1998, B. Kageyama, Shionogi and Co., Osaka, Japan: strain SHS 2006

doi: 10.13145/bacdive5178.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Erwiniaceae
  • genus: Tatumella
  • species: Tatumella punctata
  • full scientific name: Tatumella punctata (Kageyama et al. 1992) Brady et al. 2010

  • synonyms

    • @ref: 20215
    • synonym: Pantoea punctata

@ref: 5123

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Erwiniaceae

genus: Tatumella

species: Tatumella punctata

full scientific name: Tatumella punctata (Kageyama et al. 1992) Brady et al. 2010

strain designation: BD 876

type strain: yes

Morphology

cell morphology

  • @ref: 122060
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5123REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
35847MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122060CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
5123positivegrowth28mesophilic
35847positivegrowth25mesophilic
49943positivegrowth30mesophilic
67770positivegrowth30mesophilic
122060positivegrowth25-37mesophilic
122060nogrowth5psychrophilic
122060nogrowth10psychrophilic
122060nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
49943aerobe
122060facultative anaerobe

compound production

  • @ref: 5123
  • compound: 2,5 diketo-D-gulonic 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
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371amygdalin-builds acid from27613
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
68371galactitol-builds acid from16813
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-arabinose-builds acid from17108
68371erythritol-builds acid from17113
122060mannitol-fermentation29864
122060citrate+carbon source16947
122060glucose+fermentation17234
122060lactose-fermentation17716
122060nitrate+reduction17632
122060nitrite-reduction16301
122060malonate-assimilation15792
122060sodium thiosulfate-builds gas from132112
122060glucose+degradation17234

antibiotic resistance

  • @ref: 122060
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 122060
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12206015688acetoin-
12206017234glucose+

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
122060oxidase-
122060beta-galactosidase-3.2.1.23
122060alcohol dehydrogenase+1.1.1.1
122060gelatinase-
122060catalase+1.11.1.6
122060lysine decarboxylase-4.1.1.18
122060ornithine decarboxylase-4.1.1.17
122060phenylalanine ammonia-lyase-4.3.1.24
122060tryptophan deaminase-
122060urease-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
122060-+++-++---++-----+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122060+/---+/-+/-+/----++++--------+-+/-+/-+/-+/---+++/---+/----+/----+/----+/-+/-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122060+++++--+-----------------------+-----------------+---+--++-++---------+--------++-----+--+++-------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
5123mandarin orangeJapanJPNAsia
49943Mandarin orangeJapanJPNAsia
67770Mandarin orangeJapanJPNAsia
122060Mandarin orangeJapanJPNAsia1977

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Plant
  • Cat3: #Fruit (Seed)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
51231Risk group (German classification)
1220601Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pantoea punctata strain JCM 8885 16S ribosomal RNA gene, partial sequenceDQ8380971305ena399969
20218Pantoea punctata strain CIP 105598 16S ribosomal RNA gene, complete sequenceJN1753421527ena399969
5123Pantoea punctata strain DSM 13700 16S ribosomal RNA gene, partial sequenceFJ7563511505ena399969
5123Pantoea punctata strain LMG 22050 16S ribosomal RNA gene, partial sequenceEF6880061494ena399969

GC content

@refGC-contentmethod
512350.7
6777050.7high performance liquid chromatography (HPLC)
6777050.3high performance liquid chromatography (HPLC)

External links

@ref: 5123

culture collection no.: DSM 13700, ATCC 31626, CCUG 30159, CIP 105598, FERM P-5452, JCM 8885, LMG 22050, SHS 2006, BCRC 14443, CCM 4320, KCTC 12452, KCTC 2747, NCPPB 3820

straininfo link

  • @ref: 74670
  • straininfo: 40160

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny19654354Transfer of Pantoea citrea, Pantoea punctata and Pantoea terrea to the genus Tatumella emend. as Tatumella citrea comb. nov., Tatumella punctata comb. nov. and Tatumella terrea comb. nov. and description of Tatumella morbirosei sp. nov.Brady CL, Venter SN, Cleenwerck I, Vandemeulebroecke K, De Vos P, Coutinho TAInt J Syst Evol Microbiol10.1099/ijs.0.012070-02009Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Enterobacteriaceae/*classification/genetics/isolation & purification, Fruit/microbiology, Molecular Sequence Data, Pantoea/*classification/genetics/isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil MicrobiologyEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5123Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13700)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13700
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
35847Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17635
49943Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30159)https://www.ccug.se/strain?id=30159
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
74670Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40160.1StrainInfo: A central database for resolving microbial strain identifiers
122060Curators of the CIPCollection of Institut Pasteur (CIP 105598)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105598