Strain identifier

BacDive ID: 5177

Type strain: Yes

Species: Tatumella citrea

Strain Designation: BD 875

Strain history: CIP <- 1998, B. Kageyama, Shionogi and Co., Osaka, Japan: strain SHS 2003

NCBI tax ID(s): 53336 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 5122

BacDive-ID: 5177

DSM-Number: 13699

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

description: Tatumella citrea BD 875 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from mandarin orange.

NCBI tax id

  • NCBI tax id: 53336
  • Matching level: species

strain history

@refhistory
5122<- ATCC <- Shionogi Co, Ltd. (Erwinia citreus)
393251998, B. Kageyama, Shionogi & Co., Osaka, Japan: strain SHS 2003
67770B. Kageyama SHS 2003.
118296CIP <- 1998, B. Kageyama, Shionogi and Co., Osaka, Japan: strain SHS 2003

doi: 10.13145/bacdive5177.20230509.8.1

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

  • synonyms

    • @ref: 20215
    • synonym: Pantoea citrea

@ref: 5122

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Erwiniaceae

genus: Tatumella

species: Tatumella citrea

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

strain designation: BD 875

type strain: yes

Morphology

cell morphology

  • @ref: 118296
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5122REACTIVATION 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
39325MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118296CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
118296CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
5122positivegrowth28mesophilic
39325positivegrowth25mesophilic
49940positivegrowth30-37mesophilic
67770positivegrowth30mesophilic
118296positivegrowth25-37mesophilic
118296nogrowth5psychrophilic
118296nogrowth10psychrophilic
118296nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
49940aerobe
118296facultative anaerobe

compound production

  • @ref: 5122
  • compound: 2,5 diketo-D-gulonic acid

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-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
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose+builds acid from28053
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371arbutin-builds acid from18305
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
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-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
118296mannitol+fermentation29864
118296citrate+carbon source16947
118296glucose+fermentation17234
118296lactose-fermentation17716
118296nitrate+reduction17632
118296nitrite-reduction16301
118296malonate-assimilation15792
118296sodium thiosulfate-builds gas from132112
118296glucose+degradation17234
68374ornithine-degradation18257
68374arginine+hydrolysis29016
68374lysine-degradation25094
68374urea-hydrolysis16199
68374L-arabitol-builds acid from18403
68374D-galacturonic acid-builds acid from18024
68374Potassium 5-ketogluconate+builds acid from
68374D-mannitol+builds acid from16899
68374maltose+builds acid from17306
68374ribitol+builds acid from15963
68374palatinose+builds acid from18394
68374malonate-assimilation15792
68374tryptophan-energy source27897
68374D-glucose+builds acid from17634
68374sucrose+builds acid from17992
68374L-arabinose+builds acid from30849
68374D-arabitol+builds acid from18333
68374trehalose+builds acid from27082
68374L-rhamnose+builds acid from62345
68374myo-inositol+builds acid from17268
68374cellobiose+builds acid from17057
68374sorbitol+builds acid from30911

antibiotic resistance

  • @ref: 118296
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleno
67770182812,5-didehydro-D-gluconic acidyes
11829635581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837435581indole-
11829615688acetoin+
11829617234glucose+

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
68374L-aspartate arylamidase-3.4.11.21
68374alpha-maltosidase-
68374alpha-galactosidase-3.2.1.22
68374alpha-glucosidase-3.2.1.20
68374beta-galactosidase+3.2.1.23
68374N-acetyl-beta-glucosaminidase-3.2.1.52
68374beta-glucuronidase-3.2.1.31
68374beta-glucosidase-3.2.1.21
68374lipase-
68374urease-3.5.1.5
68374lysine decarboxylase-4.1.1.18
68374arginine dihydrolase+3.5.3.6
68374ornithine decarboxylase-4.1.1.17
118296oxidase-
118296beta-galactosidase+3.2.1.23
118296alcohol dehydrogenase-1.1.1.1
118296gelatinase-
118296catalase+1.11.1.6
118296lysine decarboxylase-4.1.1.18
118296ornithine decarboxylase-4.1.1.17
118296phenylalanine ammonia-lyase-4.3.1.24
118296tryptophan deaminase-
118296urease-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
118296-+---+----++---++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118296+--+++/----++++----+/----+--+/-+/--++/-+-+------+/---++/--+-+/--+

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
49940-+----+---++++----+++++--+++++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118296+++++----++++++----++-----+----+-+------+-------+++--+--++-++------------------++-+---+--+++-------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
5122mandarin orangeJapanJPNAsia
49940Mandarin orangeJapanJPNAsia
67770Mandarin orangeJapanJPNAsia
118296Mandarin orangeJapanJPNAsia1976

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
51221Risk group (German classification)
1182961Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pantoea citrea strain DSM 13699 16S ribosomal RNA gene, partial sequenceFJ7563521361ena53336
5122Pantoea citrea strain JCM 8882 16S ribosomal RNA, partial sequenceDQ8380961351ena53336
5122Pantoea citrea strain LMG 22049 16S ribosomal RNA gene, partial sequenceEF6880081422ena53336

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tatumella citrea DSM 13699GCA_002163585completencbi53336
66792Tatumella citrea strain ATCC 3162353336.10plasmidpatric53336
66792Tatumella citrea strain DSM 1369953336.7completepatric53336
66792Tatumella citrea strain DSM 1369953336.11plasmidpatric53336
66792Tatumella citrea DSM 136992757320934completeimg53336

GC content

@refGC-contentmethod
512249.8high performance liquid chromatography (HPLC)
6777049.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno79.119no
gram-positiveno98.473no
anaerobicno98.867yes
aerobicno68.437no
halophileno81.794no
spore-formingno96.736no
thermophileno99.48yes
glucose-utilyes93.31no
motileyes87.91no
glucose-fermentyes86.443no

External links

@ref: 5122

culture collection no.: DSM 13699, ATCC 31623, CCUG 30156, CIP 105599, FERM P-5449, JCM 8882, LMG 22049, SHS 2003, CCM 4319, KCTC 12451, KCTC 2805, NCPPB 3826

straininfo link

  • @ref: 74669
  • straininfo: 46735

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
Genetics33764372A modified pCas/pTargetF system for CRISPR-Cas9-assisted genome editing in Escherichia coli.Li Q, Sun B, Chen J, Zhang Y, Jiang Y, Yang SActa Biochim Biophys Sin (Shanghai)10.1093/abbs/gmab0362021*CRISPR-Cas Systems, Escherichia coli/*genetics, *Gene Editing, *Genome, Bacterial, Plasmids/genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5122Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13699)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13699
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
39325Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17636
49940Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30156)https://www.ccug.se/strain?id=30156
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/
68371Automatically annotated from API 50CH acid
68374Automatically annotated from API ID32E
68382Automatically annotated from API zym
74669Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46735.1StrainInfo: A central database for resolving microbial strain identifiers
118296Curators of the CIPCollection of Institut Pasteur (CIP 105599)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105599