Strain identifier

BacDive ID: 4379

Type strain: Yes

Species: Lelliottia nimipressuralis

Strain Designation: E 62

Strain history: CIP <- 1996, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain E 62, Enterobacter nimipressuralis

NCBI tax ID(s): 69220 (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: 7801

BacDive-ID: 4379

DSM-Number: 18955

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

description: Lelliottia nimipressuralis E 62 is an aerobe, mesophilic, motile plant pathogen that was isolated from elm tree.

NCBI tax id

  • NCBI tax id: 69220
  • Matching level: species

strain history

@refhistory
7801<- CIP <- P. A. D. Grimont, Inst. Pasteur; E 62
328341996, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain E 62, Enterobacter nimipressuralis
67770ATCC 9912 <-- J. C. Carter 41-173.
121304CIP <- 1996, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain E 62, Enterobacter nimipressuralis

doi: 10.13145/bacdive4379.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Lelliottia
  • species: Lelliottia nimipressuralis
  • full scientific name: Lelliottia nimipressuralis (Carter 1945) Brady et al. 2013

  • synonyms

    @refsynonym
    20215Erwinia nimipressuralis
    20215Enterobacter nimipressuralis

@ref: 7801

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Lelliottia

species: Lelliottia nimipressuralis

full scientific name: Lelliottia nimipressuralis (Carter 1945) Brady et al. 2013

strain designation: E 62

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes94.479
6948099.984negative
121304yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7801TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
32834MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121304CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
121304CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7801positivegrowth30mesophilic
32834positivegrowth30mesophilic
48286positivegrowth30mesophilic
67770positivegrowth37mesophilic
121304positivegrowth30-41
121304nogrowth5psychrophilic
121304nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
48286aerobe
121304facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.966

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate+builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
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
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
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
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-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
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
68368ornithine+degradation18257
68368lysine-degradation25094
68368arginine+hydrolysis29016
121304mannitol+fermentation29864
121304citrate+carbon source16947
121304glucose+fermentation17234
121304lactose+fermentation17716
121304nitrate+reduction17632
121304nitrite-reduction16301
121304malonate+assimilation15792
121304sodium thiosulfate-builds gas from132112
121304glucose+degradation17234

antibiotic resistance

  • @ref: 121304
  • 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
12130435581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12130415688acetoin+
12130417234glucose-

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
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23
121304oxidase-
121304beta-galactosidase+3.2.1.23
121304alcohol dehydrogenase+1.1.1.1
121304gelatinase-
121304catalase+1.11.1.6
121304lysine decarboxylase-4.1.1.18
121304ornithine decarboxylase+4.1.1.17
121304phenylalanine ammonia-lyase-4.3.1.24
121304tryptophan deaminase-
121304urease-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
121304-+---+----++++-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
7801++-++----+-++-++-+++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121304+--+++---++++-+-----++-+++++++-+------+-+/-+-----+-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121304+++++-+--+++-+++++++++++------++-++-+--+-+-++----+---++++--+++-------------++--++--------++++++----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7801elm treeUSAUSANorth America
48286Elm,Ulmus sp.USAUSANorth America
67770Elm treeUSAUSANorth America
121304ElmUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_11116.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_78;99_11116&stattab=map
  • Last taxonomy: Enterobacteriaceae
  • 16S sequence: Z96077
  • Sequence Identity:
  • Total samples: 477
  • soil counts: 67
  • aquatic counts: 49
  • animal counts: 316
  • plant counts: 45

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
7801yes1Risk group (German classification)
1213042Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lelliottia nimipressuralis strain DSMZ 18955 16S ribosomal RNA gene, partial sequenceKF5162601347ena69220
7801Enterobacter nimipressuralis LMG 10245-T 16S ribosomal RNAZ960771498ena69220
7801Enterobacter nimipressuralis strain LMG 10245 16S ribosomal RNA gene, partial sequenceJF430421616ena69220

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lelliottia nimipressuralis strain CCUG 2589469220.11wgspatric69220
66792Lelliottia nimipressuralis strain CIP 10498069220.3wgspatric69220
66792Lelliottia nimipressuralis CIP 1049802843132434draftimg69220
67770Lelliottia nimipressuralis CIP 104980GCA_001875645contigncbi69220
67770Lelliottia nimipressuralis CCUG 25894GCA_004115925contigncbi69220

GC content

  • @ref: 67770
  • GC-content: 58.4-59.6
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.25no
anaerobicno95.84yes
halophileno87.887no
spore-formingno93.557no
glucose-utilyes94.635no
flagellatedno61.281no
thermophileno98.974yes
motileyes88.363no
aerobicyes86.12yes
glucose-fermentyes93.025yes

External links

@ref: 7801

culture collection no.: DSM 18955, ATCC 9912, CIP 104980, LMG 10245, NCPPB 2045, CCUG 25894, JCM 6050, ICMP 1577

straininfo link

  • @ref: 73870
  • straininfo: 11790

literature

Pubmed-IDtitleauthorsjournalDOIyeartopicmeshtopic2
29472760Genetic Diversity and Functional Analysis of Sigma Factors in Enterobacter cloacae Complex Resourced From Various Niche.Nazir F, Ibrahim M, Zaman G, Hussain A, Yar AM, Bo ZEvol Bioinform Online10.1177/11769343187548782018
29583116Lelliottia jeotgali sp. nov., isolated from a traditional Korean fermented clam.Yuk KJ, Kim YT, Huh CS, Lee JHInt J Syst Evol Microbiol10.1099/ijsem.0.0027372018PhylogenyAnimals, Bacterial Typing Techniques, Base Composition, Bivalvia/*microbiology, DNA, Bacterial/genetics, Enterobacter/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Fermented Foods/*microbiology, Genes, Bacterial, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seafood/*microbiology, Sequence Analysis, DNATranscriptome
35829834Lelliottia steviae sp. nov. isolated from Stevia rebaudiana Bertoni.Lin J, Huang K, Huang JY, Xiong YR, Wei MM, Xiao N, Gao J, Ding XK, Ma ZY, Sang JH, Kong LX, Hong ZY, Li OArch Microbiol10.1007/s00203-022-03033-22022PhylogenyBacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal, Fatty Acids/analysis, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Stevia/geneticsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7801Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18955)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18955
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
32834Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16948
48286Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 25894)https://www.ccug.se/strain?id=25894
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
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
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
73870Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID11790.1StrainInfo: A central database for resolving microbial strain identifiers
121304Curators of the CIPCollection of Institut Pasteur (CIP 104980)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104980