Strain identifier

BacDive ID: 4372

Type strain: Yes

Species: Enterobacter ludwigii

Strain Designation: EN-119

Strain history: CIP <- 2004, J. Heesemann, LM Munich Univ., Gauting, Germany: strain EN-119

NCBI tax ID(s): 299767 (species)

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General

@ref: 6567

BacDive-ID: 4372

DSM-Number: 16688

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

description: Enterobacter ludwigii EN-119 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from mid-stream urine.

NCBI tax id

  • NCBI tax id: 299767
  • Matching level: species

strain history

@refhistory
6567<- H. Hoffmann; EN-119
120664CIP <- 2004, J. Heesemann, LM Munich Univ., Gauting, Germany: strain EN-119

doi: 10.13145/bacdive4372.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Enterobacter
  • species: Enterobacter ludwigii
  • full scientific name: Enterobacter ludwigii Hoffmann et al. 2005

@ref: 6567

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Enterobacter

species: Enterobacter ludwigii

full scientific name: Enterobacter ludwigii Hoffmann et al. 2005

strain designation: EN-119

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
120664negativerod-shapedyes
125439negative98
125438negative99.5

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6567COLUMBIA 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
6567CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
37435MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120664CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
6567positivegrowth37
37435positivegrowth30
59148positivegrowth30-37
120664positivegrowth10-41
120664nogrowth5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59148aerobe
120664facultative anaerobe

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 96.4

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12066429864mannitol+fermentation
12066416947citrate+carbon source
12066417234glucose+fermentation
12066417716lactose-fermentation
12066417632nitrate+reduction
12066416301nitrite-reduction
12066415792malonate+assimilation
120664132112sodium thiosulfate-builds gas from
12066417234glucose+degradation
68371Potassium 5-ketogluconate-builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin-builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol+builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol+builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol+fermentation
6836817268myo-inositol+fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis

antibiotic resistance

  • @ref: 120664
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
12066435581indoleno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-testindole test
12066415688acetoin+
12066417234glucose-
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
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
120664oxidase-
120664beta-galactosidase+3.2.1.23
120664alcohol dehydrogenase+1.1.1.1
120664gelatinase-
120664catalase+1.11.1.6
120664lysine decarboxylase-4.1.1.18
120664ornithine decarboxylase+4.1.1.17
120664phenylalanine ammonia-lyase-4.3.1.24
120664tryptophan deaminase-
120664urease-3.5.1.5
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    59148C12:0512
    59148C13:00.713
    59148C14:07.514
    59148C15:03.715
    59148C16:022.716
    59148C17:01.617
    59148C18:00.218
    59148C12:0 ALDE ?0.810.915
    59148C13:0 3OH/C15:1 i I/H0.514.469
    59148C14:0 3OH/C16:1 ISO I7.315.485
    59148C16:1 ω7c20.315.819
    59148C17:0 CYCLO12.716.888
    59148C17:1 ω8c0.416.792
    59148C18:1 ω7c /12t/9t14.317.824
    59148C18:2 ω6,9c/C18:0 ANTE0.317.724
    59148C19:0 CYCLO ω8c0.218.9
    59148Unidentified0.29.152
    59148Unidentified0.413.94
    59148Unidentified0.315.176
    59148Unidentified0.319.069
    59148unknown 14.5030.514.503
    59148unknown 18.5550.418.555
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120664-+---+----++++-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
6567-+-++----+++++++++++-
6567++-++----+-+++++++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120664+--+++---++++-+-+++-++-+++++++++--+---++/----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120664+++++-++++++-+++++++++++-------++++-+--+-++++----+++-++++--+++-------------+---++-----+-++++++++--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6567mid-stream urineMunich, Grosshadern HospitalGermanyDEUEurope
59148Human mid-stream urine,18-yr-old maleMünchenGermanyDEUEurope
120664Human, UrineMünchenGermanyDEUEurope2000

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Urine

taxonmaps

  • @ref: 69479
  • File name: preview.99_66.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_17;99_66&stattab=map
  • Last taxonomy: Enterobacterales
  • 16S sequence: NR_042349
  • Sequence Identity:
  • Total samples: 14221
  • soil counts: 575
  • aquatic counts: 888
  • animal counts: 11838
  • plant counts: 920

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65672Risk group (German classification)
1206642Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Enterobacter ludwigii 16S rRNA gene, type strain EN-119TAJ8538911513nuccore299767
20218Enterobacter ludwigii strain DSMZ 16688 16S ribosomal RNA gene, partial sequenceKF5162571347nuccore299767
6567Enterobacter ludwigii strain EN-119 16S ribosomal RNA, partial sequenceNR_0423491513nuccore299767

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Enterobacter ludwigii EN-119GCA_001750725completencbi299767
66792Enterobacter ludwigii EN-119GCA_000818595contigncbi299767
66792Enterobacter ludwigii EN-119299767.3wgspatric299767
66792Enterobacter ludwigii strain FDAARGOS 1436299767.200completepatric299767
66792Enterobacter ludwigii EN-1192718218030completeimg299767
66792Enterobacter ludwigii EN-1192636415448draftimg299767

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.82yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no65.79no
125438spore-formingspore-formingAbility to form endo- or exosporesno88.648no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno100yes
125438motile2+flagellatedAbility to perform flagellated movementyes80.403no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno96.4
125439BacteriaNetmotilityAbility to perform movementyes63.6
125439BacteriaNetgram_stainReaction to gram-stainingnegative98
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe88.6

External links

@ref: 6567

culture collection no.: CCUG 51323, DSM 16688, CCM 8602, CIP 108491, KCTC 23921

straininfo link

  • @ref: 73863
  • straininfo: 138308

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15900967Description of Enterobacter ludwigii sp. nov., a novel Enterobacter species of clinical relevance.Hoffmann H, Stindl S, Stumpf A, Mehlen A, Monget D, Heesemann J, Schleifer KH, Roggenkamp ASyst Appl Microbiol10.1016/j.syapm.2004.12.0092005Bacterial Typing Techniques, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Enterobacter/*classification/isolation & purification/physiology, Enterobacteriaceae Infections/*microbiology, Fermentation, Genes, rRNA, Gentian Violet, Humans, Inositol/metabolism, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phenazines, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology
Phylogeny24824638Enterobacter xiangfangensis sp. nov., isolated from Chinese traditional sourdough, and reclassification of Enterobacter sacchari Zhu et al. 2013 as Kosakonia sacchari comb. nov.Gu CT, Li CY, Yang LJ, Huo GCInt J Syst Evol Microbiol10.1099/ijs.0.064709-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Enterobacter/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Fermentation, *Food Microbiology, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNABiotechnology
Phylogeny25412475Characterization of exoelectrogenic bacteria enterobacter strains isolated from a microbial fuel cell exposed to copper shock load.Feng C, Li J, Qin D, Chen L, Zhao F, Chen S, Hu H, Yu CPPLoS One10.1371/journal.pone.01133792014Bioelectric Energy Sources/*microbiology, Copper/*physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Electricity, Electron Transport, Enterobacter/*classification/genetics/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis, Sequence Analysis, DNA, Spectrum Analysis, RamanGenetics
Genetics25724532Whole genome sequence of Enterobacter ludwigii type strain EN-119T, isolated from clinical specimens.Li G, Hu Z, Zeng P, Zhu B, Wu LFEMS Microbiol Lett10.1093/femsle/fnv0332015Base Sequence, DNA, Bacterial/genetics, Enterobacter/*genetics/*isolation & purification, Enterobacter cloacae/genetics, *Genome, Bacterial, Molecular Sequence Data, *Sequence Analysis, DNA, SyntenyTranscriptome
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

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6567Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16688)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16688
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
37435Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6119
59148Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51323)https://www.ccug.se/strain?id=51323
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
73863Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138308.1StrainInfo: A central database for resolving microbial strain identifiers
120664Curators of the CIPCollection of Institut Pasteur (CIP 108491)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108491
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1