Strain identifier

BacDive ID: 4365

Type strain: No

Species: Enterobacter ludwigii

Strain Designation: EK4

Strain history: <- E. Katsivela; EK4

NCBI tax ID(s): 299767 (species)

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General

@ref: 5760

BacDive-ID: 4365

DSM-Number: 15213

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

description: Enterobacter ludwigii EK4 is a mesophilic, Gram-negative bacterium that was isolated from soil from a landfarm for treatment of refinery waste sludge.

NCBI tax id

  • NCBI tax id: 299767
  • Matching level: species

strain history

  • @ref: 5760
  • history: <- E. Katsivela; EK4

doi: 10.13145/bacdive4365.20250331.9.3

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: 5760

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: EK4

type strain: no

Morphology

cell morphology

@refgram stainconfidence
125439negative95.7
125438negative99.5

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5760COLUMBIA 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
5760TRYPTICASE 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

culture temp

  • @ref: 5760
  • growth: positive
  • type: growth
  • temperature: 30

Physiology and metabolism

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 90.2

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol+fermentation
6836817268myo-inositol+fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
5760++-++----+-+++++++++-

Isolation, sampling and environmental information

isolation

  • @ref: 5760
  • sample type: soil from a landfarm for treatment of refinery waste sludge
  • geographic location: Korinthos
  • country: Greece
  • origin.country: GRC
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Engineered#Waste
#Environmental#Terrestrial#Mud (Sludge)
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 5760
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 5760
  • description: Enterobacter sp. EK4 partial 16S rRNA gene, isolate EK4
  • accession: AJ457062
  • length: 481
  • database: nuccore
  • NCBI tax ID: 192167

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Enterobacter ludwigii strain FDAARGOS_1475299767.207completepatric299767
66792Enterobacter ludwigii strain FDAARGOS_1475299767.225completepatric299767
66792Enterobacter ludwigii strain FDAARGOS_1475299767.235completepatric299767
66792Enterobacter ludwigii strain FDAARGOS_1475299767.215completepatric299767

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.298no
125438spore-formingspore-formingAbility to form endo- or exosporesno89.137no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no66.965no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno100yes
125438motile2+flagellatedAbility to perform flagellated movementyes78.607no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno90.2
125439BacteriaNetmotilityAbility to perform movementyes72.7
125439BacteriaNetgram_stainReaction to gram-stainingnegative95.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe89.1

External links

@ref: 5760

culture collection no.: DSM 15213

straininfo link

  • @ref: 73856
  • straininfo: 144473

Reference

@idauthorscataloguedoi/urltitle
5760Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15213)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15213
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
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
73856Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID144473.1StrainInfo: A central database for resolving microbial strain identifiers
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