Strain identifier

BacDive ID: 4323

Type strain: Yes

Species: Citrobacter amalonaticus

Strain history: CIP <- 1982, NCTC <- 1971, V.M. Young: strain 9823, Levinea amalonatica

NCBI tax ID(s): 35703 (species)

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General

@ref: 1784

BacDive-ID: 4323

DSM-Number: 4593

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

description: Citrobacter amalonaticus CCUG 4860 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Human feces.

NCBI tax id

  • NCBI tax id: 35703
  • Matching level: species

strain history

@refhistory
1784<- CIP <- NCTC
67770Y. Kosako 82056 <-- R. Sakazaki 18 <-- ATCC 25405 <-- V. M. Young 9823.
116318CIP <- 1982, NCTC <- 1971, V.M. Young: strain 9823, Levinea amalonatica

doi: 10.13145/bacdive4323.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Citrobacter
  • species: Citrobacter amalonaticus
  • full scientific name: Citrobacter amalonaticus (Young et al. 1971) Brenner and Farmer 1982

  • synonyms

    • @ref: 20215
    • synonym: Levinea amalonatica

@ref: 1784

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Citrobacter

species: Citrobacter amalonaticus

full scientific name: Citrobacter amalonaticus (Young et al. 1971) Brenner and Farmer 1982

type strain: yes

Morphology

cell morphology

  • @ref: 116318
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1784REACTIVATION 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
38207MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116318CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116318CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1784positivegrowth30mesophilic
38207positivegrowth30mesophilic
44799positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44799aerobe
116318facultative anaerobe

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
11631817632nitrate+reduction
11631816301nitrite+reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno
11631835581indoleyes

metabolite tests

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

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
116318oxidase-
116318catalase+1.11.1.6
116318urease-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
116318-+---++-+-++-+-+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
1784++-++---+--++-++--++-

Isolation, sampling and environmental information

isolation

@refsample type
44799Human feces
67770Stool
116318Stool

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_363.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_307;99_363&stattab=map
  • Last taxonomy: Enterobacteriaceae
  • 16S sequence: HQ992946
  • Sequence Identity:
  • Total samples: 2518
  • soil counts: 59
  • aquatic counts: 191
  • animal counts: 2129
  • plant counts: 139

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17842Risk group (German classification)
1163182Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Citrobacter amalonaticus partial 16S rRNA gene, type strain CECT 863TFR8704411504ena35703
20218Citrobacter amalonaticus strain LMG 7873 16S ribosomal RNA gene, partial sequenceHQ9929461494ena35703

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Citrobacter amalonaticus JCM 1661GCA_018323885completencbi35703
66792Citrobacter amalonaticus strain FDAARGOS_148935703.130completepatric35703
66792Citrobacter amalonaticus strain JCM 166135703.125completepatric35703
66792Citrobacter amalonaticus strain NCTC1080535703.59wgspatric35703
67770Citrobacter amalonaticus NCTC10805GCA_900460855contigncbi35703
66792Citrobacter amalonaticus strain FDAARGOS_148935703.138completepatric35703
66792Citrobacter amalonaticus strain FDAARGOS_148935703.132completepatric35703
66792Citrobacter amalonaticus strain FDAARGOS_148935703.135completepatric35703

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno53.727no
gram-positiveno98.453no
anaerobicno94.641no
aerobicyes77.61no
halophileno91.216no
spore-formingno94.059no
thermophileno99.327yes
glucose-utilyes96.166no
motileyes88.668no
glucose-fermentyes92.565yes

External links

@ref: 1784

culture collection no.: CCUG 4860, CECT 863, DSM 4593, ATCC 25405, CIP 82.89, NCTC 10805, JCM 1661, BCRC 14802, CGMCC 1.2020, LMG 7873, NCCB 92007, NCIMB 13274, NRRL B-41228

straininfo link

  • @ref: 73815
  • straininfo: 10382

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism2644212Nucleotide sequence of a citrate utilization gene from Citrobacter amalonaticus.Daimon H, Ishiguro N, Shinagawa M, Sato GJ Bacteriol10.1128/jb.171.1.620-623.19891989Base Sequence, Blotting, Southern, Citrates/*metabolism, Citrobacter/*genetics/metabolism, Cloning, Molecular, Escherichia coli/genetics, *Genes, *Genes, Bacterial, Molecular Sequence Data, Mutation, Nucleic Acid Hybridization, Restriction MappingEnzymology
Metabolism3941048Conservation of DNA sequences for plasmid-mediated citrate utilization within the enterobacteria.Hirato T, Ishiguro N, Shinagawa M, Sato GJ Bacteriol10.1128/jb.165.1.324-327.19861986*Base Sequence, Citrates/*metabolism, Citric Acid, DNA, Bacterial/*analysis, Enterobacteriaceae/*genetics/metabolism, Plasmids, *Sequence Homology, Nucleic Acid
Phylogeny30079059Superficieibacter electus gen. nov., sp. nov., an Extended-Spectrum beta-Lactamase Possessing Member of the Enterobacteriaceae Family, Isolated From Intensive Care Unit Surfaces.Potter RF, D'Souza AW, Wallace MA, Shupe A, Patel S, Gul D, Kwon JH, Beatty W, Andleeb S, Burnham CD, Dantas GFront Microbiol10.3389/fmicb.2018.016292018

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1784Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4593)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4593
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
38207Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11364
44799Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 4860)https://www.ccug.se/strain?id=4860
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
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
73815Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10382.1StrainInfo: A central database for resolving microbial strain identifiers
116318Curators of the CIPCollection of Institut Pasteur (CIP 82.89)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2082.89