Strain identifier

BacDive ID: 140426

Type strain: Yes

Species: Citrobacter portucalensis

Strain Designation: A60

Strain history: CIP <- 2017, L. Peixe, Porto Univ., Porto, Portugal: strain A60

NCBI tax ID(s): 1639133 (species)

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General

@ref: 43033

BacDive-ID: 140426

DSM-Number: 104542

keywords: genome sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped, human pathogen

description: Citrobacter portucalensis A60 is a facultative anaerobe, Gram-negative, motile human pathogen that was isolated from water well.

NCBI tax id

  • NCBI tax id: 1639133
  • Matching level: species

strain history

@refhistory
43033<- L. Vieira Peixe; Faculty of Pharmacy, University of Porto, Porto, Portugal; A60 <- E. Machado
121947CIP <- 2017, L. Peixe, Porto Univ., Porto, Portugal: strain A60

doi: 10.13145/bacdive140426.20230509.8.1

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 portucalensis
  • full scientific name: Citrobacter portucalensis Ribeiro et al. 2017

@ref: 43033

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Citrobacter

species: Citrobacter portucalensis

full scientific name: Citrobacter portucalensis Ribeiro et al. 2017

strain designation: A60

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
43514negative4-5 µm1-2 µmrod-shapedyes
121947negativerod-shapedyes

colony morphology

  • @ref: 43514
  • colony color: bright, translucent
  • medium used: TSB

multimedia

  • @ref: 43033
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_104542.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43514TSByes
43033COLUMBIA 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
43033TRYPTICASE 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
121947CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
43514positivegrowth20-37
43514positivegrowth50thermophilic
43033positivegrowth37mesophilic

culture pH

  • @ref: 43514
  • ability: positive
  • type: growth
  • pH: 5-10
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 43514
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 43514
  • spore formation: no

halophily

  • @ref: 43514
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-15 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4351416467L-arginine-assimilation
4351418019L-lysine-assimilation
4351415729L-ornithine-assimilation
4351416828L-tryptophan-assimilation
4351427613amygdalin-builds acid from
4351415963ribitol-builds acid from
4351417108D-arabinose-builds acid from
4351418333D-arabitol-builds acid from
4351428847D-fucose-builds acid from
4351462318D-lyxose-builds acid from
4351416443D-tagatose-builds acid from
4351416813galactitol-builds acid from
4351417113erythritol-builds acid from
43514esculin ferric citrate-builds acid from
4351428087glycogen-builds acid from
4351415443inulin-builds acid from
4351418403L-arabitol-builds acid from
4351465328L-xylose-builds acid from
435146731melezitose-builds acid from
43514320061methyl alpha-D-glucopyranoside-builds acid from
4351443943methyl alpha-D-mannoside-builds acid from
4351474863methyl beta-D-xylopyranoside-builds acid from
4351428017starch-builds acid from
4351432528turanose-builds acid from
4351417151xylitol-builds acid from
435145291gelatin-degradation
4351427897tryptophan-energy source
43514168082-dehydro-D-gluconate+builds acid from
43514581435-dehydro-D-gluconate+builds acid from
4351418305arbutin+builds acid from
4351417057cellobiose+builds acid from
4351415824D-fructose+builds acid from
4351412936D-galactose+builds acid from
4351417634D-glucose+builds acid from
4351416899D-mannitol+builds acid from
4351416024D-mannose+builds acid from
4351416988D-ribose+builds acid from
4351417924D-sorbitol+builds acid from
4351465327D-xylose+builds acid from
4351428066gentiobiose+builds acid from
4351417754glycerol+builds acid from
4351417268myo-inositol+builds acid from
4351430849L-arabinose+builds acid from
4351418287L-fucose+builds acid from
4351462345L-rhamnose+builds acid from
4351417266L-sorbose+builds acid from
4351417716lactose+builds acid from
4351417306maltose+builds acid from
4351428053melibiose+builds acid from
43514506227N-acetylglucosamine+builds acid from
4351432032potassium gluconate+builds acid from
4351416634raffinose+builds acid from
4351417814salicin+builds acid from
4351417992sucrose+builds acid from
4351427082trehalose+builds acid from
4351416947citrate+carbon source
4351417234glucose+fermentation
4351417632nitrate+reduction
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol+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
4351415688acetoinno
4351417997dinitrogenno
4351435581indoleno
4351416136hydrogen sulfideyes
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideyes

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testindole test
4351417234glucose+
4351415688acetoin-
4351435581indole-
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
43514catalase-1.11.1.6
43514cytochrome oxidase-1.9.3.1
43514tryptophan deaminase-4.1.99.1
43514urease+3.5.1.5
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
43033+---++-----++-++++++-
43033+---++-----+++++++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
43033water wellTaboeira, Cadima, CantanhedePortugalPRTEurope
43514water well sample collected in Cantanhede CityCantanhede CityPortugalPRTEurope2008
121947Environment, Water wellPortugalPRTEurope2006

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
43033yes, in single cases1Risk group (German classification)
1219471Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Citrobacter portucalensis A60GCA_002042885contigncbi1639133
66792Citrobacter portucalensis A602874289006draftimg1639133

GC content

@refGC-content
4351452
4303352.0

External links

@ref: 43033

culture collection no.: DSM 104542, CECT 9236, CIP 111602

straininfo link

  • @ref: 96699
  • straininfo: 408082

literature

  • topic: Phylogeny
  • Pubmed-ID: 28857032
  • title: Citrobacter portucalensis sp. nov., isolated from an aquatic sample.
  • authors: Ribeiro TG, Goncalves BR, da Silva MS, Novais A, Machado E, Carrico JA, Peixe L
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002154
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, Citrobacter/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Genes, Bacterial, Multilocus Sequence Typing, *Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Microbiology, *Water Wells
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
43033Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104542Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104542)
43514Teresa Gonçalves Ribeiro, Bruno Ribeiro Gonçalves, Mickael Santos da Silva, Ângela Novais, Elisabete Machado, Joao Andre Carriço, Luísa PeixeCitrobacter portucalensis sp. nov., isolated from an aquatic sample10.1099/ijsem.0.002154IJSEM 67: 3513-3517 201728857032
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68368Automatically annotated from API 20E
96699Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID408082.1
121947Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111602Collection of Institut Pasteur (CIP 111602)