Strain identifier

BacDive ID: 5159

Type strain: Yes

Species: Serratia rubidaea

Strain Designation: 864, 2199-72

Strain history: CIP <- 1988, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 864 <- H. Ewing, CDC: strain 2199-72

NCBI tax ID(s): 1218096 (strain), 61652 (species)

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General

@ref: 1693

BacDive-ID: 5159

DSM-Number: 4480

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped, animal pathogen

description: Serratia rubidaea 864 is a facultative anaerobe, mesophilic, Gram-negative animal pathogen of the family Yersiniaceae.

NCBI tax id

NCBI tax idMatching level
1218096strain
61652species

strain history

@refhistory
1693<- ATCC <- W.H. Ewing; 2199-72
67770R. Sakazaki 306 <-- W. H. Ewing 2199-72.
122283CIP <- 1988, P.A.D. Grimont, Inst. Pasteur, Paris, France: strain 864 <- H. Ewing, CDC: strain 2199-72

doi: 10.13145/bacdive5159.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Yersiniaceae
  • genus: Serratia
  • species: Serratia rubidaea
  • full scientific name: Serratia rubidaea (Stapp 1940) Ewing et al. 1973 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Bacterium rubidaeum
    20215Serratia marinorubra

@ref: 1693

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Serratia

species: Serratia rubidaea

full scientific name: Serratia rubidaea (Stapp 1940) Ewing et al. 1973

strain designation: 864, 2199-72

type strain: yes

Morphology

cell morphology

  • @ref: 122283
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1693NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
39850MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122283CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
1693positivegrowth26mesophilic
39850positivegrowth30mesophilic
67770positivegrowth37mesophilic
122283positivegrowth30-41
122283nogrowth5psychrophilic
122283nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122283
  • oxygen tolerance: facultative anaerobe

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
68371D-lyxose-builds acid from62318
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
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
68371glycerol+builds acid from17754
68368L-arabinose+fermentation30849
68368amygdalin+fermentation27613
68368melibiose+fermentation28053
68368sucrose+fermentation17992
68368L-rhamnose+fermentation62345
68368myo-inositol+fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin+hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate+assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
122283mannitol+fermentation29864
122283citrate+carbon source16947
122283glucose+fermentation17234
122283lactose-fermentation17716
122283nitrate+reduction17632
122283nitrite-reduction16301
122283malonate+assimilation15792
122283sodium thiosulfate-builds gas from132112
122283glucose+degradation17234

antibiotic resistance

  • @ref: 122283
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12228335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12228315688acetoin+
12228317234glucose-

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
122283oxidase-
122283beta-galactosidase+3.2.1.23
122283alcohol dehydrogenase-1.1.1.1
122283gelatinase-
122283catalase+1.11.1.6
122283lysine decarboxylase+4.1.1.18
122283ornithine decarboxylase-4.1.1.17
122283phenylalanine ammonia-lyase-4.3.1.24
122283tryptophan deaminase-
122283urease-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
122283-++++++-+-++-+-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
1693+---+----+++++++++++-
1693+---+----+++++-+++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122283++/--+++-+-++++---++--+++/-+++++++++-++-+-++----+-++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122283+++++-++++++-++++++++++-+++-+--+++++-+--++-++----+++-++++--++++-+--+--++++-+---++-+---+--++++++--++

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_2238.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_1744;99_2238&stattab=map
  • Last taxonomy: Serratia
  • 16S sequence: AJ233436
  • Sequence Identity:
  • Total samples: 3342
  • soil counts: 211
  • aquatic counts: 371
  • animal counts: 2469
  • plant counts: 291

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
1693yes2Risk group (German classification)
1222831Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Serratia rubidaea 16S rRNA gene (strain DSM 4480)AJ2334361509ena61652
20218Serratia rubidaea gene for 16S ribosomal RNA, partial sequenceAB0047511442ena61652
20218Serratia rubidaea gene for 16S rRNA, partial sequence, strain: NBRC 103169AB6819761467ena61652

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Serratia rubidaea NBRC 1031691218096.3wgspatric1218096
66792Serratia rubidaea strain CIP 10323461652.4wgspatric61652
66792Serratia rubidaea strain FDAARGOS_92661652.34completepatric61652
66792Serratia rubidaea NBRC 1031692731957709draftimg1218096
66792Serratia rubidaea CIP 1032342645727870draftimg61652
67770Serratia rubidaea NBRC 103169GCA_001598675contigncbi1218096
67770Serratia rubidaea CIP 103234GCA_001304675contigncbi61652

GC content

  • @ref: 67770
  • GC-content: 53.6
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.05no
anaerobicno98.719no
halophileno85.509no
spore-formingno94.047no
glucose-utilyes94.999no
thermophileno99.376yes
flagellatedno50.903no
aerobicyes86.218no
motileyes90.432no
glucose-fermentyes92.934yes

External links

@ref: 1693

culture collection no.: DSM 4480, ATCC 27593, JCM 1240, BCRC 13990, CCUG 10981, CECT 868, CIP 103234, IAM 13545, LMG 5019, NBRC 103169, NCTC 12971

straininfo link

  • @ref: 74651
  • straininfo: 323074

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21318365Isolation and characterization of a chromium-resistant bacterium Serratia sp. Cr-10 from a chromate-contaminated site.Zhang K, Li FAppl Microbiol Biotechnol10.1007/s00253-011-3120-y2011Chromates/*metabolism, Chromium/*metabolism, Molecular Sequence Data, Phylogeny, Serratia/classification/genetics/*isolation & purification/*metabolism, *Soil Microbiology, Soil Pollutants/*metabolismMetabolism
Genetics26586886Draft Genome Sequence of the Serratia rubidaea CIP 103234T Reference Strain, a Human-Opportunistic Pathogen.Bonnin RA, Girlich D, Imanci D, Dortet L, Naas TGenome Announc10.1128/genomeA.01340-152015
Metabolism27956418Chromosome-Encoded Broad-Spectrum Ambler Class A beta-Lactamase RUB-1 from Serratia rubidaea.Bonnin RA, Didi J, Ergani A, Lima S, Naas TAntimicrob Agents Chemother10.1128/AAC.01908-162017Bacterial Proteins/genetics/metabolism, Chromosomes, Bacterial/*genetics, DNA, Complementary/genetics, Escherichia coli/drug effects/enzymology/metabolism, Microbial Sensitivity Tests, Penicillinase/genetics/metabolism, Serratia/drug effects/*enzymology/*metabolism, beta-Lactamases/genetics/*metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1693Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4480)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4480
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
39850Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15009
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
74651Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323074.1StrainInfo: A central database for resolving microbial strain identifiers
122283Curators of the CIPCollection of Institut Pasteur (CIP 103234)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103234