Strain identifier

BacDive ID: 5078

Type strain: Yes

Species: Providencia rettgeri

Strain Designation: 1163

Strain history: CIP <- 1988, ATCC <- D.J. Brenner, CDC: strain 1163, Proteus rettgeri

NCBI tax ID(s): 587 (species)

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General

@ref: 1723

BacDive-ID: 5078

DSM-Number: 4542

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

description: Providencia rettgeri 1163 is a facultative anaerobe, mesophilic, Gram-negative bacterium of the family Morganellaceae.

NCBI tax id

  • NCBI tax id: 587
  • Matching level: species

strain history

@refhistory
1723<- ATCC <- D.J. Brenner, 1163
67770R. Sakazaki 396 <-- D. J. Brenner 1163.
122168CIP <- 1988, ATCC <- D.J. Brenner, CDC: strain 1163, Proteus rettgeri

doi: 10.13145/bacdive5078.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Morganellaceae
  • genus: Providencia
  • species: Providencia rettgeri
  • full scientific name: Providencia rettgeri (Hadley et al. 1918) Brenner et al. 1978 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Bacterium rettgeri
    20215Proteus rettgeri

@ref: 1723

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Providencia

species: Providencia rettgeri

full scientific name: Providencia rettgeri (Hadley et al. 1918) Brenner et al. 1978

strain designation: 1163

type strain: yes

Morphology

cell morphology

  • @ref: 122168
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1723NUTRIENT 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
41334MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122168CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1723positivegrowth37mesophilic
41334positivegrowth30mesophilic
67770positivegrowth37mesophilic
122168positivegrowth10-41
122168nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122168
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-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
68371amygdalin-builds acid from27613
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
68368sorbitol-fermentation30911
68368myo-inositol+fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan+energy source27897
68368urea+hydrolysis16199
68368citrate+assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine+hydrolysis29016
122168mannitol+fermentation29864
122168citrate+carbon source16947
122168glucose+fermentation17234
122168lactose-fermentation17716
122168nitrate+reduction17632
122168nitrite+reduction16301
122168malonate-assimilation15792
122168sodium thiosulfate-builds gas from132112
122168glucose+degradation17234

antibiotic resistance

  • @ref: 122168
  • 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
6836835581indoleyes
6836816136hydrogen sulfideno
12216835581indoleyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole+
12216815688acetoin-
12216817234glucose+

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
122168oxidase-
122168beta-galactosidase-3.2.1.23
122168alcohol dehydrogenase-1.1.1.1
122168gelatinase-
122168catalase+1.11.1.6
122168lysine decarboxylase-4.1.1.18
122168ornithine decarboxylase-4.1.1.17
122168phenylalanine ammonia-lyase+4.3.1.24
122168tryptophan deaminase+
122168urease+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
122168-+---+++--++--------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
1723-+--+-++++-+++-+--+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122168++/---+--+-++++-+-++---+-+++------------------++++/--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122168+++-+------------+++---+--++---+++---+--+-------+++--+--+-++++----------------+++-----+--+++--+--++

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_1898.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_362;97_407;98_466;99_1898&stattab=map
  • Last taxonomy: Providencia
  • 16S sequence: NR_042413
  • Sequence Identity:
  • Total samples: 2430
  • soil counts: 73
  • aquatic counts: 275
  • animal counts: 1908
  • plant counts: 174

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17232Risk group (German classification)
1221682Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Providencia rettgeri strain ATCC 29944 16S ribosomal RNA gene, partial sequenceFJ971874795ena587
20218Providencia rettgeri 16S rRNA gene, type strain DSM 4542AM0404921497ena587
20218Providencia rettgeri strain DSM 4542 16S ribosomal RNA gene, partial sequenceEU587035978ena587
20218Providencia rettgeri strain NCTC 11801 16S ribosomal RNA gene, partial sequenceDQ8852631485ena587
1723Providencia rettgeri strain DSM 4542 16S ribosomal RNA, partial sequenceNR_0424131497nuccore587

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Providencia rettgeri strain FDAARGOS 1450587.336completepatric587
66792Providencia rettgeri strain NCTC11801587.90wgspatric587
67770Providencia rettgeri NCTC11801GCA_900455085contigncbi587

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.23no
anaerobicno98.664no
halophileno86.422no
spore-formingno96.418no
glucose-utilyes93.92no
thermophileno99.174no
flagellatedno79.499no
aerobicyes85.768no
motileyes55.777no
glucose-fermentyes87.082yes

External links

@ref: 1723

culture collection no.: DSM 4542, ATCC 29944, CCUG 14804, CECT 865, JCM 1675, BCRC 13994, CDC 1163, CIP 103182, LMG 3259, NCTC 11801

straininfo link

  • @ref: 74573
  • straininfo: 125692

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1723Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4542)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4542
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
41334Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14951
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
74573Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID125692.1StrainInfo: A central database for resolving microbial strain identifiers
122168Curators of the CIPCollection of Institut Pasteur (CIP 103182)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103182