Strain identifier

BacDive ID: 5082

Type strain: Yes

Species: Providencia rustigianii

Strain Designation: 132-68

Strain history: CIP <- 1987, ATCC <- F.W. Hickman, CDC: strain 132-68 <- Alaska State Hlth. Dept.

NCBI tax ID(s): 500637 (strain), 158850 (species)

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General

@ref: 1722

BacDive-ID: 5082

DSM-Number: 4541

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

description: Providencia rustigianii 132-68 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces.

NCBI tax id

NCBI tax idMatching level
158850species
500637strain

strain history

@refhistory
1722<- ATCC <- F.W. Hickman, CDC, 132-68
67770Y. Kosako 85551 <-- R. Sakazaki 85013 <-- CDC 132-68.
122320CIP <- 1987, ATCC <- F.W. Hickman, CDC: strain 132-68 <- Alaska State Hlth. Dept.

doi: 10.13145/bacdive5082.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Morganellaceae
  • genus: Providencia
  • species: Providencia rustigianii
  • full scientific name: Providencia rustigianii Hickman-Brenner et al. 1983

  • synonyms

    • @ref: 20215
    • synonym: Providencia friedericiana

@ref: 1722

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Providencia

species: Providencia rustigianii

full scientific name: Providencia rustigianii Hickman-Brenner et al. 1983

strain designation: 132-68

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
122320negativerod-shapedyes
125438negative99.5
125439negative98.8

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1722NUTRIENT 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
34102MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122320CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
122320CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
1722positivegrowth37
34102positivegrowth30
67770positivegrowth37
122320positivegrowth5-41

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
122320facultative anaerobe
125439obligate aerobe97.2

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 95.1

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12232029864mannitol-fermentation
12232016947citrate+carbon source
12232017234glucose+fermentation
12232017716lactose-fermentation
12232017632nitrate+reduction
12232016301nitrite-reduction
12232015792malonate-assimilation
122320132112sodium thiosulfate-builds gas from
68371Potassium 5-ketogluconate-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837117754glycerol+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from

antibiotic resistance

  • @ref: 122320
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 122320
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12232015688acetoin-
12232017234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
122320oxidase-
122320beta-galactosidase-3.2.1.23
122320alcohol dehydrogenase-1.1.1.1
122320gelatinase-
122320catalase+1.11.1.6
122320lysine decarboxylase-4.1.1.18
122320ornithine decarboxylase-4.1.1.17
122320phenylalanine ammonia-lyase+4.3.1.24
122320tryptophan deaminase+
122320urease-3.5.1.5
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382valine arylamidase-

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122320-+---+--+-++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122320+---+----++++--------+------------------------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122320+++-+--------------+-----------+-----------------+++-+----++++----------------+++-----+--+++--+--++

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
1722human faeces
122320Human, Feces1968

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_935.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_362;97_407;98_466;99_935&stattab=map
  • Last taxonomy: Providencia
  • 16S sequence: DQ885264
  • Sequence Identity:
  • Total samples: 373
  • soil counts: 23
  • aquatic counts: 44
  • animal counts: 258
  • plant counts: 48

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17222Risk group (German classification)
1223202Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Providencia rustigianii 16S rRNA gene, type strain DSM 4541AM0404891516nuccore158850
20218Providencia rustigianii strain DSM 4541 16S ribosomal RNA gene, partial sequenceEU587030978nuccore158850
20218Providencia rustigianii strain NCTC 11802 16S ribosomal RNA gene, partial sequenceDQ8852641476nuccore158850
124043Providencia rustigianii strain DSM 4541 16S ribosomal RNA gene, partial sequence.ON386151881nuccore158850

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Providencia rustigianii NCTC11802GCA_900455075contigncbi158850
66792Providencia rustigianii DSM 4541500637.6wgspatric500637
66792Providencia rustigianii strain NCTC11802158850.6wgspatric158850
66792Providencia rustigianii DSM 4541642979318draftimg500637
67770Providencia rustigianii DSM 4541GCA_000156395scaffoldncbi500637

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.872yes
125438spore-formingspore-formingAbility to form endo- or exosporesno89.699no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no67.134yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.942yes
125438motile2+flagellatedAbility to perform flagellated movementyes70.895no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno95.1
125439BacteriaNetmotilityAbility to perform movementyes64.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.2

External links

@ref: 1722

culture collection no.: CCUG 15723, DSM 4541, ATCC 33673, CDC 132-68, JCM 3953, BCRC 13997, CIP 103032, NCTC 11802, RIMD 1659001

straininfo link

  • @ref: 74577
  • straininfo: 40613

literature

  • topic: Phylogeny
  • Pubmed-ID: 6874899
  • title: Providencia rustigianii: a new species in the family Enterobacteriaceae formerly known as Providencia alcalifaciens biogroup 3.
  • authors: Hickman-Brenner FW, Farmer JJ 3rd, Steigerwalt AG, Brenner DJ
  • journal: J Clin Microbiol
  • DOI: 10.1128/jcm.17.6.1057-1060.1983
  • year: 1983
  • mesh: Anti-Bacterial Agents/pharmacology, DNA, Bacterial/analysis, Nucleic Acid Hybridization, Proteus/*classification, Providencia/*classification/drug effects/metabolism
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1722Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4541)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4541
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
34102Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14784
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/
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
74577Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40613.1StrainInfo: A central database for resolving microbial strain identifiers
122320Curators of the CIPCollection of Institut Pasteur (CIP 103032)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103032
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
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