Strain identifier

BacDive ID: 5075

Type strain: Yes

Species: Providencia heimbachae

Strain Designation: 8025-83

Strain history: CIP <- 1987, ATCC <- CDC: strain 8025-83 <- A.E. Müller, Braunschweig, Germany: strain MUA 2-110 <- F. Heimbach

NCBI tax ID(s): 1354272 (strain), 333962 (species)

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General

@ref: 1416

BacDive-ID: 5075

DSM-Number: 3591

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile, human pathogen

description: Providencia heimbachae 8025-83 is an aerobe, mesophilic, motile human pathogen that was isolated from faeces of penguin.

NCBI tax id

NCBI tax idMatching level
333962species
1354272strain

strain history

@refhistory
1416<- H.E. Müller
119857CIP <- 1987, ATCC <- CDC: strain 8025-83 <- A.E. Müller, Braunschweig, Germany: strain MUA 2-110 <- F. Heimbach

doi: 10.13145/bacdive5075.20230509.8.1

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 heimbachae
  • full scientific name: Providencia heimbachae Müller et al. 1986

@ref: 1416

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Providencia

species: Providencia heimbachae

full scientific name: Providencia heimbachae Müller et al. 1986

strain designation: 8025-83

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes94.05
6948099.976negative
119857yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1416NUTRIENT 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
34101MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119857CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
119857CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
1416positivegrowth37mesophilic
34101positivegrowth30mesophilic
46488positivegrowth37mesophilic
119857positivegrowth5-37
119857nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
46488aerobe
119857facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.889

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
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
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
68371erythritol+builds acid from17113
68371glycerol+builds acid from17754
119857mannitol-fermentation29864
119857citrate+carbon source16947
119857glucose+fermentation17234
119857lactose-fermentation17716
119857nitrate+reduction17632
119857nitrite-reduction16301
119857malonate-assimilation15792
119857sodium thiosulfate-builds gas from132112

antibiotic resistance

  • @ref: 119857
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119857
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11985715688acetoin-
11985717234glucose+

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
119857oxidase-
119857beta-galactosidase-3.2.1.23
119857alcohol dehydrogenase-1.1.1.1
119857gelatinase-
119857catalase+1.11.1.6
119857lysine decarboxylase-4.1.1.18
119857ornithine decarboxylase-4.1.1.17
119857phenylalanine ammonia-lyase+4.3.1.24
119857tryptophan deaminase+
119857urease-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
119857-++--+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119857++--+--+-++++-+-++/----+-----+--+-------------++++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119857+++-+----++--------+---+--++---+++---+--+-------++++-+--+-++++----------------+++-----+--+++--+--+-

Isolation, sampling and environmental information

isolation

@refsample typesampling datecountryorigin.countrycontinent
1416faeces of penguin
464881984GermanyDEUEurope
119857Animal, Penguin, fecesGermanyDEUEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4782.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_362;97_407;98_466;99_4782&stattab=map
  • Last taxonomy: Providencia heimbachae
  • 16S sequence: DQ885265
  • Sequence Identity:
  • Total samples: 1016
  • soil counts: 24
  • aquatic counts: 91
  • animal counts: 871
  • plant counts: 30

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
1416yes, in single cases1Risk group (German classification)
1198572Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Providencia heimbachae 16S rRNA gene, type strain DSM 3591AM0404901518ena333962
20218Providencia heimbachae strain DSM 3591 16S ribosomal RNA gene, partial sequenceEU587018978ena333962
20218Providencia heimbachae strain NCTC 12003 16S ribosomal RNA gene, partial sequenceDQ8852651465ena333962

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Providencia heimbachae NCTC12003GCA_900475855completencbi333962
66792Providencia heimbachae ATCC 35613GCA_001655055contigncbi1354272
66792Providencia heimbachae ATCC 356131354272.4wgspatric1354272
66792Providencia heimbachae strain NCTC12003333962.4completepatric333962
66792Providencia heimbachae ATCC 356132802429662draftimg1354272

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes53.834no
gram-positiveno98.491no
anaerobicno97.82yes
aerobicyes86.285yes
halophileno88.699no
spore-formingno96.527no
thermophileno98.906yes
glucose-utilyes92.206no
motileyes88.006no
glucose-fermentyes88.372no

External links

@ref: 1416

culture collection no.: CCUG 16446, NCTC 12003, DSM 3591, ATCC 35613, CIP 103031, MUA 2-110

straininfo link

  • @ref: 74570
  • straininfo: 10836

literature

  • topic: Pathogenicity
  • Pubmed-ID: 36016188
  • title: Designing a Novel Peptide-Based Multi-Epitope Vaccine to Evoke a Robust Immune Response against Pathogenic Multidrug-Resistant Providencia heimbachae.
  • authors: Naveed M, Sheraz M, Amin A, Waseem M, Aziz T, Khan AA, Ghani M, Shahzad M, Alruways MW, Dablool AS, Elazzazy AM, Almalki AA, Alamri AS, Alhomrani M
  • journal: Vaccines (Basel)
  • DOI: 10.3390/vaccines10081300
  • year: 2022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1416Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3591)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3591
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
34101Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14783
46488Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 16446)https://www.ccug.se/strain?id=16446
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
74570Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10836.1StrainInfo: A central database for resolving microbial strain identifiers
119857Curators of the CIPCollection of Institut Pasteur (CIP 103031)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103031