Strain identifier

BacDive ID: 5065

Type strain: Yes

Species: Proteus penneri

Strain Designation: 1808-73

Strain history: CIP <- 1987, ATCC <- CDC: strain 1808-73 <- Alaska State Hlth. Dept., USA

NCBI tax ID(s): 102862 (species)

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General

@ref: 1725

BacDive-ID: 5065

DSM-Number: 4544

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

description: Proteus penneri 1808-73 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from urine.

NCBI tax id

  • NCBI tax id: 102862
  • Matching level: species

strain history

@refhistory
1725<- ATCC; ATCC 33519 <- CDC, Atlanta; CDC 1808-73
67770Y. Kosako 85546 <-- R. Sakazaki 85008 <-- CDC 1808-73.
121660CIP <- 1987, ATCC <- CDC: strain 1808-73 <- Alaska State Hlth. Dept., USA

doi: 10.13145/bacdive5065.20250331.9.3

Name and taxonomic classification

LPSN

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

@ref: 1725

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Proteus

species: Proteus penneri

full scientific name: Proteus penneri Hickman et al. 1983

strain designation: 1808-73

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121660negativerod-shapedno
125438negative99.985
125439negative97.7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1725NUTRIENT 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
34100MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
1725TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
1725COLUMBIA 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
121660CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121660CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
1725positivegrowth37
34100positivegrowth30
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 96.9

spore formation

@refspore formationconfidence
125438no90.231
125439no99.1

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose+fermentation
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

  • @ref: 68368
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68368
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
68368cytochrome oxidase-1.9.3.1
68368tryptophan deaminase+4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
1725-----+/-++-++/-+----+----
1725-----+++---+----+----
1725-----+++-+++----+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1725urine
67770Urine
121660Human, UrineAnchorage, AlaskaUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Urine

taxonmaps

  • @ref: 69479
  • File name: preview.99_739.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_12;97_12;98_14;99_739&stattab=map
  • Last taxonomy: Proteus
  • 16S sequence: DQ885258
  • Sequence Identity:
  • Total samples: 89
  • soil counts: 4
  • aquatic counts: 10
  • animal counts: 74
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17252Risk group (German classification)
1216602Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Proteus penneri strain ATCC 33519 16S ribosomal RNA gene, partial sequenceFJ971869797nuccore102862
20218Proteus penneri strain NCTC 12737 16S ribosomal RNA gene, partial sequenceDQ8852581383nuccore102862
124043Proteus penneri gene for 16S rRNA, partial sequence, strain: NBRC 105705.AB6822771468nuccore102862
124043Proteus penneri partial 16S rRNA gene, type strain DSM 4544TLN8098841445nuccore102862

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Proteus penneri strain ATCC 33519102862.7wgspatric102862
66792Proteus penneri strain FDAARGOS_874102862.20completepatric102862
66792Proteus penneri strain NCTC12737102862.13wgspatric102862
66792Proteus penneri ATCC 335192858358578draftimg102862
67770Proteus penneri ATCC 33519GCA_003144535contigncbi102862
67770Proteus penneri NCTC12737GCA_900455015contigncbi102862

GC content

  • @ref: 67770
  • GC-content: 38
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe96.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative97.7
125439BacteriaNetmotilityAbility to perform movementno62.3
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.1
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.985no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no89.791no
125438spore-formingspore-formingAbility to form endo- or exosporesno90.231no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no78.768no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.697no
125438motile2+flagellatedAbility to perform flagellated movementyes71.676no

External links

@ref: 1725

culture collection no.: DSM 4544, ATCC 33519, CCUG 15722, CECT 864, NCTC 12737, CDC 1808-73, JCM 3948, BCRC 14123, CIP 103030, LMG 7877, NBRC 105705, NCIMB 12597

straininfo link

  • @ref: 74560
  • straininfo: 10834

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7050147Identification of Proteus penneri sp. nov., formerly known as Proteus vulgaris indole negative or as Proteus vulgaris biogroup 1.Hickman FW, Steigerwalt AG, Farmer JJ 3rd, Brenner DJJ Clin Microbiol10.1128/jcm.15.6.1097-1102.19821982Anti-Bacterial Agents/pharmacology, Base Composition, Cytosine/analysis, DNA, Bacterial/analysis, Guanine/analysis, Indoles/metabolism, Nucleic Acid Hybridization, Proteus/*classification/physiology, Proteus vulgaris/classification, Terminology as TopicMetabolism
Genetics7541754Structure and epitope specificity of the O-specific polysaccharide of Proteus penneri strain 12 (ATCC 33519) containing the amide of D-galacturonic acid with L-threonine.Sidorczyk Z, Swierzko A, Knirel YA, Vinogradov EV, Chernyak AY, Kononov LO, Cedzynski M, Rozalski A, Kaca W, Shashkov AS, et al.Eur J Biochem1995Amides/chemistry, Carbohydrate Conformation, Carbohydrate Sequence, Epitopes/*chemistry/immunology, Hexuronic Acids/*chemistry, Magnetic Resonance Spectroscopy, Molecular Sequence Data, O Antigens, Polysaccharides, Bacterial/*chemistry/immunology, Proteus/*chemistry, Serology, Threonine/*chemistry
Phylogeny29297845Proteus columbae sp. nov., isolated from a pigeon in Ma'anshan, China.Dai H, Wang Y, Fang Y, Xiao T, Huang Z, Kan B, Wang DInt J Syst Evol Microbiol10.1099/ijsem.0.0025412018Animals, Bacterial Typing Techniques, Base Composition, China, Columbidae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, *Phylogeny, Proteus/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1725Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4544)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4544
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
34100Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14782
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
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
74560Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10834.1StrainInfo: A central database for resolving microbial strain identifiers
121660Curators of the CIPCollection of Institut Pasteur (CIP 103030)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103030
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