Strain identifier

BacDive ID: 5074

Type strain: Yes

Species: Providencia alcalifaciens

Strain history: CIP <- 1982, NCTC <- 1962, ATCC <- 1945, R.E. Buchanan, Iowa <- L. de Salles Gomes, Brazil, Eberthella alcalifaciens

NCBI tax ID(s): 520999 (strain), 126385 (species)

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General

@ref: 9143

BacDive-ID: 5074

DSM-Number: 30120

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, human pathogen

description: Providencia alcalifaciens DSM 30120 is an aerobe, mesophilic, Gram-negative human pathogen that was isolated from faeces.

NCBI tax id

NCBI tax idMatching level
126385species
520999strain

strain history

@refhistory
9143<- ATCC; ATCC 9886 <- R. E. Buchanan; <- L. de Salles Gomes; (Eberthella alcalifaciens)
67770R. Sakazaki <-- ATCC 9886 <-- R. E. Buchanan <-- L. de Salles Gomes.
116205CIP <- 1982, NCTC <- 1962, ATCC <- 1945, R.E. Buchanan, Iowa <- L. de Salles Gomes, Brazil, Eberthella alcalifaciens

doi: 10.13145/bacdive5074.20250331.9.3

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 alcalifaciens
  • full scientific name: Providencia alcalifaciens (de Salles Gomes 1944) Ewing 1962 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Proteus inconstans
    20215Eberthella alcalifaciens
    20215Bacillus inconstans

@ref: 9143

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Providencia

species: Providencia alcalifaciens

full scientific name: Providencia alcalifaciens (de Salles Gomes 1944) Ewing 1962

type strain: yes

Morphology

cell morphology

  • @ref: 125438
  • gram stain: negative
  • confidence: 100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9143TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf
9143COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf
37725MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116205CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
9143positivegrowth37
37725positivegrowth30
44887positivegrowth30-37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 44887
  • oxygen tolerance: aerobe

spore formation

  • @ref: 125438
  • spore formation: no
  • confidence: 90.76

compound production

  • @ref: 9143
  • compound: restriction endonuclease PalI

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
683685291gelatin-hydrolysis
6836827897tryptophan+energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleyes
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole+

enzymes

@refvalueactivityec
68368beta-galactosidase-3.2.1.23
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
9143----+--+++-+---------

Isolation, sampling and environmental information

isolation

@refsample type
9143faeces
44887Human feces
67770Feces
116205Faeces

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Gastrointestinal tract
  • Cat3: #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: DQ885261
  • Sequence Identity:
  • Total samples: 373
  • soil counts: 23
  • aquatic counts: 44
  • animal counts: 258
  • plant counts: 48

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
9143yesyes2Risk group (German classification)
1162052Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Providencia alcalifaciens 16S rRNA gene, strain CIP8290TAJ3016841507nuccore520999
20218Providencia alcalifaciens strain DSM 30120 16S ribosomal RNA gene, partial sequenceEU587047978nuccore520999
20218Providencia alcalifaciens DSM 30120 strain NCTC 10286 16S ribosomal RNA gene, partial sequenceDQ8852611479nuccore520999
124043Providencia alcalifaciens gene for 16S rRNA, partial sequence, strain: NBRC 105687.AB6822621466nuccore126385

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Providencia alcalifaciens NCTC10286GCA_900478095completencbi126385
66792Providencia alcalifaciens DSM 30120520999.6wgspatric520999
66792Providencia alcalifaciens strain NCTC10286126385.9completepatric126385
66792Providencia alcalifaciens sv. 019:H2 DSM 30120642979317draftimg520999
67770Providencia alcalifaciens DSM 30120GCA_000173415contigncbi520999

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe70.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative67.8
125439BacteriaNetmotilityAbility to perform movementno51.2
125439BacteriaNetspore_formationAbility to form endo- or exosporesno89.2
125438gram-positivegram-positivePositive reaction to Gram-stainingno100no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.973no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no61.716yes
125438spore-formingspore-formingAbility to form endo- or exosporesno90.76no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.75yes
125438motile2+flagellatedAbility to perform flagellated movementyes71.094no

External links

@ref: 9143

culture collection no.: DSM 30120, ATCC 9886, CCUG 6325, NCTC 10286, JCM 1673, BCRC 13995, CGMCC 1.6768, CIP 82.90, NBRC 105687

straininfo link

  • @ref: 74569
  • straininfo: 10835

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9143Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30120)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30120
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
37725Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11365
44887Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 6325)https://www.ccug.se/strain?id=6325
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
74569Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10835.1StrainInfo: A central database for resolving microbial strain identifiers
116205Curators of the CIPCollection of Institut Pasteur (CIP 82.90)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2082.90
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