Strain identifier

BacDive ID: 5128

Type strain: Yes

Species: Salmonella enterica subsp. diarizonae

Strain history: CIP <- 1982, L. Le Minor, Inst. Pasteur, Paris, France: strain Salmonella choleraesuis subsp. diarizonae

NCBI tax ID(s): 59204 (subspecies)

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General

@ref: 5575

BacDive-ID: 5128

DSM-Number: 14847

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

description: Salmonella enterica subsp. diarizonae CCUG 30040 is a mesophilic, Gram-negative, motile bacterium of the family Enterobacteriaceae.

NCBI tax id

  • NCBI tax id: 59204
  • Matching level: subspecies

strain history

@refhistory
5575<- CIP <- L. Le Minor
402321982, L. Le Minor, Inst. Pasteur, Paris, France, Salmonella choleraesuis subsp. diarizonae
119039CIP <- 1982, L. Le Minor, Inst. Pasteur, Paris, France: strain Salmonella choleraesuis subsp. diarizonae

doi: 10.13145/bacdive5128.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Salmonella
  • species: Salmonella enterica subsp. diarizonae
  • full scientific name: Salmonella enterica subsp. diarizonae (Le Minor et al. 1985) Le Minor and Popoff 1987

  • synonyms

    @refsynonym
    20215Salmonella diarizonae
    20215Salmonella choleraesuis subsp. diarizonae

@ref: 5575

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Salmonella

species: Salmonella enterica subsp. diarizonae

full scientific name: Salmonella enterica subsp. diarizonae (Le Minor et al. 1985) Le Minor and Popoff 1987

type strain: yes

Morphology

cell morphology

  • @ref: 119039
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5575COLUMBIA 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
5575TRYPTICASE 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
5575CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
40232MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119039CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119039CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
5575positivegrowth30mesophilic
40232positivegrowth30mesophilic
49870positivegrowth30mesophilic

Physiology and metabolism

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
6837418257ornithine+degradation
6837429016arginine+hydrolysis
6837425094lysine+degradation
6837416199urea-hydrolysis
6837418403L-arabitol-builds acid from
6837418024D-galacturonic acid-builds acid from
68374Potassium 5-ketogluconate-builds acid from
6837416899D-mannitol+builds acid from
6837417306maltose+builds acid from
6837415963ribitol-builds acid from
6837418394palatinose-builds acid from
6837415792malonate+assimilation
6837427897tryptophan-energy source
6837417634D-glucose+builds acid from
6837417992sucrose-builds acid from
6837430849L-arabinose+builds acid from
6837418333D-arabitol-builds acid from
6837427082trehalose+builds acid from
6837462345L-rhamnose+builds acid from
6837417268myo-inositol-builds acid from
6837417057cellobiose-builds acid from
6837430911sorbitol+builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6837435581indole-
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68374L-aspartate arylamidase-3.4.11.21
68374alpha-maltosidase-
68374alpha-galactosidase+3.2.1.22
68374alpha-glucosidase-3.2.1.20
68374beta-galactosidase+3.2.1.23
68374N-acetyl-beta-glucosaminidase-3.2.1.52
68374beta-glucuronidase+3.2.1.31
68374beta-glucosidase-3.2.1.21
68374lipase+
68374urease-3.5.1.5
68374lysine decarboxylase+4.1.1.18
68374arginine dihydrolase+3.5.3.6
68374ornithine decarboxylase+4.1.1.17
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
5575++++++-----++-++-+-+-
49870++++++-----++-++-+-+-

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
49870+++----+--++--++--++-+--+++--+--

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_9.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_8;99_9&stattab=map
  • Last taxonomy: Salmonella enterica
  • 16S sequence: EU014688
  • Sequence Identity:
  • Total samples: 28103
  • soil counts: 1084
  • aquatic counts: 2005
  • animal counts: 23018
  • plant counts: 1996

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
55752Risk group (German classification)
1190392Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5575
  • description: Salmonella enterica subsp. diarizonae strain DSM 14847 16S ribosomal RNA gene, partial sequence
  • accession: EU014688
  • length: 1368
  • database: ena
  • NCBI tax ID: 59204

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salmonella enterica subsp. diarizonae NCTC10060GCA_900456375contigncbi59204
66792Salmonella enterica subsp. diarizonae strain NCTC1006059204.31wgspatric59204
66792Salmonella enterica subsp. diarizonae CCUG30040GCA_016030095contigncbi59204

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.493no
anaerobicno92.553no
halophileno91.722no
spore-formingno91.97no
glucose-utilyes94.016no
thermophileno98.89yes
flagellatedno55.399no
aerobicyes72.723no
motileyes89.374no
glucose-fermentyes92.324no

External links

@ref: 5575

culture collection no.: CCUG 30040, DSM 14847, ATCC 43973, CIP 82.31, NCTC 10060

straininfo link

  • @ref: 74620
  • straininfo: 45180

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25908712Mangrovibacter yixingensis sp. nov., isolated from farmland soil.Zhang H, Guo SH, Sun B, Zhang J, Cheng MG, Li Q, Hong Q, Huang XInt J Syst Evol Microbiol10.1099/ijs.0.0002812015Agriculture, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Enterobacteriaceae/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny28086074Mangrovibacter phragmitis sp. nov., an endophyte isolated from the roots of Phragmites karka.Behera P, Venkata Ramana V, Maharana B, Joseph N, Vaishampayan P, Singh NK, Shouche Y, Bhadury P, Mishra SR, Raina V, Suar M, Pattnaik AK, Rastogi GInt J Syst Evol Microbiol10.1099/ijsem.0.0017892017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Enterobacteriaceae/*classification/genetics/isolation & purification, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, Poaceae/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology

Reference

@idauthorscataloguedoi/urltitle
5575Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14847)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14847
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
40232Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11301
49870Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30040)https://www.ccug.se/strain?id=30040
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)
68368Automatically annotated from API 20E
68374Automatically annotated from API ID32E
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
74620Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45180.1StrainInfo: A central database for resolving microbial strain identifiers
119039Curators of the CIPCollection of Institut Pasteur (CIP 82.31)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2082.31