Strain identifier

BacDive ID: 5126

Type strain: Yes

Species: Salmonella subterranea

Strain Designation: FRCl

Strain history: CIP <- 2005, DSMZ <- E.S. Shelobolina, Massachusetts Univ., Massachusetts, USA: strain FRC1

NCBI tax ID(s): 1123238 (strain), 255519 (species)

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General

@ref: 6326

BacDive-ID: 5126

DSM-Number: 16208

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

description: Salmonella subterranea FRCl is an aerobe, Gram-negative, motile bacterium that was isolated from uranium contaminated subsurface sediment.

NCBI tax id

NCBI tax idMatching level
255519species
1123238strain

strain history

@refhistory
6326<- E. S. Shelobolina, Uni Massachusetts; FRCl
123352CIP <- 2005, DSMZ <- E.S. Shelobolina, Massachusetts Univ., Massachusetts, USA: strain FRC1

doi: 10.13145/bacdive5126.20240510.9

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 subterranea
  • full scientific name: Salmonella subterranea Shelobolina et al. 2005

  • synonyms

    • @ref: 20215
    • synonym: Atlantibacter subterranea

@ref: 6326

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Salmonella

species: Salmonella subterranea

full scientific name: Salmonella subterranea Shelobolina et al. 2005

strain designation: FRCl

type strain: yes

Morphology

cell morphology

  • @ref: 123352
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

colony morphology

@refincubation period
606161 day
123352

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6326TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
6326CASO 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
6326LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
38374MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123352CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
6326positivegrowth30
38374positivegrowth25
60616positivegrowth25
6326positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60616aerobe
123352facultative anaerobe

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
68371turanose-builds acid from32528
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
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
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
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
68368L-arabinose+fermentation30849
68368amygdalin+fermentation27613
68368melibiose-fermentation28053
68368sucrose-fermentation17992
68368L-rhamnose+fermentation62345
68368sorbitol-fermentation30911
68368myo-inositol-fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan+energy source27897
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine+degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
123352nitrate+reduction17632
123352nitrite+reduction16301

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno
12335235581indoleyes

metabolite tests

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

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
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
123352oxidase-
123352alcohol dehydrogenase-1.1.1.1
123352catalase+1.11.1.6
123352lysine decarboxylase-4.1.1.18
123352ornithine decarboxylase+4.1.1.17
123352urease-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
123352-+---+----++-+-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
6326+--+----+--++--+--++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123352+/--++++---++++-++/--+---+-+/---++---+------+/--+/---++-++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6326uranium contaminated subsurface sedimentTNUSAUSANorth America
60616Uranium contaminated subsurface sedimentUSAUSANorth America
123352Environment, Uranium contaminated subsurface sedimentUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Aquatic#Sediment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
63261Risk group (German classification)
1233522Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Atlantibacter subterranea strain FRCl 16S ribosomal RNA gene, partial sequenceAY3738291363nuccore255519
124043Salmonella subterranea gene for 16S ribosomal RNA, partial sequence, strain: JNBP 5029.LC1262691065nuccore255519

Genome sequences

  • @ref: 66792
  • description: Atlantibacter subterranea DSM 16208
  • accession: 2574180435
  • assembly level: draft
  • database: img
  • NCBI tax ID: 1123238

External links

@ref: 6326

culture collection no.: CCUG 55500, DSM 16208, ATCC BAA-836, CIP 109002, FRC 1

straininfo link

  • @ref: 74618
  • straininfo: 138028

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6326Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16208)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16208
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
38374Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6696
60616Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55500)https://www.ccug.se/strain?id=55500
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
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
74618Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138028.1StrainInfo: A central database for resolving microbial strain identifiers
123352Curators of the CIPCollection of Institut Pasteur (CIP 109002)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109002
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy