Strain identifier

BacDive ID: 13664

Type strain: Yes

Species: Jannaschia rubra

Strain Designation: 4SM3

Strain history: CIP <- 2004, M.J. Pujalte, Burjassot, Spain: strain 4SM3

NCBI tax ID(s): 282197 (species)

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General

@ref: 6269

BacDive-ID: 13664

DSM-Number: 16279

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

description: Jannaschia rubra 4SM3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Mediterranean sea water.

NCBI tax id

  • NCBI tax id: 282197
  • Matching level: species

strain history

@refhistory
6269<- M. J. Pujalte; 4SM3 <- M. Ortigosa et al.
382752004, M.J. Pujalte, Burjassot, Spain: strain 4SM3
122284CIP <- 2004, M.J. Pujalte, Burjassot, Spain: strain 4SM3

doi: 10.13145/bacdive13664.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Jannaschia
  • species: Jannaschia rubra
  • full scientific name: Jannaschia rubra Macián et al. 2005

@ref: 6269

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Jannaschia

species: Jannaschia rubra

full scientific name: Jannaschia rubra Macián et al. 2005

strain designation: 4SM3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31367negative1.5 µm0.5 µmrod-shapedyes
69480no93.883
69480negative99.999
122284negativerod-shapedno

colony morphology

@refincubation period
585532 days
122284

pigmentation

  • @ref: 31367
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6269BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
38275Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122284CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6269positivegrowth25mesophilic
31367positivegrowth04-25
31367positiveoptimum14.5psychrophilic
38275positivegrowth25mesophilic
58553positivegrowth24-26
122284positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31367aerobe
58553aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
31367NaClpositivegrowth<9 %
31367NaClpositiveoptimum4.5 %
122284NaClpositivegrowth4-10 %
122284NaClnogrowth0 %
122284NaClnogrowth2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3136730089acetate+carbon source
3136729016arginine+carbon source
3136735391aspartate+carbon source
3136728757fructose+carbon source
3136728260galactose+carbon source
3136717234glucose+carbon source
3136717754glycerol+carbon source
3136727570histidine+carbon source
3136724996lactate+carbon source
3136725017leucine+carbon source
3136725115malate+carbon source
3136717306maltose+carbon source
3136729864mannitol+carbon source
3136737684mannose+carbon source
3136718257ornithine+carbon source
3136717148putrescine+carbon source
3136715361pyruvate+carbon source
3136717822serine+carbon source
3136730911sorbitol+carbon source
3136730031succinate+carbon source
3136718222xylose+carbon source
12228416947citrate-carbon source
1222844853esculin+hydrolysis
122284606565hippurate+hydrolysis
12228417632nitrate-builds gas from
12228417632nitrate+reduction
12228416301nitrite-builds gas from
12228416301nitrite+reduction
12228415792malonate-assimilation
12228417632nitrate-respiration

metabolite production

  • @ref: 122284
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 122284
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
31367cytochrome oxidase+1.9.3.1
122284oxidase+
122284beta-galactosidase+3.2.1.23
122284alcohol dehydrogenase-1.1.1.1
122284gelatinase-
122284amylase+
122284caseinase-3.4.21.50
122284catalase+1.11.1.6
122284tween esterase+
122284gamma-glutamyltransferase+2.3.2.2
122284lecithinase-
122284lipase-
122284lysine decarboxylase-4.1.1.18
122284ornithine decarboxylase-4.1.1.17
122284phenylalanine ammonia-lyase+4.3.1.24
122284tryptophan deaminase+
122284urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122284-+++-++----+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
6269Mediterranean sea waternear ValenciaSpainESPEurope
58553Oyster meatValenciaSpainESPEurope1990-04-01
122284Environment, Sea waterValenciaSpainESPEurope1990

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_1708.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_971;97_1131;98_1348;99_1708&stattab=map
  • Last taxonomy: Jannaschia rubra
  • 16S sequence: AJ748747
  • Sequence Identity:
  • Total samples: 390
  • soil counts: 48
  • aquatic counts: 320
  • animal counts: 22

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
62691Risk group (German classification)
1222841Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Jannaschia rubra strain CECT5088 16S ribosomal RNA gene, partial sequenceDQ9156041308ena282197
6269Jannaschia rubra 16S rRNA gene, type strain 4SM3TAJ7487471462ena282197

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Jannaschia rubra DSM 16279GCA_900113265scaffoldncbi282197
66792Jannaschia rubra CECT 5088GCA_001403735contigncbi282197
66792Jannaschia rubra strain CECT 5088282197.4wgspatric282197
66792Jannaschia rubra strain DSM 16279282197.5wgspatric282197
66792Jannaschia rubra CECT 50882711768026draftimg282197
66792Jannaschia rubra DSM 162792622736430draftimg282197

GC content

  • @ref: 6269
  • GC-content: 64.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes50.736yes
flagellatedno90.308no
gram-positiveno98.26no
anaerobicno97.883yes
aerobicyes91.94yes
halophileyes80.97yes
spore-formingno96.485no
glucose-fermentno90.531no
thermophileno94.883yes
glucose-utilyes78.683yes

External links

@ref: 6269

culture collection no.: DSM 16279, CECT 5088, DSM 14425, CCUG 49434, CIP 108401

straininfo link

  • @ref: 82847
  • straininfo: 138008

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774638Jannaschia rubra sp. nov., a red-pigmented bacterium isolated from sea water.Macian MC, Arahal DR, Garay E, Ludwig W, Schleifer KH, Pujalte MJInt J Syst Evol Microbiol10.1099/ijs.0.63412-02005DNA, Bacterial/analysis, DNA, Ribosomal, Genes, rRNA, Genotype, Mediterranean Sea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Pigments, Biological/*metabolism, RNA, Ribosomal, 16S, Rhodobacteraceae/*classification/genetics/isolation & purification/metabolism, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny33724173Jannaschia marina sp. nov., isolated from the gut of a gastropod, Onchidium reevesii.Chen S, He M, Lai Q, Xu Y, Shang CInt J Syst Evol Microbiol10.1099/ijsem.0.0047562021

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6269Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16279)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16279
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
31367Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127680
38275Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6020
58553Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49434)https://www.ccug.se/strain?id=49434
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
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
82847Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138008.1StrainInfo: A central database for resolving microbial strain identifiers
122284Curators of the CIPCollection of Institut Pasteur (CIP 108401)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108401