Strain identifier

BacDive ID: 17933

Type strain: Yes

Species: Rubrivivax gelatinosus

Strain history: CIP <- 2001, CCUG <- K. Kersters <- 1973, NCIB, Rhodopseudomonas gelatinosa <- 1951, C. van Niel

NCBI tax ID(s): 28068 (species)

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General

@ref: 866

BacDive-ID: 17933

DSM-Number: 1709

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile

description: Rubrivivax gelatinosus DSM 1709 is an anaerobe, mesophilic, motile bacterium that was isolated from Acetate enrichment .

NCBI tax id

  • NCBI tax id: 28068
  • Matching level: species

strain history

@refhistory
866<- NCIB <- C.B. van Niel
67770IAM 14808 <-- DSM 1709 <-- NCIB 8290 <-- C. B. Van Niel.
119561CIP <- 2001, CCUG <- K. Kersters <- 1973, NCIB, Rhodopseudomonas gelatinosa <- 1951, C. van Niel

doi: 10.13145/bacdive17933.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Rubrivivax
  • species: Rubrivivax gelatinosus
  • full scientific name: Rubrivivax gelatinosus (Molisch 1907) Willems et al. 1991

  • synonyms

    @refsynonym
    20215Rhodocyclus gelatinosus
    20215Rhodopseudomonas gelatinosa
    20215Rhodocystis gelatinosa

@ref: 866

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Rubrivivax

species: Rubrivivax gelatinosus

full scientific name: Rubrivivax gelatinosus (Molisch 1907) Willems et al. 1991

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes96.719
6948099.997negative
119561yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
866RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)yeshttps://mediadive.dsmz.de/medium/27Name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27) Composition: Disodium succinate 1.0 g/l KH2PO4 0.5 g/l Ammonium acetate 0.5 g/l NaCl 0.4 g/l NH4Cl 0.4 g/l MgSO4 x 7 H2O 0.4 g/l Yeast extract 0.3 g/l L-Cysteine HCl 0.3 g/l CaCl2 x 2 H2O 0.05 g/l Fe(III) citrate 0.005 g/l Resazurin 0.005 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Vitamin B12 Distilled water
40648MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
119561CIP Medium 403yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=403
119561CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
866positivegrowth25mesophilic
40648positivegrowth25mesophilic
67770positivegrowth27mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 866
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.821

compound production

  • @ref: 866
  • compound: carotenoids

halophily

@refsaltgrowthtested relationconcentration
119561NaClpositivegrowth0 %
119561NaClnogrowth2 %
119561NaClnogrowth4 %
119561NaClnogrowth6 %
119561NaClnogrowth8 %
119561NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11956116947citrate-carbon source
1195614853esculin-hydrolysis
11956117234glucose-fermentation
11956117716lactose-fermentation
11956117632nitrate-reduction
11956116301nitrite+reduction
119561132112sodium thiosulfate-builds gas from
11956117632nitrate+respiration

antibiotic resistance

  • @ref: 119561
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119561
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 119561
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
119561oxidase-
119561beta-galactosidase-3.2.1.23
119561gelatinase+
119561amylase+
119561DNase-
119561caseinase-3.4.21.50
119561catalase-1.11.1.6
119561tween esterase+
119561gamma-glutamyltransferase+2.3.2.2
119561lecithinase-
119561lipase-
119561phenylalanine ammonia-lyase-4.3.1.24
119561tryptophan deaminase-
119561urease-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
119561-+++-++----+--------

Isolation, sampling and environmental information

isolation

@refsample type
67770Acetate enrichment (pH 6.6)
119561Acetate enrichment

taxonmaps

  • @ref: 69479
  • File name: preview.99_3294.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_1718;97_2057;98_2526;99_3294&stattab=map
  • Last taxonomy: Rubrivivax
  • 16S sequence: D16213
  • Sequence Identity:
  • Total samples: 3901
  • soil counts: 714
  • aquatic counts: 2410
  • animal counts: 348
  • plant counts: 429

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
8661Risk group (German classification)
1195611Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhodocyclus gelatinosus 16S ribosomal RNAM606821532ena28068
866Rubrivivax gelatinosus gene for 16S ribosomal RNA, partial sequence, strain: ATCC 17011D162131451ena28068

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rubrivivax gelatinosus DSM 1709GCA_016583525contigncbi28068
66792Rubrivivax gelatinosus strain DSM 170928068.10wgspatric28068
66792Rubrivivax gelatinosus strain DSM 170928068.13wgspatric28068
66792Rubrivivax gelatinosus DSM 17092795385456draftimg28068
67770Rubrivivax gelatinosus DSM 1709GCA_004340905scaffoldncbi28068

GC content

  • @ref: 67770
  • GC-content: 71.9
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes91.336no
gram-positiveno99.169no
anaerobicyes60.491no
halophileno95.963no
spore-formingno93.414no
glucose-utilyes69.779no
flagellatedyes82.216no
aerobicno75.853yes
thermophileno98.96yes
glucose-fermentno84.057no

External links

@ref: 866

culture collection no.: DSM 1709, ATCC 17011, NCIB 8290, JCM 21318, ATCC 11169, CCTM 1912, CCUG 15841, CCUG 21977, CCUG 21990, CIP 107072, IAM 14808, IFO 16663, LMG 4311, LMG 4438, NBRC 16663, NCIMB 8290

straininfo link

  • @ref: 86922
  • straininfo: 4936

literature

  • topic: Phylogeny
  • Pubmed-ID: 31730031
  • title: Rubrivivax albus sp. nov., isolated from a freshwater pond.
  • authors: Sheu SY, Li ZH, Young CC, Chen WM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003829
  • year: 2020
  • mesh: Bacterial Typing Techniques, Base Composition, Burkholderiales/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistry
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
866Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1709)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1709
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
40648Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19272
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/
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
86922Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4936.1StrainInfo: A central database for resolving microbial strain identifiers
119561Curators of the CIPCollection of Institut Pasteur (CIP 107072)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107072