Strain identifier

BacDive ID: 13801

Type strain: Yes

Species: Ruegeria gelatinovorans

Strain Designation: B6

Strain history: CIP <- 1999, IAM <- ATCC <- R. Ahrens, strain B6

NCBI tax ID(s): 53501 (species)

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General

@ref: 2345

BacDive-ID: 13801

DSM-Number: 5887

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

description: Ruegeria gelatinovorans B6 is a mesophilic, Gram-negative, motile bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 53501
  • Matching level: species

strain history

@refhistory
2345<- ATCC <- R. Ahrens, B6
67770IAM 12617 <-- ATCC 25655 <-- R. Ahrens B6.
119562CIP <- 1999, IAM <- ATCC <- R. Ahrens, strain B6

doi: 10.13145/bacdive13801.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Ruegeria
  • species: Ruegeria gelatinovorans
  • full scientific name: Ruegeria gelatinovorans corrig. (Rüger and Höfle 1992 ex Ahrens 1968) Uchino et al. 1999

  • synonyms

    @refsynonym
    20215Thalassovita gelatinovora
    20215Agrobacterium gelatinovorum
    20215Ruegeria gelatinovora
    20215Thalassobius gelatinovorus

@ref: 2345

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Thalassobius

species: Thalassobius gelatinovorus

full scientific name: Thalassobius gelatinovorus (Rüger and Höfle 1992) Arahal et al. 2006

strain designation: B6

type strain: yes

Morphology

cell morphology

  • @ref: 119562
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2345MARINE AGAR (DSMZ Medium 123)yeshttps://mediadive.dsmz.de/medium/123Name: MARINE AGAR (DSMZ Medium 123) Composition: NaCl 24.0 g/l Agar 15.0 g/l MgCl2 x 6 H2O 11.0 g/l Bacto peptone 5.0 g/l Na2SO4 4.0 g/l CaCl2 x 6 H2O 2.0 g/l Yeast extract 1.0 g/l KCl 0.7 g/l KBr 0.1 g/l SrCl2 x 6 H2O 0.04 g/l H3BO3 0.03 g/l NaSiO3 x 9 H2O 0.005 g/l NaF 0.003 g/l NH4NO3 0.002 g/l Fe(III)PO4 x 4 H2O 0.001 g/l Distilled water
39413Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119562CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
2345positivegrowth26mesophilic
39413positivegrowth25mesophilic
67770positivegrowth25mesophilic
119562positivegrowth5-30
119562nogrowth37mesophilic
119562nogrowth41thermophilic
119562nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
119562NaClnogrowth0 %
119562NaClnogrowth2 %
119562NaClnogrowth4 %
119562NaClnogrowth6 %
119562NaClnogrowth8 %
119562NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11956216947citrate-carbon source
1195624853esculin-hydrolysis
119562606565hippurate-hydrolysis
11956217632nitrate-builds gas from
11956217632nitrate+reduction
11956216301nitrite-builds gas from
11956216301nitrite-reduction
11956215792malonate-assimilation
11956217234glucose-degradation

metabolite production

  • @ref: 119562
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11956215688acetoin-
11956217234glucose-

enzymes

@refvalueactivityec
119562oxidase-
119562beta-galactosidase-3.2.1.23
119562alcohol dehydrogenase-1.1.1.1
119562gelatinase+/-
119562amylase-
119562caseinase-3.4.21.50
119562catalase+1.11.1.6
119562tween esterase-
119562gamma-glutamyltransferase-2.3.2.2
119562lecithinase-
119562lipase-
119562lysine decarboxylase-4.1.1.18
119562ornithine decarboxylase-4.1.1.17
119562phenylalanine ammonia-lyase-4.3.1.24
119562protease-
119562tryptophan deaminase-
119562urease-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
119562-+++-+-----+--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119562------------------------------------------------------------+--------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2345seawaterKiel FjordGermanyDEUEurope
67770SedimentBaltic Sea
119562Environment, Sediment from the Kiel Fjord of the Baltic SeaKiel FjordBaltic Sea

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4780.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_2363;97_2877;98_3582;99_4780&stattab=map
  • Last taxonomy: Thalassobius gelatinovorus subclade
  • 16S sequence: D88523
  • Sequence Identity:
  • Total samples: 851
  • soil counts: 7
  • aquatic counts: 783
  • animal counts: 25
  • plant counts: 36

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
23451Risk group (German classification)
1195621Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Agrobacterium gelatinovorum gene for 16S rRNA, partial sequenceD885231390ena53501
20218Thalassobius gelatinovorus gene for 16S ribosomal RNA, partial sequenceAB2895911389ena53501
20218Thalassobius gelatinovorus strain NBRC15761 16S ribosomal RNA gene, partial sequenceDQ9156391307ena53501

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thalassobius gelatinovorus strain CECT 435753501.3wgspatric53501
66792Thalassobius gelatinovorus strain DSM 588753501.6wgspatric53501
66792Thalassobius gelatinovorus DSM 58872622736435draftimg53501
66792Thalassobius gelatinovorus CECT 43572684622622draftimg53501
67770Thalassovita gelatinovora CECT 4357GCA_001458355contigncbi53501
67770Thalassovita gelatinovora DSM 5887GCA_900111045contigncbi53501

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.73no
anaerobicno97.306no
halophileyes76.76no
spore-formingno95.939no
glucose-utilyes58.397no
thermophileno95.353yes
aerobicyes81.502no
motileyes60.077no
glucose-fermentno88.232no
flagellatedno73.871no

External links

@ref: 2345

culture collection no.: DSM 5887, ATCC 25655, CECT 4357, IAM 12617, JCM 20688, CIP 105976, IFO 15761, LMG 129, LMG 8174, NBRC 15761, NCIMB 2206

straininfo link

  • @ref: 82979
  • straininfo: 412

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Enzymology1369292Purification, properties and determinations of recognition sequence and cleavage site of restriction endonuclease from "Agrobacterium gelatinovorum" IAM 12617, a marine bacterium (AgeI).Mizuno H, Suzuki T, Akagawa M, Yamasato K, Yamada YAgric Biol Chem1990Base Sequence, Cations, Divalent/pharmacology, DNA Restriction Enzymes/*isolation & purification/metabolism, DNA, Viral/metabolism, Electrophoresis, Polyacrylamide Gel/methods, Enzyme Stability, Hot Temperature, Hydrogen-Ion Concentration, Isoelectric Point, Molecular Sequence Data, Molecular Weight, Rhizobium/*enzymologyMetabolism
Phylogeny1371058Marine star-shaped-aggregate-forming bacteria: Agrobacterium atlanticum sp. nov.; Agrobacterium meteori sp. nov.; Agrobacterium ferrugineum sp. nov., nom. rev.; Agrobacterium gelatinovorum sp. nov., nom. rev.; and Agrobacterium stellulatum sp. nov., nom. rev.Ruger HJ, Hofle MGInt J Syst Bacteriol1992DNA, Bacterial/analysis, Genotype, Phenotype, RNA, Bacterial/analysis, Rhizobium/*classification/genetics/physiology, Seawater, *Water MicrobiologyGenetics10.1099/00207713-42-1-133
Enzymology8901102Cloning and nucleotide sequence of the AgeI methylase gene from Agrobacterium gelatinovorum IAM 12617, a marine bacterium.Suzuki T, Sugimoto E, Tahara Y, Yamada YBiosci Biotechnol Biochem1996Amino Acid Sequence, Bacterial Proteins/*genetics/metabolism, Base Sequence, Cloning, Molecular, DNA-Cytosine Methylases/*genetics/metabolism, Molecular Sequence Data, Rhizobium/*enzymology/*genetics, Sequence Homology, Amino AcidMetabolism10.1271/bbb.60.444
Phylogeny12501429Reclassification of marine Agrobacterium species: Proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev.Uchino Y, Hirata A, Yokota A, Sugiyama JJ Gen Appl Microbiol199810.2323/jgam.44.201
Phylogeny17684282Thalassococcus halodurans gen. nov., sp. nov., a novel halotolerant member of the Roseobacter clade isolated from the marine sponge Halichondria panicea at Friday Harbor, USA.Lee OO, Tsoi MMY, Li X, Wong PK, Qian PYInt J Syst Evol Microbiol2007Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/chemistry/*classification/isolation & purification/physiology, Roseobacter/chemistry/*classification/isolation & purification/physiology, WashingtonGenetics10.1099/ijs.0.64801-0
Phylogeny33974534Isolation of Thalassobius mangrovi sp. nov., a novel bacterium in the family Rhodobacteraceae, from marine mangrove sediment.Chen S, Zheng S, Zhang D, Hetharua B, Gui J, An X, Xu HInt J Syst Evol Microbiol2021Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, WetlandsTranscriptome10.1099/ijsem.0.004801

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2345Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5887)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5887
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
39413Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18054
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
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
82979Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID412.1StrainInfo: A central database for resolving microbial strain identifiers
119562Curators of the CIPCollection of Institut Pasteur (CIP 105976)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105976