Strain identifier

BacDive ID: 5665

Type strain: Yes

Species: Zobellia galactanivorans

Strain Designation: Dsij

Strain history: CIP <- 2000, T. Barbeyron, C.E.O.B.M., Bretagne, France: strain Dsij <- 1989, P. Potin, Roscoff, France

NCBI tax ID(s): 63186 (species)

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General

@ref: 4827

BacDive-ID: 5665

DSM-Number: 12802

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

description: Zobellia galactanivorans Dsij is an aerobe, mesophilic, Gram-negative bacterium that was isolated from red alga .

NCBI tax id

  • NCBI tax id: 63186
  • Matching level: species

strain history

@refhistory
4827<- T. Barbeyron; Dsij
119503CIP <- 2000, T. Barbeyron, C.E.O.B.M., Bretagne, France: strain Dsij <- 1989, P. Potin, Roscoff, France

doi: 10.13145/bacdive5665.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Zobellia
  • species: Zobellia galactanivorans
  • full scientific name: Zobellia galactanivorans corrig. Barbeyron et al. 2001

  • synonyms

    • @ref: 20215
    • synonym: Zobellia galactanovorans

@ref: 4827

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Zobellia

species: Zobellia galactanivorans

full scientific name: Zobellia galactanivorans Barbeyron et al. 2001

strain designation: Dsij

type strain: yes

Morphology

cell morphology

  • @ref: 119503
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 119503
  • production: yes
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4827BACTO 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
38637MEDIUM 308 - for Stappia stellulata and RuegeriayesAgar (15.000 g);Yeast extract (1.000 g);Peptone (5.000 g);Synthetic sea solution - M0527 (1000.000 ml)
119503CIP Medium 308yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=308

culture temp

@refgrowthtypetemperaturerange
4827positivegrowth35mesophilic
38637positivegrowth30mesophilic
57507positivegrowth25-28mesophilic
119503positivegrowth15-41
119503nogrowth5psychrophilic
119503nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 57507
  • oxygen tolerance: aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1195034853esculin-hydrolysis
119503606565hippurate-hydrolysis
11950317632nitrate+reduction
11950316301nitrite-reduction

antibiotic resistance

  • @ref: 119503
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119503
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11950315688acetoin-
11950317234glucose-

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
119503oxidase+
119503beta-galactosidase+3.2.1.23
119503alcohol dehydrogenase-1.1.1.1
119503gelatinase+
119503amylase+
119503caseinase+3.4.21.50
119503catalase+1.11.1.6
119503tween esterase-
119503gamma-glutamyltransferase+2.3.2.2
119503lecithinase-
119503lipase-
119503lysine decarboxylase-4.1.1.18
119503ornithine decarboxylase-4.1.1.17
119503phenylalanine ammonia-lyase-4.3.1.24
119503protease+
119503tryptophan deaminase-
119503urease-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
119503-+++-++-+-++-+--++++

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
4827red alga (Delesseria sanguinea)Delesseria sanguineaBrittany, English Channel near RoscoffFranceFRAEurope
119503Red algaeRoscoffFranceFRAEurope1989

isolation source categories

  • Cat1: #Host
  • Cat2: #Algae
  • Cat3: #Red algae

taxonmaps

  • @ref: 69479
  • File name: preview.99_716.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_141;96_439;97_501;98_575;99_716&stattab=map
  • Last taxonomy: Zobellia
  • 16S sequence: AF208293
  • Sequence Identity:
  • Total samples: 529
  • soil counts: 69
  • aquatic counts: 434
  • animal counts: 18
  • plant counts: 8

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
48271Risk group (German classification)
1195031Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4827
  • description: Zobellia galactanovora 16S ribosomal RNA gene, partial sequence
  • accession: AF208293
  • length: 1483
  • database: ena
  • NCBI tax ID: 63186

Genome sequences

  • @ref: 66792
  • description: Zobellia galactanivorans strain Dsij
  • accession: 63186.3
  • assembly level: complete
  • database: patric
  • NCBI tax ID: 63186

GC content

  • @ref: 4827
  • GC-content: 43-44
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.367no
anaerobicno99.316yes
halophileno64.027no
spore-formingno95.038no
glucose-utilyes90.695no
flagellatedno94.369no
aerobicyes91.9yes
thermophileno99.379yes
motileno85.777no
glucose-fermentno88.908no

External links

@ref: 4827

culture collection no.: DSM 12802, CIP 106680, CCUG 47099, KCTC 12921

straininfo link

  • @ref: 75147
  • straininfo: 49363

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11411725Zobellia galactanovorans gen. nov., sp. nov., a marine species of Flavobacteriaceae isolated from a red alga, and classification of [Cytophaga] uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Zobellia uliginosa gen. nov., comb. nov.Barbeyron T, L'Haridon S, Corre E, Kloareg B, Potin PInt J Syst Evol Microbiol10.1099/00207713-51-3-9852001Anti-Bacterial Agents/pharmacology, Cytophaga/*classification/drug effects/genetics/isolation & purification, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Escherichia coli/genetics, Fatty Acids/analysis, Flavobacterium/*classification/drug effects/genetics/isolation & purification, Microbial Sensitivity Tests, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodophyta/*microbiology, Seawater/microbiologyEnzymology
Biotechnology20686828Hyper-production and characterization of the iota-carrageenase useful for iota-carrageenan oligosaccharide production from a deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94T, and insight into the unusual catalytic mechanism.Hatada Y, Mizuno M, Li Z, Ohta YMar Biotechnol (NY)10.1007/s10126-010-9312-02010Alteromonadaceae/chemistry/*enzymology, Amino Acid Sequence, Bacterial Proteins/*genetics, Base Sequence, Biotechnology/*methods, Carrageenan/*biosynthesis, Catalysis, Genes, Bacterial/*genetics, Glycoside Hydrolases/*genetics, Hot Temperature, *Models, Molecular, Molecular Sequence Data, Mutagenesis, Site-Directed, Sequence Analysis, DNA, Sequence Homology, Species SpecificityStress

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4827Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12802)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12802
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
38637Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18837
57507Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47099)https://www.ccug.se/strain?id=47099
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
75147Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49363.1StrainInfo: A central database for resolving microbial strain identifiers
119503Curators of the CIPCollection of Institut Pasteur (CIP 106680)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106680