Strain identifier

BacDive ID: 5664

Type strain: Yes

Species: Zobellia uliginosa

Strain Designation: 553 (843)

Strain history: CIP <- 1996, IFO <- ATCC <- C.E. ZoBell: strain 553, Flavobacterium uliginosum

NCBI tax ID(s): 143224 (species)

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General

@ref: 697

BacDive-ID: 5664

DSM-Number: 2061

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

description: Zobellia uliginosa 553 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 143224
  • Matching level: species

strain history

@refhistory
697<- NCMB <- ATCC (Agarbacterium uliginosum) <- C.E. ZoBell, 553
67770IAM 14312 <-- NCIMB l863 <-- ATCC 14397 ("Agarbacterium uliginosum") <-- C. E. ZoBell 553.
123712CIP <- 1996, IFO <- ATCC <- C.E. ZoBell: strain 553, Flavobacterium uliginosum

doi: 10.13145/bacdive5664.20230509.8.1

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 uliginosa
  • full scientific name: Zobellia uliginosa (ZoBell and Upham 1944) Barbeyron et al. 2001

  • synonyms

    @refsynonym
    20215Flavobacterium uliginosum
    20215Cellulophaga uliginosa
    20215Cytophaga uliginosa

@ref: 697

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Zobellia

species: Zobellia uliginosa

full scientific name: Zobellia uliginosa (ZoBell and Upham 1944) Barbeyron et al. 2001

strain designation: 553 (843)

type strain: yes

Morphology

cell morphology

  • @ref: 123712
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
697SEAWATER YEAST PEPTONE AGAR (DSMZ Medium 243)yeshttps://mediadive.dsmz.de/medium/243Name: SEAWATER YEAST PEPTONE AGAR (DSMZ Medium 243) Composition: Agar 12.0 g/l Peptone 5.0 g/l Yeast extract 3.0 g/l Sea water Distilled water
37581MEDIUM 167 - for Cytophaga uliginosa, Demetria terragena and Marinococcus al busyesDistilled water make up to (1000.000 ml);Sodium chloride (50.000 g);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Yeast extract (5.000 g);Peptone (10.000 g);Tween 80 (50.000 mg);Glycerol (2.000 g);Malt extract (5.000 g);Beef extract (2.000 g);
123712CIP Medium 167yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=167
123712CIP Medium 234yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=234

culture temp

@refgrowthtypetemperaturerange
697positivegrowth26mesophilic
37581positivegrowth25mesophilic
67770positivegrowth25mesophilic
123712positivegrowth15-37
123712nogrowth5psychrophilic
123712nogrowth41thermophilic
123712nogrowth45thermophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1237124853esculin-hydrolysis
123712606565hippurate-hydrolysis
12371217632nitrate+reduction
12371216301nitrite-reduction

antibiotic resistance

  • @ref: 123712
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123712
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
123712oxidase+
123712beta-galactosidase-3.2.1.23
123712alcohol dehydrogenase-1.1.1.1
123712gelatinase-
123712catalase+1.11.1.6
123712gamma-glutamyltransferase+2.3.2.2
123712lysine decarboxylase-4.1.1.18
123712ornithine decarboxylase-4.1.1.17
123712phenylalanine ammonia-lyase-4.3.1.24
123712tryptophan deaminase-
123712urease-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
123712-+++-++-+-++++-+-+--

Isolation, sampling and environmental information

isolation

@refsample type
697seawater
67770Marine bottom sediment

isolation source categories

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

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: AB680724
  • 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
6971Risk group (German classification)
1237121Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Zobellia uliginosa gene for 16S rRNA, partial sequence, strain: NBRC 14962AB6807241449ena143224
697Zobellia uliginosa strain ATCC 14397 16S ribosomal RNA gene, partial sequenceM627991527ena143224

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Zobellia uliginosa DSM 2061GCA_900156625contigncbi143224
66792Zobellia uliginosa strain DSM 2061143224.8wgspatric143224
66792Zobellia uliginosa DSM 20612681813510draftimg143224

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno87.913no
gram-positiveno98.295no
anaerobicno99.211no
halophileno70.298no
spore-formingno95.593no
thermophileno99.416no
glucose-utilyes90.747no
aerobicyes90.073no
flagellatedno94.041no
glucose-fermentno87.708no

External links

@ref: 697

culture collection no.: DSM 2061, ATCC 14397, IAM 14312, IFO 14962, NBRC 14962, NCMB 1863, JCM 21152, ACAM 538, CCUG 33448, CECT 4277, CIP 104808, LMG 3809, NCIMB 1863

straininfo link

  • @ref: 75146
  • straininfo: 2837

literature

  • topic: Phylogeny
  • Pubmed-ID: 11411725
  • title: Zobellia 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.
  • authors: Barbeyron T, L'Haridon S, Corre E, Kloareg B, Potin P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-51-3-985
  • year: 2001
  • mesh: Anti-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/microbiology
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
697Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2061)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2061
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
37581Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16758
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
75146Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2837.1StrainInfo: A central database for resolving microbial strain identifiers
123712Curators of the CIPCollection of Institut Pasteur (CIP 104808)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104808