Strain identifier

BacDive ID: 134091

Type strain: Yes

Species: Zobellia russellii

Strain history: CIP <- 2004, CCUG <- 2002, KMM

NCBI tax ID(s): 248907 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 8.1 (current version)

General

@ref: 31228

BacDive-ID: 134091

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

description: Zobellia russellii LMG 22071 is an aerobe, Gram-negative, motile bacterium that was isolated from Green alga,Acrosiphonia sonderi.

NCBI tax id

  • NCBI tax id: 248907
  • Matching level: species

strain history

  • @ref: 122318
  • history: CIP <- 2004, CCUG <- 2002, KMM

doi: 10.13145/bacdive134091.20230509.8.1

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 russellii
  • full scientific name: Zobellia russellii Nedashkovskaya et al. 2004

@ref: 31228

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Zobellia

species: Zobellia russellii

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityflagellum arrangementconfidencecell shape
31228negative1.3 µm0.45 µmyesgliding
69480negative99.97
122318negativenorod-shaped

colony morphology

  • @ref: 122318

pigmentation

@refproductionname
31228yes
122318yesFlexirubin

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
38282Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122318CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
31228positivegrowth04-38
31228positiveoptimum26.5mesophilic
38282positivegrowth25mesophilic
57502positivegrowth25-28mesophilic
122318positivegrowth5-37
122318nogrowth41thermophilic
122318nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31228aerobe
57502aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
31228NaClpositivegrowth01-10 %
31228NaClpositiveoptimum2.5 %
122318NaClnogrowth0 %
122318NaClnogrowth2 %
122318NaClnogrowth4 %
122318NaClnogrowth6 %
122318NaClnogrowth8 %
122318NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3122822599arabinose+carbon source
3122817057cellobiose+carbon source
3122833984fucose+carbon source
3122817234glucose+carbon source
3122817716lactose+carbon source
3122817306maltose+carbon source
3122829864mannitol+carbon source
3122837684mannose+carbon source
3122826546rhamnose+carbon source
3122817992sucrose+carbon source
3122853424tween 20+carbon source
3122853423tween 40+carbon source
3122853426tween 80+carbon source
3122818222xylose+carbon source
3122817632nitrate+reduction
1223184853esculin-hydrolysis
122318606565hippurate-hydrolysis
12231817632nitrate+reduction
12231816301nitrite-reduction
12231815792malonate-assimilation
12231817632nitrate-respiration

metabolite production

  • @ref: 122318
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12231815688acetoin-
12231817234glucose-

enzymes

@refvalueactivityec
31228alkaline phosphatase+3.1.3.1
31228catalase+1.11.1.6
31228gelatinase+
31228cytochrome oxidase+1.9.3.1
122318oxidase+
122318beta-galactosidase+3.2.1.23
122318alcohol dehydrogenase-1.1.1.1
122318gelatinase+/-
122318amylase+
122318caseinase+3.4.21.50
122318catalase+1.11.1.6
122318tween esterase+
122318gamma-glutamyltransferase+2.3.2.2
122318lecithinase+
122318lipase-
122318lysine decarboxylase-4.1.1.18
122318ornithine decarboxylase-4.1.1.17
122318phenylalanine ammonia-lyase-4.3.1.24
122318protease+
122318tryptophan deaminase-
122318urease-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
122318-+++-++++-++++-+++++

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryisolation date
57502Green alga,Acrosiphonia sonderi2000-06-01Sea of JapanPacific Ocean
122318Green alga, Accrosiphonia sonderiPacific OceanSea of Japan2000

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_26386.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_141;96_439;97_501;98_575;99_26386&stattab=map
  • Last taxonomy: Zobellia russellii
  • 16S sequence: AB121976
  • Sequence Identity:
  • Total samples: 499
  • soil counts: 30
  • aquatic counts: 382
  • animal counts: 83
  • plant counts: 4

Safety information

risk assessment

  • @ref: 122318
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31228
  • description: Zobellia russellii gene for 16S ribosomal RNA, partial sequence
  • accession: AB121976
  • length: 1408
  • database: nuccore
  • NCBI tax ID: 248907

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Zobellia russellii KMM 3677GCA_018728565contigncbi248907
66792Zobellia russellii strain KMM 3677248907.4wgspatric248907

GC content

  • @ref: 31228
  • GC-content: 38.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno85.901no
gram-positiveno98.174yes
anaerobicno99.504no
aerobicyes92.498yes
halophileno66.023no
spore-formingno95.963no
glucose-utilyes89.42yes
flagellatedno93.274yes
thermophileno99.589yes
glucose-fermentno88.136no

External links

@ref: 31228

culture collection no.: LMG 22071, CCUG 47084, KMM 3677, CIP 108564, KMM 3677T

straininfo link

  • @ref: 91700
  • straininfo: 127802

literature

  • topic: Phylogeny
  • Pubmed-ID: 15388723
  • title: Zobellia amurskyensis sp. nov., Zobellia laminariae sp. nov. and Zobellia russellii sp. nov., novel marine bacteria of the family Flavobacteriaceae.
  • authors: Nedashkovskaya OI, Suzuki M, Vancanneyt M, Cleenwerck I, Lysenko AM, Mikhailov VV, Swings J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63091-0
  • year: 2004
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis, Flavobacteriaceae/*classification/*isolation & purification/physiology, Genes, rRNA, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Pacific Ocean, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Water Microbiology
  • topic2: Enzymology

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
31228Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172755428776041
38282Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6200
57502Curators of the CCUGhttps://www.ccug.se/strain?id=47084Culture Collection University of Gothenburg (CCUG) (CCUG 47084)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91700Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID127802.1
122318Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108564Collection of Institut Pasteur (CIP 108564)