Strain identifier

BacDive ID: 134089

Type strain: Yes

Species: Zobellia amurskyensis

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

NCBI tax ID(s): 248905 (species)

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General

@ref: 31228

BacDive-ID: 134089

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

description: Zobellia amurskyensis LMG 22069 is an aerobe, Gram-negative, motile bacterium that was isolated from Sea water.

NCBI tax id

  • NCBI tax id: 248905
  • Matching level: species

strain history

  • @ref: 116348
  • history: CIP <- 2004, CCUG <- 2002, KMM

doi: 10.13145/bacdive134089.20230509.8.1

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

@ref: 31228

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Zobellia

species: Zobellia amurskyensis

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityflagellum arrangementconfidencecell shape
31228negative1.3 µm0.45 µmyesgliding
69480negative99.983
116348negativenorod-shaped

colony morphology

  • @ref: 116348

pigmentation

@refproductionname
31228yes
116348yesFlexirubin

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
40020Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
116348CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
31228positivegrowth04-32
31228positiveoptimum24psychrophilic
40020positivegrowth25mesophilic
57500positivegrowth22-25
116348positivegrowth5-25psychrophilic
116348nogrowth30mesophilic
116348nogrowth37mesophilic
116348nogrowth41thermophilic
116348nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31228aerobe
57500aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
31228NaClpositivegrowth01-06 %
31228NaClpositiveoptimum2 %
116348NaClnogrowth0 %
116348NaClnogrowth2 %
116348NaClnogrowth4 %
116348NaClnogrowth6 %
116348NaClnogrowth8 %
116348NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3122822599arabinose+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
3122853426tween 80+carbon source
3122817632nitrate+reduction
1163484853esculin-hydrolysis
116348606565hippurate+hydrolysis
11634817632nitrate+reduction
11634816301nitrite-reduction
11634815792malonate-assimilation
11634817632nitrate-respiration

metabolite production

  • @ref: 116348
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11634815688acetoin-
11634817234glucose+

enzymes

@refvalueactivityec
31228alkaline phosphatase+3.1.3.1
31228catalase+1.11.1.6
31228gelatinase+
31228cytochrome oxidase+1.9.3.1
116348oxidase+
116348beta-galactosidase+3.2.1.23
116348alcohol dehydrogenase-1.1.1.1
116348gelatinase+/-
116348amylase+
116348DNase+
116348caseinase-3.4.21.50
116348catalase+1.11.1.6
116348tween esterase+
116348gamma-glutamyltransferase+2.3.2.2
116348lecithinase+
116348lysine decarboxylase-4.1.1.18
116348ornithine decarboxylase-4.1.1.17
116348phenylalanine ammonia-lyase-4.3.1.24
116348protease-
116348tryptophan deaminase-
116348urease-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
116348-+++-++---+-++-++++-

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryisolation date
57500Sea water2000-06-01Sea of Japan,Amursky BayPacific Ocean
116348Environment, Sea waterPacific OceanSea of Japan2000

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4433.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_141;96_439;97_501;98_575;99_4433&stattab=map
  • Last taxonomy: Zobellia
  • 16S sequence: AB121974
  • Sequence Identity:
  • Total samples: 211
  • soil counts: 2
  • aquatic counts: 178
  • animal counts: 30
  • plant counts: 1

Safety information

risk assessment

  • @ref: 116348
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31228
  • description: Zobellia amurskyensis gene for 16S ribosomal RNA, partial sequence
  • accession: AB121974
  • length: 1448
  • database: nuccore
  • NCBI tax ID: 248905

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Zobellia amurskyensis KMM 3526GCA_009725985contigncbi248905
66792Zobellia amurskyensis strain KMM 3526248905.6wgspatric248905
66792Zobellia amurskyensis KMM 35262910286357draftimg248905

GC content

  • @ref: 31228
  • GC-content: 37.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno85.552no
gram-positiveno98.26yes
anaerobicno99.572no
aerobicyes92.4no
halophileno66.544no
spore-formingno95.753no
glucose-utilyes88.967no
flagellatedno92.846no
thermophileno99.642yes
glucose-fermentno87.802no

External links

@ref: 31228

culture collection no.: LMG 22069, CCUG 47080, KMM 3526, CIP 108562

straininfo link

  • @ref: 91698
  • straininfo: 127804

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15388723Zobellia amurskyensis sp. nov., Zobellia laminariae sp. nov. and Zobellia russellii sp. nov., novel marine bacteria of the family Flavobacteriaceae.Nedashkovskaya OI, Suzuki M, Vancanneyt M, Cleenwerck I, Lysenko AM, Mikhailov VV, Swings JInt J Syst Evol Microbiol10.1099/ijs.0.63091-02004Bacterial 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 MicrobiologyEnzymology
Genetics31771309Comparative Genomics and CAZyme Genome Repertoires of Marine Zobellia amurskyensis KMM 3526(T) and Zobellia laminariae KMM 3676(T).Chernysheva N, Bystritskaya E, Stenkova A, Golovkin I, Nedashkovskaya O, Isaeva MMar Drugs10.3390/md171206612019Aquatic Organisms/enzymology/*genetics, Bacterial Proteins/*genetics/metabolism, Biotechnology/methods, Carbohydrate Metabolism, Flavobacteriaceae/enzymology/*genetics, Genome, Bacterial/*genetics, *Genomics, Phylogeny, Polysaccharides/metabolism, Seaweed/chemistry/metabolism, Sequence Analysis, DNAMetabolism
Phylogeny34346862Zobellia roscoffensis sp. nov. and Zobellia nedashkovskayae sp. nov., two flavobacteria from the epiphytic microbiota of the brown alga Ascophyllum nodosum, and emended description of the genus Zobellia.Barbeyron T, Thiebaud M, Le Duff N, Martin M, Corre E, Tanguy G, Vandenbol M, Thomas FInt J Syst Evol Microbiol10.1099/ijsem.0.0049132021*Ascophyllum/microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Flavobacteriaceae/classification/isolation & purification, France, Microbiota, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNATranscriptome

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
40020Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6198
57500Curators of the CCUGhttps://www.ccug.se/strain?id=47080Culture Collection University of Gothenburg (CCUG) (CCUG 47080)
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
91698Reimer, 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-ID127804.1
116348Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108562Collection of Institut Pasteur (CIP 108562)