Strain identifier

BacDive ID: 134090

Type strain: Yes

Species: Zobellia laminariae

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

NCBI tax ID(s): 248906 (species)

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General

@ref: 31228

BacDive-ID: 134090

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

description: Zobellia laminariae KMM 3676 is an aerobe, Gram-negative, motile bacterium that was isolated from Brown alga,Laminaria japonica.

NCBI tax id

  • NCBI tax id: 248906
  • Matching level: species

strain history

  • @ref: 120552
  • history: CIP <- 2004, CCUG <- 2002, KMM

doi: 10.13145/bacdive134090.20230509.8.1

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

@ref: 31228

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Zobellia

species: Zobellia laminariae

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityflagellum arrangementconfidencecell shape
31228negative1.3 µm0.45 µmyesgliding
69480negative99.997
120552negativenorod-shaped

colony morphology

  • @ref: 120552
  • hemolysis ability: 1

pigmentation

@refproductionname
31228yes
120552yesFlexirubin

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
40023Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120552CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
31228positivegrowth04-30
31228positiveoptimum22psychrophilic
40023positivegrowth25mesophilic
57501positivegrowth22-25
120552positivegrowth5-30
120552nogrowth37mesophilic
120552nogrowth41thermophilic
120552nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31228aerobe
57501aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
31228NaClpositivegrowth1.5-6 %
31228NaClpositiveoptimum2 %
120552NaClpositivegrowth2-6 %
120552NaClnogrowth0 %
120552NaClnogrowth8 %
120552NaClnogrowth10 %

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
3122816634raffinose+carbon source
3122826546rhamnose+carbon source
3122817992sucrose+carbon source
3122853423tween 40+carbon source
3122817632nitrate+reduction
1205524853esculin-hydrolysis
120552606565hippurate-hydrolysis
12055217632nitrate+reduction
12055216301nitrite-reduction
12055215792malonate-assimilation
12055217632nitrate-respiration

metabolite production

  • @ref: 120552
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12055215688acetoin-
12055217234glucose-

enzymes

@refvalueactivityec
31228alkaline phosphatase+3.1.3.1
31228catalase+1.11.1.6
31228gelatinase+
31228cytochrome oxidase+1.9.3.1
120552oxidase+
120552beta-galactosidase+3.2.1.23
120552alcohol dehydrogenase-1.1.1.1
120552gelatinase+/-
120552amylase-
120552caseinase-3.4.21.50
120552catalase+1.11.1.6
120552tween esterase+
120552gamma-glutamyltransferase+2.3.2.2
120552lecithinase-
120552lipase-
120552lysine decarboxylase-4.1.1.18
120552ornithine decarboxylase-4.1.1.17
120552phenylalanine ammonia-lyase-4.3.1.24
120552protease+
120552tryptophan deaminase-
120552urease-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
120552-+++-++++-++++-++++-

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryisolation date
57501Brown alga,Laminaria japonica2000-06-01Sea of JapanPacific Ocean
120552Brown alga, laminaria japonicaPacific OceanSea of Japan2000

isolation source categories

  • Cat1: #Host
  • Cat2: #Algae
  • Cat3: #Brown Algae

taxonmaps

  • @ref: 69479
  • File name: preview.99_46887.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_141;96_439;97_501;98_575;99_46887&stattab=map
  • Last taxonomy: Zobellia laminariae
  • 16S sequence: AB121975
  • Sequence Identity:
  • Total samples: 458
  • soil counts: 16
  • aquatic counts: 431
  • animal counts: 4
  • plant counts: 7

Safety information

risk assessment

  • @ref: 120552
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31228
  • description: Zobellia laminariae gene for 16S ribosomal RNA, partial sequence
  • accession: AB121975
  • length: 1384
  • database: nuccore
  • NCBI tax ID: 248906

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Zobellia laminariae KMM 3676GCA_009725995scaffoldncbi248906
66792Zobellia laminariae strain KMM 3676248906.8wgspatric248906
66792Zobellia laminariae KMM 36762910277695draftimg248906

GC content

  • @ref: 31228
  • GC-content: 36.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno94.44no
gram-positiveno98.01no
anaerobicno99.66yes
aerobicyes92.18yes
halophileno61.472no
spore-formingno95.234no
thermophileno99.792yes
glucose-utilyes90.433yes
motileno86.594no
glucose-fermentno85.578no

External links

@ref: 31228

culture collection no.: KMM 3676, CIP 108563, LMG 22070, CCUG 47083

straininfo link

  • @ref: 91699
  • straininfo: 127803

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
40023Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6199
57501Curators of the CCUGhttps://www.ccug.se/strain?id=47083Culture Collection University of Gothenburg (CCUG) (CCUG 47083)
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
91699Reimer, 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-ID127803.1
120552Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108563Collection of Institut Pasteur (CIP 108563)