Strain identifier

BacDive ID: 6230

Type strain: Yes

Species: Idiomarina zobellii

Strain history: CIP <- 2002, KMM

NCBI tax ID(s): 86103 (species)

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General

@ref: 6187

BacDive-ID: 6230

DSM-Number: 15924

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, motile

description: Idiomarina zobellii DSM 15924 is a psychrophilic, motile bacterium that was isolated from sea water.

NCBI tax id

  • NCBI tax id: 86103
  • Matching level: species

strain history

@refhistory
6187<- E. P. Ivanova; KMM 231 <- L. A. Romanenko
331242002, KMM
124032CIP <- 2002, KMM

doi: 10.13145/bacdive6230.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Idiomarinaceae
  • genus: Idiomarina
  • species: Idiomarina zobellii
  • full scientific name: Idiomarina zobellii Ivanova et al. 2000

@ref: 6187

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Idiomarinaceae

genus: Idiomarina

species: Idiomarina zobellii

full scientific name: Idiomarina zobellii Ivanova et al. 2000

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.092
6948099.994negative
124032yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6187BACTO 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
33124Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
124032CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6187positivegrowth22psychrophilic
33124positivegrowth25mesophilic
124032positivegrowth5-41

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
124032NaClpositivegrowth2-10 %
124032NaClnogrowth0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12403216947citrate-carbon source
1240324853esculin-hydrolysis
12403217632nitrate-reduction
12403216301nitrite-reduction
12403217234glucose-degradation

metabolite production

  • @ref: 124032
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12403215688acetoin-
12403217234glucose-

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
124032oxidase+
124032alcohol dehydrogenase-1.1.1.1
124032gelatinase+
124032amylase-
124032caseinase-3.4.21.50
124032catalase+1.11.1.6
124032tween esterase+
124032gamma-glutamyltransferase+2.3.2.2
124032lecithinase-
124032lipase+
124032lysine decarboxylase-4.1.1.18
124032ornithine decarboxylase-4.1.1.17
124032phenylalanine ammonia-lyase-4.3.1.24
124032protease-
124032tryptophan deaminase-
124032urease-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
124032-+++-+----++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryisolation date
6187sea waterPacific Ocean
124032Environment, Deep sea waterPacific Ocean1985

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61871Risk group (German classification)
1240321Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Idiomarina zobellii strain KM231(EI5) 16S ribosomal RNA gene, partial sequence
  • accession: AF052741
  • length: 1464
  • database: ena
  • NCBI tax ID: 86103

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Idiomarina zobellii KMM 231GCA_900100855scaffoldncbi86103
66792Idiomarina zobellii KMM 231GCA_001294745contigncbi86103
66792Idiomarina zobellii strain KMM 23186103.7wgspatric86103
66792Idiomarina zobellii strain KMM 23186103.6wgspatric86103
66792Idiomarina zobellii KMM 2312643221445draftimg86103
66792Idiomarina zobellii KMM 2312713896804draftimg86103

GC content

  • @ref: 6187
  • GC-content: 48

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.157no
flagellatedno52.791no
gram-positiveno99.204no
anaerobicno97.706no
aerobicyes81.29no
halophileyes68.948no
spore-formingno96.759no
glucose-fermentno80.101no
thermophileno97.984no
glucose-utilyes85.237no

External links

@ref: 6187

culture collection no.: DSM 15924, KMM 231, CIP 107407, ATCC BAA 313

straininfo link

  • @ref: 75709
  • straininfo: 93235

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10758902Idiomarina gen. nov., comprising novel indigenous deep-sea bacteria from the Pacific Ocean, including descriptions of two species, Idiomarina abyssalis sp. nov. and Idiomarina zobellii sp. nov.Ivanova EP, Romanenko LA, Chun J, Matte MH, Matte GR, Mikhailov VV, Svetashev VI, Huq A, Maugel T, Colwell RRInt J Syst Evol Microbiol10.1099/00207713-50-2-9012000Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gram-Negative Aerobic Bacteria/*classification/cytology/isolation & purification/physiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Water MicrobiologyGenetics
15013384Structure of the O-polysaccharide of Idiomarina zobellii KMM 231T containing two unusual amino sugars with the free amino group, 4-amino-4,6-dideoxy-D-glucose and 2-amino-2-deoxy-L-guluronic acid.Kilcoyne M, Perepelov AV, Tomshich SV, Komandrova NA, Shashkov AS, Romanenko LA, Knirel YA, Savage AVCarbohydr Res10.1016/j.carres.2003.11.0202004Amino Sugars/*analysis/*chemistry, Gammaproteobacteria/*chemistry, Glucosamine/*analogs & derivatives/*analysis/chemistry, Hexuronic Acids/*analysis/chemistry, Magnetic Resonance Spectroscopy, Molecular Structure, O Antigens/*chemistry
Phylogeny26382219Idiomarina aquatica sp. nov., a moderately halophilic bacterium isolated from salterns.Jose Leon M, Martinez-Checa F, Ventosa A, Sanchez-Porro CInt J Syst Evol Microbiol10.1099/ijsem.0.0006192015Alteromonadaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Spain, Ubiquinone/chemistry, *Water MicrobiologyGenetics
Genetics26514764Draft Whole-Genome Sequence of the Marine Bacterium Idiomarina zobellii KMM 231T.Mithoefer S, Rheaume BA, MacLea KSGenome Announc10.1128/genomeA.01257-152015
Phylogeny36355023Structure of the Lipooligosaccharide from the Deep-Sea Marine Bacterium Idiomarina zobellii KMM 231(T), Isolated at a Depth of 4000 Meters.Kokoulin MS, Dmitrenok PS, Romanenko LAMar Drugs10.3390/md201107002022*Lipopolysaccharides/chemistry, Gas Chromatography-Mass Spectrometry, *Alteromonadaceae, Fatty Acids/analysis

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6187Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15924)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15924
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
33124Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4840
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)
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75709Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID93235.1StrainInfo: A central database for resolving microbial strain identifiers
124032Curators of the CIPCollection of Institut Pasteur (CIP 107407)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107407