Strain identifier

BacDive ID: 3833

Type strain: Yes

Species: Ekhidna lutea

Strain Designation: BiosLi/39

Strain history: CIP <- 2007, K. Alain, CNRS, Banyuls sur mer, France: strain BiosLi/39

NCBI tax ID(s): 447679 (species)

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General

@ref: 8028

BacDive-ID: 3833

DSM-Number: 19307

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

description: Ekhidna lutea BiosLi/39 is an aerobe, Gram-negative, motile bacterium that was isolated from oligotrophic seawater at a depth of 5 m .

NCBI tax id

  • NCBI tax id: 447679
  • Matching level: species

strain history

@refhistory
8028<- K. Alain, Lab. d'Océanographie Biologique de Banyuls, Univ. Pierre et Marie Curie, France; BIOSLi/39 <- L. Intertaglia
377802007, K. Alain, CNRS, Banyuls/mer, France: strain BiosLi/39
120682CIP <- 2007, K. Alain, CNRS, Banyuls sur mer, France: strain BiosLi/39

doi: 10.13145/bacdive3833.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Reichenbachiellaceae
  • genus: Ekhidna
  • species: Ekhidna lutea
  • full scientific name: Ekhidna lutea Alain et al. 2010

@ref: 8028

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Reichenbachiellaceae

genus: Ekhidna

species: Ekhidna lutea

full scientific name: Ekhidna lutea Alain et al. 2010

strain designation: BiosLi/39

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityflagellum arrangementconfidence
29691negativerod-shapedyesgliding
120682negativerod-shapedno
69480negative92.816

pigmentation

  • @ref: 29691
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8028BACTO 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
37780Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120682CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
8028positivegrowth28
29691positivegrowth20-37
29691positiveoptimum30
37780positivegrowth30

culture pH

@refabilitytypepHPH range
29691positivegrowth07-09alkaliphile
29691positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 29691
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29691no
69480no90.108
69481no100

observation

  • @ref: 29691
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
296914853esculin+hydrolysis
12068217632nitrate-reduction
12068216301nitrite-reduction

metabolite production

  • @ref: 120682
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29691alkaline phosphatase+3.1.3.1
29691catalase+1.11.1.6
29691cytochrome oxidase+1.9.3.1
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
120682oxidase+
120682catalase+1.11.1.6
120682urease-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
120682-++--++++-++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationlatitudelongitudecountryorigin.countrycontinentisolation date
8028oligotrophic seawater at a depth of 5 m (21 °C, 35.9% salinity)South East Pacific Gyre (28° 32.176' S 104° 18.480' W)-28.5363-104.308
120682Environment, Sea water, PacificBanyuls sur merFranceFRAEurope2004

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_40265.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15905;96_11870;97_16060;98_29399;99_40265&stattab=map
  • Last taxonomy: Ekhidna lutea subclade
  • 16S sequence: AM746475
  • Sequence Identity:
  • Total samples: 106
  • soil counts: 2
  • aquatic counts: 104

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
80281Risk group (German classification)
1206821Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8028
  • description: Ekhidna lutea partial 16S rRNA gene, type strain BiosLi/39T
  • accession: AM746475
  • length: 1368
  • database: nuccore
  • NCBI tax ID: 447679

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ekhidna lutea DSM 19307GCA_900188325contigncbi447679
66792Ekhidna lutea strain DSM 19307447679.3wgspatric447679
66792Ekhidna lutea DSM 193072687453772draftimg447679

GC content

@refGC-contentmethod
802837.2high performance liquid chromatography (HPLC)
2969137.2

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno92.816no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.508no
69480spore-formingspore-formingAbility to form endo- or exosporesno90.108yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes85.885yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno91.967yes
69480flagellatedmotile2+Ability to perform flagellated movementno86.095yes

External links

@ref: 8028

culture collection no.: DSM 19307, CIP 109600, OOB 398, BiosLi 39

straininfo link

  • @ref: 73343
  • straininfo: 374231

literature

  • topic: Phylogeny
  • Pubmed-ID: 20118290
  • title: Ekhidna lutea gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from the South East Pacific Ocean.
  • authors: Alain K, Tindall BJ, Catala P, Intertaglia L, Lebaron P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.018804-0
  • year: 2010
  • mesh: Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8028Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19307)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19307
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
29691Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2607628776041
37780Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7362
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
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
73343Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID374231.1StrainInfo: A central database for resolving microbial strain identifiers
120682Curators of the CIPCollection of Institut Pasteur (CIP 109600)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109600