Strain identifier

BacDive ID: 23035

Type strain: Yes

Species: Endozoicomonas numazuensis

Strain Designation: HC50

Strain history: <- M. Nishijima, Marine Biotechnology Institute, Kamaishi, Japan; HC50

NCBI tax ID(s): 1137799 (species)

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General

@ref: 19246

BacDive-ID: 23035

DSM-Number: 25634

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped

description: Endozoicomonas numazuensis HC50 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from purple sponge, order Haplosclerida, from tidal area.

NCBI tax id

  • NCBI tax id: 1137799
  • Matching level: species

strain history

  • @ref: 19246
  • history: <- M. Nishijima, Marine Biotechnology Institute, Kamaishi, Japan; HC50

doi: 10.13145/bacdive23035.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Endozoicomonadaceae
  • genus: Endozoicomonas
  • species: Endozoicomonas numazuensis
  • full scientific name: Endozoicomonas numazuensis Nishijima et al. 2013

@ref: 19246

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Endozoicomonadaceae

genus: Endozoicomonas

species: Endozoicomonas numazuensis

full scientific name: Endozoicomonas numazuensis Nishijima et al. 2013

strain designation: HC50

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30690negative6.5 µm0.6 µmrod-shapedno
69480negative99.992

pigmentation

  • @ref: 30690
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 19246
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
19246positivegrowth25mesophilic
30690positivegrowth15-37
30690positiveoptimum25mesophilic

culture pH

@refabilitytypepHPH range
30690positivegrowth5.5-9alkaliphile
30690positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30690
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
30690no
69481no100
69480no99.95

halophily

@refsaltgrowthtested relationconcentration
30690NaClpositivegrowth1.25-5 %
30690NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3069028757fructose+carbon source
306905417glucosamine+carbon source
3069017234glucose+carbon source
3069017754glycerol+carbon source
3069037684mannose+carbon source
3069053426tween 80+carbon source
3069017632nitrate+reduction

enzymes

@refvalueactivityec
30690acid phosphatase+3.1.3.2
30690alkaline phosphatase+3.1.3.1
30690alpha-galactosidase+3.2.1.22
30690catalase+1.11.1.6
30690gelatinase+
30690cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 19246
  • sample type: purple sponge, order Haplosclerida, from tidal area
  • host species: Haplosclerida
  • geographic location: Shizuoka Prefecture, Numazu
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Tidal flat
#Host#Invertebrates (Other)#Porifera (Sponges)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6831.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_202;96_709;97_828;98_2822;99_6831&stattab=map
  • Last taxonomy: Endozoicomonas numazuensis subclade
  • 16S sequence: AB695088
  • Sequence Identity:
  • Total samples: 231
  • soil counts: 1
  • aquatic counts: 218
  • animal counts: 11
  • plant counts: 1

Safety information

risk assessment

  • @ref: 19246
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19246
  • description: Endozoicomonas numazuensis gene for 16S rRNA, partial sequence
  • accession: AB695088
  • length: 1466
  • database: ena
  • NCBI tax ID: 1137799

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Endozoicomonas numazuensis DSM 25634GCA_000722635scaffoldncbi1137799
66792Endozoicomonas numazuensis strain DSM 256341137799.5wgspatric1137799
66792Endozoicomonas numazuensis DSM 256342574179790draftimg1137799

GC content

@refGC-contentmethod
1924648.7high performance liquid chromatography (HPLC)
3069048.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes81.892yes
flagellatedyes69.748yes
gram-positiveno98.602yes
anaerobicno98.801no
aerobicyes76.443yes
halophileyes58.24no
spore-formingno93.931yes
glucose-utilyes90.241yes
thermophileno98.835yes
glucose-fermentno68.774no

External links

@ref: 19246

culture collection no.: DSM 25634, NBRC 108893

straininfo link

  • @ref: 87275
  • straininfo: 404913

literature

  • topic: Phylogeny
  • Pubmed-ID: 22544802
  • title: Endozoicomonas numazuensis sp. nov., a gammaproteobacterium isolated from marine sponges, and emended description of the genus Endozoicomonas Kurahashi and Yokota 2007.
  • authors: Nishijima M, Adachi K, Katsuta A, Shizuri Y, Yamasato K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.042077-0
  • year: 2012
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification, Japan, Molecular Sequence Data, *Phylogeny, Porifera/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
19246Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25634)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25634
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
30690Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2702128776041
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
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
87275Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404913.1StrainInfo: A central database for resolving microbial strain identifiers