Strain identifier

BacDive ID: 23576

Type strain: Yes

Species: Halioglobus japonicus

Strain Designation: S1-36

Strain history: <- NBRC <- S. Yoshizawa, Univ. Tokyo, Japan; S1-36

NCBI tax ID(s): 930805 (species)

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General

@ref: 21236

BacDive-ID: 23576

DSM-Number: 27941

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, coccus-shaped

description: Halioglobus japonicus S1-36 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 930805
  • Matching level: species

strain history

  • @ref: 21236
  • history: <- NBRC <- S. Yoshizawa, Univ. Tokyo, Japan; S1-36

doi: 10.13145/bacdive23576.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Cellvibrionales
  • family: Halieaceae
  • genus: Halioglobus
  • species: Halioglobus japonicus
  • full scientific name: Halioglobus japonicus Park et al. 2012

@ref: 21236

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Halieaceae, not assigned to order

family: Halieaceae

genus: Halioglobus

species: Halioglobus japonicus

full scientific name: Halioglobus japonicus Park et al. 2012

strain designation: S1-36

type strain: yes

Morphology

cell morphology

  • @ref: 30236
  • gram stain: negative
  • cell width: 0.4 µm
  • cell shape: coccus-shaped
  • motility: no

multimedia

  • @ref: 21236
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27941.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 21236
  • name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514c
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 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 Na2CO3 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
21236positivegrowth25mesophilic
30236positivegrowth15-30
30236positiveoptimum22.5psychrophilic

culture pH

@refabilitytypepHPH range
30236positivegrowth06-09alkaliphile
30236positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30236
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
30236NaClpositivegrowth<4 %
30236NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3023628757fructose+carbon source
3023617234glucose+carbon source
3023617306maltose+carbon source
3023633942ribose+carbon source
302364853esculin+hydrolysis
3023617632nitrate+reduction
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
30236acid phosphatase+3.1.3.2
30236alkaline phosphatase+3.1.3.1
30236gelatinase+
30236cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
21236-----+-+------------+

Isolation, sampling and environmental information

isolation

  • @ref: 21236
  • sample type: seawater
  • geographic location: western North Pacific Ocean
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4746.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_305;96_2349;97_2860;98_3557;99_4746&stattab=map
  • Last taxonomy: Halioglobus japonicus subclade
  • 16S sequence: AB602427
  • Sequence Identity:
  • Total samples: 5161
  • soil counts: 116
  • aquatic counts: 4890
  • animal counts: 139
  • plant counts: 16

Safety information

risk assessment

  • @ref: 21236
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21236
  • description: Halioglobus japonicus gene for 16S rRNA, partial sequence
  • accession: AB602427
  • length: 1367
  • database: ena
  • NCBI tax ID: 930805

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halioglobus japonicus S1-36GCA_002869505contigncbi930805
66792Halioglobus japonicus NBRC 107739GCA_001983995completencbi930805
66792Halioglobus japonicus KCTC 23429GCA_014652255scaffoldncbi930805
66792Halioglobus japonicus strain KCTC 23429930805.12wgspatric930805
66792Halioglobus japonicus strain NBRC 107739930805.8plasmidpatric930805
66792Halioglobus japonicus strain NBRC 107739930805.7plasmidpatric930805
66792Halioglobus japonicus strain NBRC 107739930805.6plasmidpatric930805
66792Halioglobus japonicus strain NBRC 107739930805.5completepatric930805

GC content

  • @ref: 30236
  • GC-content: 59.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes59.396no
gram-positiveno98.539yes
anaerobicno98.501no
aerobicyes90.482yes
halophileyes70.23no
spore-formingno96.929no
glucose-utilyes78.338no
thermophileno98.12yes
motileyes81.364no
glucose-fermentno89.936yes

External links

@ref: 21236

culture collection no.: DSM 27941, KCTC 23429, NBRC 107739

straininfo link

  • @ref: 87668
  • straininfo: 406445

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21986723Halioglobus japonicus gen. nov., sp. nov. and Halioglobus pacificus sp. nov., members of the class Gammaproteobacteria isolated from seawater.Park S, Yoshizawa S, Inomata K, Kogure K, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.031443-02011Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification, Heterotrophic Processes, Japan, Molecular Sequence Data, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity, Water MicrobiologyGenetics
Phylogeny30908180Halioglobus sediminis sp. nov., isolated from coastal sediment.Han JR, Ye MQ, Wang C, Du ZJInt J Syst Evol Microbiol10.1099/ijsem.0.0033662019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/isolation & purification, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny31985391Halioglobus maricola sp. nov., isolated from coastal seawater.Li SH, Song J, Lim Y, Joung Y, Kang I, Cho JCInt J Syst Evol Microbiol10.1099/ijsem.0.0039852020Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/isolation & purification, Genome Size, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, Whole Genome SequencingGenetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
21236Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27941Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27941)
30236Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172657828776041
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
68369Automatically annotated from API 20NE
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/
87668Reimer, 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-ID406445.1