Strain identifier

BacDive ID: 6221

Type strain: Yes

Species: Henriciella marina

Strain Designation: IS4

Strain history: <- ZX Quan, KRIBB

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 8199

BacDive-ID: 6221

DSM-Number: 19595

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

description: Henriciella marina IS4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Sea water.

NCBI tax id

NCBI tax idMatching level
1121949strain
453851species

strain history

@refhistory
8199<- S. W. Roh, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; Iso4
67770S. W. Roh Iso4.
67771<- ZX Quan, KRIBB

doi: 10.13145/bacdive6221.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Caulobacterales
  • family: Hyphomonadaceae
  • genus: Henriciella
  • species: Henriciella marina
  • full scientific name: Henriciella marina Quan et al. 2009

@ref: 8199

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Caulobacterales

family: Hyphomonadaceae

genus: Henriciella

species: Henriciella marina

full scientific name: Henriciella marina Quan et al. 2009

strain designation: IS4

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
67771negative
69480negative99.998

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_19595_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19595_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19595_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19595_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19595_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 8199
  • 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
8199positivegrowth28mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

observation

  • @ref: 67770
  • observation: quinones: Q-10

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
8199Sea waterRepublic of KoreaKORAsia
67770Seawater
67771From sea waterRepublic of KoreaKORAsiaGoseong, East Sea

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7202.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_269;96_2377;97_2893;98_3605;99_7202&stattab=map
  • Last taxonomy: Henriciella
  • 16S sequence: EF660760
  • Sequence Identity:
  • Total samples: 1463
  • soil counts: 30
  • aquatic counts: 1366
  • animal counts: 59
  • plant counts: 8

Safety information

risk assessment

  • @ref: 8199
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8199
  • description: Henriciella marina DSM 19595 strain Iso4 16S ribosomal RNA gene, partial sequence
  • accession: EF660760
  • length: 1391
  • database: ena
  • NCBI tax ID: 1121949

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Henriciella marina DSM 195951121949.8wgspatric1121949
66792Henriciella marina DSM 195952519103046draftimg1121949
67770Henriciella marina DSM 19595GCA_000376805contigncbi1121949

GC content

  • @ref: 67770
  • GC-content: 56.2
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.944no
flagellatedno70.663no
gram-positiveno98.741yes
anaerobicno97.791yes
halophileno62.748no
spore-formingno96.373no
thermophileno98.512yes
glucose-utilyes78.58no
aerobicyes92.059yes
glucose-fermentno94.881no

External links

@ref: 8199

culture collection no.: DSM 19595, JCM 15116, KCTC 12513, ISO Iso4, ISO 4

straininfo link

  • @ref: 75700
  • straininfo: 399096

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19412598Henriciella marina gen. nov., sp. nov., a novel member of the family Hyphomonadaceae isolated from the East Sea.Quan ZX, Zeng DN, Xiao YP, Roh SW, Nam YD, Chang HW, Yoon JH, Oh HM, Bae JWJ Microbiol10.1007/s12275-008-0290-02009Alphaproteobacteria/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Phylogeny28820101Henriciella pelagia sp. nov., isolated from seawater.Wu YH, Cheng H, Huo YY, Jin XB, Wang CS, Xu XWInt J Syst Evol Microbiol10.1099/ijsem.0.0020662017Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny34296989Physiological and genomic features of Henriciella with the description of Henriciella mobilis sp. nov.Ren WT, Cheng H, Wang CS, Xu XW, Zhou P, Wu YHInt J Syst Evol Microbiol10.1099/ijsem.0.0048892021Alphaproteobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8199Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19595)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19595
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
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
75700Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399096.1StrainInfo: A central database for resolving microbial strain identifiers