Strain identifier

BacDive ID: 6222

Type strain: Yes

Species: Henriciella litoralis

Strain Designation: SD10

Strain history: <- C. O. Jeon, Chung-Ang Univ., Seoul, Republic of Korea; SD10

NCBI tax ID(s): 568102 (species)

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General

@ref: 16102

BacDive-ID: 6222

DSM-Number: 22014

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

description: Henriciella litoralis SD10 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat sediment.

NCBI tax id

  • NCBI tax id: 568102
  • Matching level: species

strain history

  • @ref: 16102
  • history: <- C. O. Jeon, Chung-Ang Univ., Seoul, Republic of Korea; SD10

doi: 10.13145/bacdive6222.20230509.8.1

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 litoralis
  • full scientific name: Henriciella litoralis Lee et al. 2011

@ref: 16102

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Caulobacterales

family: Hyphomonadaceae

genus: Henriciella

species: Henriciella litoralis

full scientific name: Henriciella litoralis Lee et al. 2011

strain designation: SD10

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29766negative1.8 µm0.5 µmrod-shapedyes
69480negative99.996

pigmentation

  • @ref: 29766
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16102
  • 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
16102positivegrowth25mesophilic
29766positivegrowth15-40
29766positiveoptimum27.5mesophilic

culture pH

@refabilitytypepHPH range
29766positivegrowth06-09alkaliphile
29766positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 29766
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29766no
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
29766NaClpositivegrowth01-10 %
29766NaClpositiveoptimum3.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2976630089acetate+carbon source
2976621217L-alaninamide+carbon source
2976616449alanine+carbon source
2976622599arabinose+carbon source
2976635391aspartate+carbon source
2976616947citrate+carbon source
2976623652dextrin+carbon source
2976628757fructose+carbon source
2976633984fucose+carbon source
2976628260galactose+carbon source
2976624175galacturonate+carbon source
2976624265gluconate+carbon source
2976617754glycerol+carbon source
2976617596inosine+carbon source
2976637684mannose+carbon source
2976637657methyl D-glucoside+carbon source
2976617268myo-inositol+carbon source
29766506227N-acetylglucosamine+carbon source
2976618257ornithine+carbon source
2976650048phenylethylamine+carbon source
2976626490quinate+carbon source
2976616634raffinose+carbon source
2976626546rhamnose+carbon source
2976617822serine+carbon source
2976630031succinate+carbon source
2976626986threonine+carbon source
2976616704uridine+carbon source
297664853esculin+hydrolysis

enzymes

@refvalueactivityec
29766acid phosphatase+3.1.3.2
29766alkaline phosphatase+3.1.3.1
29766catalase+1.11.1.6
29766cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 16102
  • sample type: tidal flat sediment
  • geographic location: Taean coast
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Tidal flat
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_4815.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_269;96_2377;97_2893;98_3605;99_4815&stattab=map
  • Last taxonomy: Henriciella litoralis
  • 16S sequence: FJ230835
  • Sequence Identity:
  • Total samples: 216
  • soil counts: 9
  • aquatic counts: 200
  • animal counts: 6
  • plant counts: 1

Safety information

risk assessment

  • @ref: 16102
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16102
  • description: Henriciella litoralis strain SD10 16S ribosomal RNA gene, partial sequence
  • accession: FJ230835
  • length: 1332
  • database: ena
  • NCBI tax ID: 568102

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Henriciella litoralis DSM 22014GCA_002088935scaffoldncbi568102
66792Henriciella litoralis strain DSM 22014568102.3wgspatric568102
66792Henriciella litoralis DSM 220142831707323draftimg568102

GC content

@refGC-contentmethod
1610255.2high performance liquid chromatography (HPLC)
2976655.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno82.681no
gram-positiveno98.582no
anaerobicno98.171no
aerobicyes92.958yes
halophileno63.189no
spore-formingno97.262yes
glucose-utilyes81.305no
thermophileno97.144no
motileyes87.271yes
glucose-fermentno93.793no

External links

@ref: 16102

culture collection no.: DSM 22014, KACC 13700

straininfo link

  • @ref: 75701
  • straininfo: 405495

literature

  • topic: Phylogeny
  • Pubmed-ID: 20418412
  • title: Henriciella litoralis sp. nov., isolated from a tidal flat, transfer of Maribaculum marinum Lai et al. 2009 to the genus Henriciella as Henriciella aquimarina nom. nov. and emended description of the genus Henriciella.
  • authors: Lee SH, Shim JK, Kim JM, Choi HK, Jeon CO
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.020396-0
  • year: 2010
  • mesh: Aerobiosis, Alphaproteobacteria/*classification/genetics/*isolation & purification/physiology, Base Composition, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16102Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22014)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22014
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
29766Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2614728776041
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)
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
75701Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405495.1StrainInfo: A central database for resolving microbial strain identifiers