Strain identifier

BacDive ID: 158757

Type strain: Yes

Species: Rheinheimera salexigens

Strain Designation: KH87

Strain history: CIP <- 2016, SP. Donachie, Hawai Univ., Honolulu, Hawai, USA: strain KH87 <- K. Hayashi

NCBI tax ID(s): 1628148 (species)

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General

@ref: 65053

BacDive-ID: 158757

DSM-Number: 100018

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

description: Rheinheimera salexigens KH87 is an obligate aerobe, halophilic, mesophilic bacterium that forms circular colonies and was isolated from shark-fishing hook.

NCBI tax id

  • NCBI tax id: 1628148
  • Matching level: species

strain history

@refhistory
65053<- K. Hayashi, Dept. Microbiology, Univ. Hawaii; KH87
122369CIP <- 2016, SP. Donachie, Hawai Univ., Honolulu, Hawai, USA: strain KH87 <- K. Hayashi

doi: 10.13145/bacdive158757.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Chromatiales
  • family: Chromatiaceae
  • genus: Rheinheimera
  • species: Rheinheimera salexigens
  • full scientific name: Rheinheimera salexigens Hayashi et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Rheinheimera salexigens

@ref: 65053

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Chromatiales

family: Chromatiaceae

genus: Rheinheimera

species: Rheinheimera salexigens

full scientific name: Rheinheimera salexigens Hayashi et al. 2018

strain designation: KH87

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
65509negative1.6-2.2 µm0.6-0.7 µmrod-shapedyesmonopolar
69480yes98.036
69480negative99.978
122369negativerod-shapedyes

colony morphology

  • @ref: 65509
  • colony size: 1-2 mm
  • colony color: orange-beige
  • colony shape: circular
  • medium used: MA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
65053BACTO 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
65509Marine agar (MA)yes
65509Reasoner's 2A agar (R2A)yeswith 0.5-7.5 %(w/v) NaCl
122369CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
65053positivegrowth28mesophilic
65509positivegrowth4-39
65509positiveoptimum33-36mesophilic

culture pH

  • @ref: 65509
  • ability: positive
  • type: optimum
  • pH: 6.5-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 65509
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69480no99.992
69481no100

halophily

@refhalophily levelsaltgrowthtested relationconcentration
65509halophilicNaClpositivegrowth0.5-5.0 %(w/v)
65509NaClnogrowth7.5 %(w/v)
65509NaClpositiveoptimum3 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
655095291gelatin+hydrolysis
6550917632nitrate+reduction
6550928017starch-hydrolysis
6550916199urea+hydrolysis

enzymes

@refvalueactivityec
65509alkaline phosphatase+3.1.3.1
65509esterase (C 4)+
65509esterase Lipase (C 8)+
65509leucine arylamidase+3.4.11.1
65509trypsin+3.4.21.4
65509alpha-chymotrypsin+3.4.21.1
65509acid phosphatase+3.1.3.2
65509naphthol-AS-BI-phosphohydrolase+
65509catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedureisolation date
65053shark-fishing hookOahu, Hawaii, Pacific Ocean, 28 km north northeast of Kaneohe BayUSAUSANorth America
65509baited fishing hook in seawater18km north-east of Kane'ohe Bay, O'ahu, Hawai'iUSAUSANorth AmericaMA3 days30in the dark
122369Fishing hook baited and suspended in seawater18 km northeast of Kaneohe bay, Oahu, Hawaii, USAUnited States of AmericaUSANorth America2013-04-16

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Engineered product
#Environmental#Aquatic#Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_45519.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_43;96_20873;97_25991;98_33007;99_45519&stattab=map
  • Last taxonomy: Rheinheimera salexigens subclade
  • 16S sequence: KP026120
  • Sequence Identity:
  • Total samples: 362
  • soil counts: 14
  • aquatic counts: 252
  • animal counts: 87
  • plant counts: 9

Safety information

risk assessment

  • @ref: 122369
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 65509
  • description: Rheinheimera salexigens strain KH87 16S ribosomal RNA gene, partial sequence
  • accession: KP026120
  • length: 1523
  • database: nuccore
  • NCBI tax ID: 1628148

Genome sequences

  • @ref: 66792
  • description: Rheinheimera salexigens KH87
  • accession: GCA_001752395
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1628148

GC content

  • @ref: 65509
  • GC-content: 42
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes79.552yes
gram-positiveno98.877no
anaerobicno98.364yes
aerobicyes87.671no
halophileno57.276yes
spore-formingno94.917no
glucose-utilyes79.577no
thermophileno99.667no
motileyes90.229yes
glucose-fermentno75.038no

External links

@ref: 65053

culture collection no.: ATCC BAA 2715, CIP 111115, DSM 100018

straininfo link

@refstraininfo
111337399342
111338413479

literature

  • topic: Phylogeny
  • Pubmed-ID: 29111971
  • title: Rheinheimera salexigens sp. nov., isolated from a fishing hook, and emended description of the genus Rheinheimera.
  • authors: Hayashi K, Busse HJ, Golke J, Anderson J, Wan X, Hou S, Chain PSG, Prescott RD, Donachie SP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002412
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, Chromatiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hawaii, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/*chemistry, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
65053Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100018Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100018)
65509Kazukuni Hayashi, Hans-Jürgen Busse, Jan Golke, James Anderson, Xuehua Wan, Shaobin Hou, Patrick S. G. Chain, Rebecca D. Prescott and Stuart P. DonachieRheinheimera salexigens sp. nov., isolated from a fishing hook, and emended description of the genus Rheinheimera10.1099/ijsem.0.002412IJSEM 68: 35-41 201829111971
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
111337Reimer, 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-ID399342.1
111338Reimer, 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-ID413479.1
122369Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111115Collection of Institut Pasteur (CIP 111115)