Strain identifier

BacDive ID: 6074

Type strain: Yes

Species: Halomonas hamiltonii

Strain Designation: T68687

Strain history: <- D A Stevens, Santa Clara Valley Medical Center, USA

NCBI tax ID(s): 502832 (species)

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General

@ref: 15439

BacDive-ID: 6074

DSM-Number: 21197

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

description: Halomonas hamiltonii T68687 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from waste handling option port of a dialysis machine.

NCBI tax id

  • NCBI tax id: 502832
  • Matching level: species

strain history

@refhistory
15439<- K. K. Kim, KCTC; T68687 <- D. A. Stevens, Santa Clara Valley Medical Center (SCVMC), San Jose, California, USA
67771<- D A Stevens, Santa Clara Valley Medical Center, USA

doi: 10.13145/bacdive6074.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Halomonadaceae
  • genus: Halomonas
  • species: Halomonas hamiltonii
  • full scientific name: Halomonas hamiltonii Kim et al. 2010

  • synonyms

    @refsynonym
    20215Halomonas johnsoniae
    20215Vreelandella hamiltonii

@ref: 15439

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas johnsoniae

full scientific name: Halomonas johnsoniae Kim et al. 2010

strain designation: T68687

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29031negative2.75 µm0.8 µmrod-shapedyes
67771negative
125439negative99.5
125439yes90.8
125438negative100

pigmentation

  • @ref: 29031
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 15439
  • name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/545
  • composition: Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

culture temp

@refgrowthtypetemperature
15439positivegrowth28
29031positivegrowth10-40
29031positiveoptimum32.5
67771positivegrowth28

culture pH

@refabilitytypepHPH range
29031positivegrowth07-10alkaliphile
29031positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29031aerobe
67771aerobe

spore formation

@refspore formationconfidence
29031no
125439no99.6

halophily

@refsaltgrowthtested relationconcentration
29031NaClpositivegrowth0-20 %
29031NaClpositiveoptimum2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
29031178794-hydroxybenzoate+carbon source
2903130089acetate+carbon source
2903116449alanine+carbon source
2903116947citrate+carbon source
2903116236ethanol+carbon source
2903128757fructose+carbon source
2903124265gluconate+carbon source
2903117234glucose+carbon source
2903117754glycerol+carbon source
2903125115malate+carbon source
2903117306maltose+carbon source
2903129864mannitol+carbon source
2903126271proline+carbon source
2903117272propionate+carbon source
2903117822serine+carbon source
2903130911sorbitol+carbon source
2903130031succinate+carbon source
2903117992sucrose+carbon source
2903127082trehalose+carbon source
2903117632nitrate+reduction

metabolite production

  • @ref: 29031
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
29031catalase+1.11.1.6
29031cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15439waste handling option port of a dialysis machineCalifornia, San Jose, Santa Clara Valley Medical CenterUSAUSANorth America
67771From dialysis center environment and machinesUSAUSANorth America

isolation source categories

Cat1Cat2
#Engineered#Waste
#Infection#Medical device

taxonmaps

  • @ref: 69479
  • File name: preview.99_136.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_104;97_111;98_121;99_136&stattab=map
  • Last taxonomy: Halomonas
  • 16S sequence: AM941399
  • Sequence Identity:
  • Total samples: 9461
  • soil counts: 614
  • aquatic counts: 3901
  • animal counts: 4865
  • plant counts: 81

Safety information

risk assessment

  • @ref: 15439
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15439
  • description: Halomonas johnsoniae partial 16S rRNA gene, type strain T68687T
  • accession: AM941399
  • length: 1455
  • database: nuccore
  • NCBI tax ID: 502832

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas johnsoniae KCTC 22157GCA_014651795contigncbi502832
66792Halomonas johnsoniae strain KCTC 22157502832.6wgspatric502832

GC content

@refGC-contentmethod
1543964.4high performance liquid chromatography (HPLC)
2903164.4-65.2

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno100yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.189yes
125438spore-formingspore-formingAbility to form endo- or exosporesno88.933yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.067yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes80.735yes
125438motile2+flagellatedAbility to perform flagellated movementyes81.702no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.6
125439BacteriaNetmotilityAbility to perform movementyes90.8
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe83.9

External links

@ref: 15439

culture collection no.: DSM 21197, KCTC 22157

straininfo link

  • @ref: 75561
  • straininfo: 405345

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19651714Halomonas stevensii sp. nov., Halomonas hamiltonii sp. nov. and Halomonas johnsoniae sp. nov., isolated from a renal care centre.Kim KK, Lee KC, Oh HM, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.004424-02009Bacteremia/etiology/*microbiology, Base Composition, Base Sequence, California, DNA, Bacterial/chemistry, Equipment and Supplies, Hospital/*microbiology, Halomonas/*classification/genetics/isolation & purification, *Hemodialysis Units, Hospital, Humans, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Renal Dialysis/*instrumentation, Sequence Homology, Nucleic AcidPathogenicity
Phylogeny24510978Halomonas songnenensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soils.Jiang J, Pan Y, Hu S, Zhang X, Hu B, Huang H, Hong S, Meng J, Li C, Wang KInt J Syst Evol Microbiol10.1099/ijs.0.056499-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Halomonas/*classification/genetics/isolation & purification, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny32195651Halomonas montanilacus sp. nov., isolated from hypersaline Lake Pengyanco on the Tibetan Plateau.Lu H, Xing P, Zhai L, Li H, Wu QInt J Syst Evol Microbiol10.1099/ijsem.0.0041092020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Halomonas/*classification/isolation & purification, Lakes/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Saline Waters, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15439Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21197)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21197
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
29031Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2546128776041
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)
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
75561Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405345.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1