Strain identifier

BacDive ID: 158384

Type strain: Yes

Species: Halomonas nigrificans

Strain Designation: G8648

Strain history: <- G.-S. Cho, Max Rubner Institut, Federal Research Institute of Nutrition and Food, Department of Microbiology and Biotechnology; G8648

NCBI tax ID(s): 2042704 (species)

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General

@ref: 65060

BacDive-ID: 158384

DSM-Number: 105749

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

description: Halomonas nigrificans G8648 is a mesophilic, Gram-negative, motile bacterium that was isolated from cheese.

NCBI tax id

  • NCBI tax id: 2042704
  • Matching level: species

strain history

  • @ref: 65060
  • history: <- G.-S. Cho, Max Rubner Institut, Federal Research Institute of Nutrition and Food, Department of Microbiology and Biotechnology; G8648

doi: 10.13145/bacdive158384.20230509.8.1

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 nigrificans
  • full scientific name: Halomonas nigrificans Oguntoyinbo et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Vreelandella nigrificans

@ref: 65060

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas nigrificans

full scientific name: Halomonas nigrificans Oguntoyinbo et al. 2018

strain designation: G8648

type strain: yes

Morphology

cell morphology

  • @ref: 65310
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: monotrichous, polar

colony morphology

  • @ref: 65310
  • colony size: 1-3 mm
  • colony color: opaque white
  • medium used: agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
65060LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
65060BACTO 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
65310agaryes
65310brain-heart infusion brothyes

culture temp

@refgrowthtypetemperaturerange
65060positivegrowth30mesophilic
65310positivegrowth4-30
65310nogrowth37mesophilic

culture pH

  • @ref: 65310
  • ability: positive
  • type: growth
  • pH: 7-9.6
  • PH range: alkaliphile

Physiology and metabolism

spore formation

  • @ref: 65310
  • spore formation: no

halophily

  • @ref: 65310
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0.5-9 %(w/v)

observation

@refobservation
65310At 16°C the colony pigmentation is black.
65310The annotation furthermore shows the strain to have genes associated with the production of the bacteriocin colicin V.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6531015963ribitol-assimilation
6531029016arginine+hydrolysis
6531017057cellobiose-assimilation
6531018333D-arabitol-assimilation
6531016899D-mannitol-assimilation
6531016988D-ribose+assimilation
6531017924D-sorbitol-assimilation
6531028757fructose+assimilation
6531024175galacturonate-assimilation
6531017234glucose+assimilation
6531017268myo-inositol-assimilation
6531030849L-arabinose-assimilation
6531018403L-arabitol-assimilation
6531017306maltose+assimilation
6531037684mannose+assimilation
6531018394palatinose-assimilation
65310potassium 5-dehydro-D-gluconate-assimilation
6531026546rhamnose+assimilation
6531017992sucrose+assimilation
6531027082trehalose+assimilation
6531027897tryptophan-energy source
6531018222xylose+assimilation

metabolite production

@refChebi-IDmetaboliteproduction
6531015688acetoinyes
6531035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6531015688acetoin+
6531035581indole-

enzymes

@refvalueactivityec
65310tryptophan deaminase-4.1.99.1
65310catalase+1.11.1.6
65310cytochrome oxidase-1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment culture
65060cheeseKielGermanyDEUEurope
65310acid curd cheese QuargelGermanyDEUEuropetryptone soy agar

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Dairy product

taxonmaps

  • @ref: 69479
  • File name: preview.99_6528.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_104;97_1197;98_4817;99_6528&stattab=map
  • Last taxonomy: Halomonas nigrificans subclade
  • 16S sequence: MG030686
  • Sequence Identity:
  • Total samples: 550
  • soil counts: 8
  • aquatic counts: 419
  • animal counts: 112
  • plant counts: 11

Safety information

risk assessment

  • @ref: 65060
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 65060
  • description: Halomonas nigrificans strain MBT G8648 16S ribosomal RNA gene, partial sequence
  • accession: MG030686
  • length: 1271
  • database: ena
  • NCBI tax ID: 2042704

GC content

  • @ref: 65310
  • GC-content: 52.8
  • method: genome sequence analysis

External links

@ref: 65060

culture collection no.: DSM 105749

straininfo link

  • @ref: 111188
  • straininfo: 403640

literature

  • topic: Phylogeny
  • Pubmed-ID: 29231158
  • title: Halomonas nigrificans sp. nov., isolated from cheese.
  • authors: Oguntoyinbo FA, Cnockaert M, Cho GS, Kabisch J, Neve H, Bockelmann W, Wenning M, Franz CMAP, Vandamme P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002515
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, Cheese/*microbiology, DNA, Bacterial/genetics, Europe, *Food Microbiology, Genes, Bacterial, Halomonas/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Biotechnology

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
65060Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105749Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105749)
65310Folarin A. Oguntoyinbo, Margo Cnockaert, Gyu-Sung Cho, Jan Kabisch, Horst Neve, Wilhelm Bockelmann, Mareike Wenning, Charles M. A. P. Franz, Peter VandammeHalomonas nigrificans sp. nov., isolated from cheese10.1099/ijsem.0.002515IJSEM 68: 371-376 201829231158
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/
111188Reimer, 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-ID403640.1