Strain identifier

BacDive ID: 5995

Type strain: Yes

Species: Chromohalobacter beijerinckii

Strain Designation: L 593

Strain history: CIP <- 2001, LMG <- 1977, ATCC <- NCIB <- 1959, LMD

NCBI tax ID(s): 86179 (species)

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General

@ref: 3056

BacDive-ID: 5995

DSM-Number: 7218

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

description: Chromohalobacter beijerinckii L 593 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from salted beans.

NCBI tax id

  • NCBI tax id: 86179
  • Matching level: species

strain history

@refhistory
3056<- ATCC <- NCIB <- Lab. Microbiol. Delft, E III.9.23.1
67770IAM 14940 <-- NCIMB 9041 <-- LMD 35.8.
116774CIP <- 2001, LMG <- 1977, ATCC <- NCIB <- 1959, LMD

doi: 10.13145/bacdive5995.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Halomonadaceae
  • genus: Chromohalobacter
  • species: Chromohalobacter beijerinckii
  • full scientific name: Chromohalobacter beijerinckii (Hof 1935) Peçonek et al. 2006

  • synonyms

    • @ref: 20215
    • synonym: Pseudomonas beijerinckii

@ref: 3056

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Chromohalobacter

species: Chromohalobacter beijerinckii

full scientific name: Chromohalobacter beijerinckii (Hof 1935) Peçonek et al. 2006

strain designation: L 593

type strain: yes

Morphology

cell morphology

  • @ref: 116774
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 116774
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
305610% MH MEDIUM (DSMZ Medium 593)yeshttps://mediadive.dsmz.de/medium/593Name: 10% MH MEDIUM (DSMZ Medium 593) Composition: NaCl 81.0 g/l Agar 15.0 g/l Yeast extract 10.0 g/l MgSO4 9.6 g/l MgCl2 7.0 g/l Proteose peptone no. 3 5.0 g/l KCl 2.0 g/l Glucose 1.0 g/l CaCl2 0.36 g/l NaHCO3 0.06 g/l NaBr 0.026 g/l Distilled water
33025Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
116774CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
3056positivegrowth26mesophilic
33025positivegrowth25mesophilic
67770positivegrowth25mesophilic
116774positivegrowth10-41
116774nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116774
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
116774NaClpositivegrowth0-8 %
116774NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11677416947citrate+carbon source
1167744853esculin+hydrolysis
11677417632nitrate+reduction
11677416301nitrite-reduction
11677417632nitrate-respiration

antibiotic resistance

  • @ref: 116774
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116774
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
116774oxidase+
116774beta-galactosidase+3.2.1.23
116774alcohol dehydrogenase-1.1.1.1
116774gelatinase+
116774amylase+
116774DNase-
116774caseinase+3.4.21.50
116774catalase-1.11.1.6
116774tween esterase-
116774lecithinase-
116774lipase-
116774lysine decarboxylase-4.1.1.18
116774ornithine decarboxylase-4.1.1.17
116774protease+
116774tryptophan deaminase-
116774urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116774-+++-+--+-++-+-++++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116774++++---+++--++-++++++++--+-----+++++------------++++-++-+--++++++-+--+----++--+++-----+-+++++++--++

Isolation, sampling and environmental information

isolation

@refsample typegeographic location
3056salted beansBaltic Sea
58653Salted beans ?
67770Salted beans

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_1780.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_1010;97_1176;98_1406;99_1780&stattab=map
  • Last taxonomy: Chromohalobacter
  • 16S sequence: AB681921
  • Sequence Identity:
  • Total samples: 165
  • soil counts: 8
  • aquatic counts: 74
  • animal counts: 45
  • plant counts: 38

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
30561Risk group (German classification)
1167741Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Chromohalobacter beijerinckii gene for 16S rRNA, strain: ATCC 19372AB0213861495ena86179
20218Chromohalobacter beijerinckii gene for 16S rRNA, partial sequence, strain: NBRC 103041AB6819211465ena86179

Genome sequences

  • @ref: 66792
  • description: Chromohalobacter beijerinckii DSM 7218
  • accession: GCA_023061185
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 86179

GC content

@refGC-contentmethod
305660.7
6777060.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno56.584no
gram-positiveno98.578no
anaerobicno99.323no
aerobicyes91.398no
halophileyes95.931no
spore-formingno97.088no
motileyes90.663no
glucose-fermentno53.317no
thermophileno98.147yes
glucose-utilyes94.022no

External links

@ref: 3056

culture collection no.: DSM 7218, ATCC 19372, NCIB 9041, CCUG 49679, CIP 106957, LMG 2148, NCCB 35008, NRRL B-3153, NCIMB 9041, JCM 21422, IAM 14940, JCM 13305, NBRC 103041, Delft E III.9.23.1, CCUG 106957

straininfo link

  • @ref: 75484
  • straininfo: 3940

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545411Chromohalobacter sarecensis sp. nov., a psychrotolerant moderate halophile isolated from the saline Andean region of Bolivia.Quillaguaman J, Delgado O, Mattiasson B, Hatti-Kaul RInt J Syst Evol Microbiol10.1099/ijs.0.63153-02004Amino Acid Oxidoreductases/analysis, Bacterial Typing Techniques, Base Composition, Bolivia, Carbohydrate Metabolism, Catalase/analysis, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA, Gentian Violet, Halomonadaceae/*classification/cytology/genetics/*isolation & purification/metabolism/physiology, Hydrogen Sulfide/metabolism, Hydrogen-Ion Concentration, Indoles/metabolism, L-Amino Acid Oxidase, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Oxidoreductases/analysis, Phenazines, Phylogeny, Pseudomonas/genetics, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Saline Solution, Hypertonic, Sequence Analysis, DNA, *Soil Microbiology, TemperatureEnzymology
Phylogeny16902036Reclassification of Pseudomonas beijerinckii Hof 1935 as Chromohalobacter beijerinckii comb. nov., and emended description of the species.Peconek J, Gruber C, Gallego V, Ventosa A, Busse HJ, Kampfer P, Radax C, Stan-Lotter HInt J Syst Evol Microbiol10.1099/ijs.0.64355-02006Animals, Bacterial Proteins/analysis, Base Composition, Benzoquinones/analysis, Chromatography, Thin Layer, DNA, Bacterial/chemistry, Fabaceae/microbiology, Fish Products/microbiology, Food Microbiology, Halomonadaceae/chemistry/*classification/isolation & purification/physiology, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/chemistry/*classification/isolation & purification/physiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species SpecificityBiotechnology
Phylogeny17911293Chromohalobacter japonicus sp. nov., a moderately halophilic bacterium isolated from a Japanese salty food.Sanchez-Porro C, Tokunaga H, Tokunaga M, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.65212-02007Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, *Food Microbiology, Genes, rRNA, Halomonadaceae/chemistry/*classification/*isolation & purification/physiology, Hydrogen-Ion Concentration, Japan, Locomotion/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, TemperatureBiotechnology
Phylogeny27129697Larsenimonas suaedae sp. nov., a moderately halophilic, endophytic bacterium isolated from the halophyte Suaeda salsa.Xia ZJ, Wu HZ, Cui CX, Chen Q, Zhao GY, Wang HX, Dai MXInt J Syst Evol Microbiol10.1099/ijsem.0.0011262016Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Halomonadaceae/*classification/genetics/isolation & purification, Hydroxybutyrates/metabolism, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Polyesters/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3056Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7218)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7218
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
33025Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19145
58653Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49679)https://www.ccug.se/strain?id=49679
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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
75484Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3940.1StrainInfo: A central database for resolving microbial strain identifiers
116774Curators of the CIPCollection of Institut Pasteur (CIP 106957)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106957