Strain identifier

BacDive ID: 1386

Type strain: Yes

Species: Pontibacillus chungwhensis

Strain Designation: BH030062

Strain history: <- C.-J. Kim; BH030062 <- J. Lim

NCBI tax ID(s): 265426 (species)

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General

@ref: 6273

BacDive-ID: 1386

DSM-Number: 16287

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, moderately halophilic, spore-forming, mesophilic, Gram-positive, motile, rod-shaped, colony-forming, pigmented

description: Pontibacillus chungwhensis BH030062 is an obligate aerobe, moderately halophilic, spore-forming bacterium that forms circular colonies and has a yellow pigmentation.

NCBI tax id

  • NCBI tax id: 265426
  • Matching level: species

strain history

  • @ref: 6273
  • history: <- C.-J. Kim; BH030062 <- J. Lim

doi: 10.13145/bacdive1386.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Pontibacillus
  • species: Pontibacillus chungwhensis
  • full scientific name: Pontibacillus chungwhensis Lim et al. 2005

@ref: 6273

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Pontibacillus

species: Pontibacillus chungwhensis

full scientific name: Pontibacillus chungwhensis Lim et al. 2005

strain designation: BH030062

type strain: yes

Morphology

cell morphology

  • @ref: 23017
  • gram stain: positive
  • cell length: 2.3-3.0 µm
  • cell width: 0.6-0.9 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: peritrichous

colony morphology

  • @ref: 23017
  • colony color: yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: MA

pigmentation

  • @ref: 23017
  • production: yes
  • color: yellow

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6273BACTO 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
23017Marine agar (MA)yes

culture temp

@refgrowthtypetemperaturerange
6273positivegrowth30mesophilic
23017positivegrowth15.0-45.0
23017positiveoptimum30.0-35.0mesophilic

culture pH

@refabilitytypepHPH range
23017positivegrowth6.5-9.5alkaliphile
23017positiveoptimum7.5-8.5

Physiology and metabolism

oxygen tolerance

  • @ref: 23017
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 23017
  • spore description: spherical,terminal,in swollen sporangia
  • type of spore: endospore
  • spore formation: yes

halophily

@refhalophily levelsaltgrowthtested relationconcentration
23017moderately halophilic
23017NaClpositivegrowth1.0-15.0 %(w/v)
23017NaClpositivegrowth2.0-5.0 %(w/v)
23017NaClnogrowth>15.0 %(w/v)

murein

  • @ref: 23017
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2301715963ribitol-builds acid from
2301736219alpha-lactose-builds acid from
2301718305arbutin-builds acid from
2301715824D-fructose-builds acid from
2301716899D-mannitol-builds acid from
2301716024D-mannose-builds acid from
2301728053melibiose-builds acid from
2301716634raffinose-builds acid from
2301765327D-xylose-builds acid from
2301730849L-arabinose-builds acid from
2301762345L-rhamnose-builds acid from
2301717814salicin-builds acid from
230174853esculin-hydrolysis
230175291gelatin-hydrolysis
2301717368hypoxanthine-hydrolysis
2301717895L-tyrosine-hydrolysis
2301716199urea-hydrolysis
2301715318xanthine-hydrolysis
2301717632nitrate-reduction
2301716988D-ribose+builds acid from
2301716551D-trehalose+builds acid from
2301717234glucose+builds acid from
2301717754glycerol+builds acid from
2301717306maltose+builds acid from
23017casein+hydrolysis
2301728017starch+hydrolysis
2301753426tween 80+hydrolysis

enzymes

@refvalueactivityec
23017catalase+1.11.1.6
23017cytochrome oxidase-1.9.3.1
23017urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationenrichment cultureenrichment culture durationenrichment culture temperature
6273solar saltern soilRepublic of KoreaKORAsia
23017Tae-An area on the Yellow Seamarine agar 2216 (MA; Difco) with the addition of 5 % (w/v) NaCl [final concentration: 6.94 % (w/v) NaCl]2 days35.0

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_18252.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1612;97_1929;98_13792;99_18252&stattab=map
  • Last taxonomy: Pontibacillus
  • 16S sequence: AY553296
  • Sequence Identity:
  • Total samples: 101
  • soil counts: 29
  • aquatic counts: 25
  • animal counts: 40
  • plant counts: 7

Safety information

risk assessment

  • @ref: 6273
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 23017
  • description: Pontibacillus chungwhensis strain BH030062 16S ribosomal RNA gene, partial sequence
  • accession: AY553296
  • length: 1427
  • database: nuccore
  • NCBI tax ID: 265426

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pontibacillus chungwhensis BH030062GCA_000770675contigncbi1385513
66792Pontibacillus chungwhensis BH0300621385513.3wgspatric1385513
66792Pontibacillus chungwhensis BH0300622627854003draftimg1385513

GC content

  • @ref: 23017
  • GC-content: 41.0
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes90.861no
gram-positiveyes87.588yes
anaerobicno98.438no
halophileyes92.663no
spore-formingyes94.082yes
thermophileno95.156yes
glucose-utilyes88.034no
aerobicyes92.869no
glucose-fermentno89.156no
flagellatedyes90.541yes

External links

@ref: 6273

culture collection no.: DSM 16287

straininfo link

  • @ref: 71037
  • straininfo: 135137

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653871Pontibacillus chungwhensis gen. nov., sp. nov., a moderately halophilic Gram-positive bacterium from a solar saltern in Korea.Lim JM, Jeon CO, Song SM, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.63315-02005Bacillaceae/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Sodium ChlorideGenetics
Phylogeny15879229Pontibacillus marinus sp. nov., a moderately halophilic bacterium from a solar saltern, and emended description of the genus Pontibacillus.Lim JM, Jeon CO, Park DJ, Kim HR, Yoon BJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.63489-02005Bacillaceae/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cyanoacrylates/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis/chemistry, Fatty Acids/analysis, Flagella, Genes, rRNA, Gentian Violet, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenazines, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/pharmacology, Spores, Bacterial/cytology, Water MicrobiologyGenetics
Phylogeny19542115Pontibacillus halophilus sp. nov., a moderately halophilic bacterium isolated from a sea urchin.Chen YG, Zhang YQ, Xiao HD, Liu ZX, Yi LB, Shi JX, Zhi XY, Cui XL, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.002469-02009Animals, Bacillaceae/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sea Urchins/*microbiology, Sequence Analysis, DNA, *Sodium Chloride, Species SpecificityGenetics
Phylogeny19654352Pontibacillus litoralis sp. nov., a facultatively anaerobic bacterium isolated from a sea anemone, and emended description of the genus Pontibacillus.Chen YG, Zhang YQ, Yi LB, Li ZY, Wang YX, Xiao HD, Chen QH, Cui XL, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.009910-02009Anaerobiosis, Anemone/*microbiology, Animals, Bacillaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Phylogeny20833883Pontibacillus yanchengensis sp. nov., a moderately halophilic bacterium isolated from salt field soil.Yang Y, Zou Z, He M, Wang GInt J Syst Evol Microbiol10.1099/ijs.0.023911-02010Bacillaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/*metabolism, *Soil MicrobiologyMetabolism
Phylogeny25368138Pontibacillus salicampi sp. nov., a moderately halophilic bacterium isolated from saltern soil.Lee JC, Kim YS, Yun BS, Whang KSInt J Syst Evol Microbiol10.1099/ijs.0.066423-02014Bacillaceae/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Salinity, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6273Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16287)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16287
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
23017Jee-Min Lim,Che Ok Jeon,Sung Min Song,Chang-Jin Kim10.1099/ijs.0.63315-0Pontibacillus chungwhensis gen. nov., sp. nov., a moderately halophilic Gram-positive bacterium from a solar saltern in KoreaIJSEM 55: 165-170 200515653871
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
71037Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID135137.1StrainInfo: A central database for resolving microbial strain identifiers