Strain identifier
BacDive ID: 1386
Type strain: 
Species: Pontibacillus chungwhensis
Strain Designation: BH030062
Strain history: <- C.-J. Kim; BH030062 <- J. Lim
NCBI tax ID(s): 265426 (species)
version 9.1 (current version)
General
@ref: 6273
BacDive-ID: 1386
DSM-Number: 16287
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, moderately halophilic, spore-forming, 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/bacdive1386.20240916.9.1
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
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 6273 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: 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 |
| 23017 | Marine agar (MA) | yes |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 6273 | positive | growth | 30 |
| 23017 | positive | growth | 15.0-45.0 |
| 23017 | positive | optimum | 30.0-35.0 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 23017 | positive | growth | 6.5-9.5 | alkaliphile |
| 23017 | positive | optimum | 7.5-8.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 23017
- oxygen tolerance: obligate aerobe
spore formation
| @ref | spore description | type of spore | spore formation | confidence |
|---|---|---|---|---|
| 23017 | spherical,terminal,in swollen sporangia | endospore | yes | |
| 69480 | yes | 95.605 |
halophily
| @ref | halophily level | salt | growth | tested relation | concentration |
|---|---|---|---|---|---|
| 23017 | moderately halophilic | ||||
| 23017 | NaCl | positive | growth | 1.0-15.0 %(w/v) | |
| 23017 | NaCl | positive | growth | 2.0-5.0 %(w/v) | |
| 23017 | NaCl | no | growth | >15.0 %(w/v) |
murein
- @ref: 23017
- murein short key: A31
- type: A1gamma m-Dpm-direct
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 23017 | 15963 | ribitol | - | builds acid from |
| 23017 | 36219 | alpha-lactose | - | builds acid from |
| 23017 | 18305 | arbutin | - | builds acid from |
| 23017 | 15824 | D-fructose | - | builds acid from |
| 23017 | 16899 | D-mannitol | - | builds acid from |
| 23017 | 16024 | D-mannose | - | builds acid from |
| 23017 | 28053 | melibiose | - | builds acid from |
| 23017 | 16634 | raffinose | - | builds acid from |
| 23017 | 65327 | D-xylose | - | builds acid from |
| 23017 | 30849 | L-arabinose | - | builds acid from |
| 23017 | 62345 | L-rhamnose | - | builds acid from |
| 23017 | 17814 | salicin | - | builds acid from |
| 23017 | 4853 | esculin | - | hydrolysis |
| 23017 | 5291 | gelatin | - | hydrolysis |
| 23017 | 17368 | hypoxanthine | - | hydrolysis |
| 23017 | 17895 | L-tyrosine | - | hydrolysis |
| 23017 | 16199 | urea | - | hydrolysis |
| 23017 | 15318 | xanthine | - | hydrolysis |
| 23017 | 17632 | nitrate | - | reduction |
| 23017 | 16988 | D-ribose | + | builds acid from |
| 23017 | 16551 | D-trehalose | + | builds acid from |
| 23017 | 17234 | glucose | + | builds acid from |
| 23017 | 17754 | glycerol | + | builds acid from |
| 23017 | 17306 | maltose | + | builds acid from |
| 23017 | casein | + | hydrolysis | |
| 23017 | 28017 | starch | + | hydrolysis |
| 23017 | 53426 | tween 80 | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 23017 | catalase | + | 1.11.1.6 |
| 23017 | cytochrome oxidase | - | 1.9.3.1 |
| 23017 | urease | - | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent | geographic location | enrichment culture | enrichment culture duration | enrichment culture temperature |
|---|---|---|---|---|---|---|---|---|
| 6273 | solar saltern soil | Republic of Korea | KOR | Asia | ||||
| 23017 | Tae-An area on the Yellow Sea | marine agar 2216 (MA; Difco) with the addition of 5 % (w/v) NaCl [final concentration: 6.94 % (w/v) NaCl] | 2 days | 35.0 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #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
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pontibacillus chungwhensis BH030062 | GCA_000770675 | contig | ncbi | 1385513 |
| 66792 | Pontibacillus chungwhensis BH030062 | 1385513.3 | wgs | patric | 1385513 |
| 66792 | Pontibacillus chungwhensis BH030062 | 2627854003 | draft | img | 1385513 |
GC content
- @ref: 23017
- GC-content: 41.0
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 82.514 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 89.272 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 95.605 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 76.027 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 94.545 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 83.844 | no |
External links
@ref: 6273
culture collection no.: DSM 16287
straininfo link
- @ref: 71037
- straininfo: 135137
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15653871 | Pontibacillus chungwhensis gen. nov., sp. nov., a moderately halophilic Gram-positive bacterium from a solar saltern in Korea. | Lim JM, Jeon CO, Song SM, Kim CJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.63315-0 | 2005 | Bacillaceae/*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 Chloride | Genetics |
| Phylogeny | 15879229 | Pontibacillus 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 CJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.63489-0 | 2005 | Bacillaceae/*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 Microbiology | Genetics |
| Phylogeny | 19542115 | Pontibacillus 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 WJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.002469-0 | 2009 | Animals, 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 Specificity | Genetics |
| Phylogeny | 19654352 | Pontibacillus 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 WJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.009910-0 | 2009 | Anaerobiosis, 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/*microbiology | Metabolism |
| Phylogeny | 20833883 | Pontibacillus yanchengensis sp. nov., a moderately halophilic bacterium isolated from salt field soil. | Yang Y, Zou Z, He M, Wang G | Int J Syst Evol Microbiol | 10.1099/ijs.0.023911-0 | 2010 | Bacillaceae/*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 Microbiology | Metabolism |
| Phylogeny | 25368138 | Pontibacillus salicampi sp. nov., a moderately halophilic bacterium isolated from saltern soil. | Lee JC, Kim YS, Yun BS, Whang KS | Int J Syst Evol Microbiol | 10.1099/ijs.0.066423-0 | 2014 | Bacillaceae/*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/chemistry | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 6273 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16287) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16287 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 23017 | Jee-Min Lim,Che Ok Jeon,Sung Min Song,Chang-Jin Kim | 10.1099/ijs.0.63315-0 | Pontibacillus chungwhensis gen. nov., sp. nov., a moderately halophilic Gram-positive bacterium from a solar saltern in Korea | IJSEM 55: 165-170 2005 | 15653871 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69479 | João 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 | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 71037 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID135137.1 | StrainInfo: A central database for resolving microbial strain identifiers |