Strain identifier

BacDive ID: 1388

Type strain: Yes

Species: Pontibacillus halophilus

Strain history: CIP <- 2009, KCTC <- Y.G. Chen and H.D. Xiao, Jishou Univ., Hunan, China: strain JSM 076056

NCBI tax ID(s): 1385510 (strain), 516704 (species)

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General

@ref: 8324

BacDive-ID: 1388

DSM-Number: 19796

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

description: Pontibacillus halophilus DSM 19796 is an obligate aerobe, moderately halophilic, spore-forming bacterium that forms circular colonies and was isolated from sea urchin.

NCBI tax id

NCBI tax idMatching level
1385510strain
516704species

strain history

@refhistory
8324<- Y.-G. Chen and H.-D. Xiao, YIM; JSM 076056
67771<- YG Chen, Yunnan Inst., China
119817CIP <- 2009, KCTC <- Y.G. Chen and H.D. Xiao, Jishou Univ., Hunan, China: strain JSM 076056

doi: 10.13145/bacdive1388.20230509.8.1

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 halophilus
  • full scientific name: Pontibacillus halophilus Chen et al. 2009

@ref: 8324

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Pontibacillus

species: Pontibacillus halophilus

full scientific name: Pontibacillus halophilus Chen et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23019positive3.5-4.0 µm0.6-0.9 µmrod-shapedyesperitrichous
67771rod-shapedyesperitrichous
67771positive
69480yes97.306
69480positive100
119817positiveovoid-shapedyes

colony morphology

  • @ref: 23019
  • colony size: 2.0-3.0 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 3-5 days
  • medium used: MA supplemented with 5 % (w/v) NaCl

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8324BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 30.0 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
23019MA supplemented with 5 % (w/v) NaClyes
36868Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119817CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
8324positivegrowth28mesophilic
23019positivegrowth15.0-40.0
23019positiveoptimum25.0-30.0mesophilic
36868positivegrowth30mesophilic
67771positivegrowth25-30mesophilic

culture pH

@refabilitytypepHPH range
23019positivegrowth6.0-10.0alkaliphile
23019positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23019obligate aerobe
67771aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
23019ellipsoidal,subterminal,in swollen sporangiaendosporeyes
67771endosporeyes
69481yes100
69480yes100

halophily

  • @ref: 23019
  • halophily level: moderately halophilic

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2301915963ribitol-builds acid from
2301915824D-fructose-builds acid from
2301912936D-galactose-builds acid from
2301917634D-glucose-builds acid from
2301916899D-mannitol-builds acid from
2301917924D-sorbitol-builds acid from
2301965327D-xylose-builds acid from
2301916813galactitol-builds acid from
2301917754glycerol-builds acid from
2301930849L-arabinose-builds acid from
2301962345L-rhamnose-builds acid from
2301917716lactose-builds acid from
2301917306maltose-builds acid from
230196731melezitose-builds acid from
2301928053melibiose-builds acid from
2301917268myo-inositol-builds acid from
2301916634raffinose-builds acid from
2301917814salicin-builds acid from
2301917992sucrose-builds acid from
2301927082trehalose-builds acid from
2301917234glucose-fermentation
23019casein-hydrolysis
2301916991dna-hydrolysis
2301917368hypoxanthine-hydrolysis
2301917895L-tyrosine-hydrolysis
2301953426tween 80-hydrolysis
2301916199urea-hydrolysis
2301915318xanthine-hydrolysis
2301917632nitrate-reduction
2301916024D-mannose+builds acid from
2301916988D-ribose+builds acid from
2301928017starch+builds acid from
230194853esculin+hydrolysis
230195291gelatin+hydrolysis
2301928017starch+hydrolysis
11981717632nitrate-reduction
11981716301nitrite-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistantresistance conc.sensitivity conc.
230196472lincomycinyesnoyes2 µg (disc)
2301927902tetracyclineyesnoyes30 µg (disc)
2301917833gentamicinyesyes10 µg (disc)
2301917076streptomycinyesyes10 µg (disc)
23019100147nalidixic acidyesyes20 µg (disc)
2301928971ampicillinyesyes30 µg (disc)
230193393carbenicillinyesyes30 µg (disc)
2301917698chloramphenicolyesyes30 µg (disc)
230196104kanamycinyesyes30 µg (disc)
2301928368novobiocinyesyes30 µg (disc)
230198309polymyxin byesyes30 µg (disc)
2301928077rifampicinyesyes5 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
2301935581indoleno
2301916136hydrogen sulfideno
2301915688acetoinno
11981735581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
2301915688acetoin-
2301917234glucose-

enzymes

@refvalueactivityec
23019acid phosphatase+/-3.1.3.2
23019alkaline phosphatase+3.1.3.1
23019alpha-chymotrypsin-3.4.21.1
23019alpha-fucosidase-3.2.1.51
23019alpha-galactosidase-3.2.1.22
23019alpha-glucosidase+3.2.1.20
23019alpha-mannosidase-3.2.1.24
23019beta-galactosidase-3.2.1.23
23019beta-glucosidase+/-3.2.1.21
23019beta-glucuronidase+3.2.1.31
23019catalase+1.11.1.6
23019cytochrome oxidase+1.9.3.1
23019esterase (C 4)-
23019esterase lipase (C 8)+
23019leucine arylamidase-3.4.11.1
23019lipase (C 14)-
23019lysine decarboxylase-4.1.1.18
23019N-acetyl-beta-glucosaminidase-3.2.1.52
23019naphthol-AS-BI-phosphohydrolase+
23019ornithine decarboxylase-4.1.1.17
23019phenylalanine deaminase-4.3.1.5
23019trypsin-3.4.21.4
23019valine arylamidase-
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
119817oxidase+
119817catalase+1.11.1.6
119817urease-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
119817-+-----------+-++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperature
8324sea urchinSouth China Sea, Leizhou BayChinaCHNAsia
67771From sea waterGuangdong ProvinceChinaCHNAsia
23019Difco marine agar 2216 (MA;pH 7.5), supplemented with 0-20 % (w/v) NaCl7-28 days28.0
119817Sea urchinSouthChinaCHNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Echinodermata

taxonmaps

  • @ref: 69479
  • File name: preview.99_8284.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1612;97_4692;98_6029;99_8284&stattab=map
  • Last taxonomy: Pontibacillus halophilus subclade
  • 16S sequence: EU583728
  • Sequence Identity:
  • Total samples: 43
  • soil counts: 16
  • aquatic counts: 20
  • animal counts: 6
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
83241Risk group (German classification)
1198171Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8324
  • description: Pontibacillus halophilus strain JSM 076056 16S ribosomal RNA gene, partial sequence
  • accession: EU583728
  • length: 1469
  • database: ena
  • NCBI tax ID: 516704

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pontibacillus halophilus JSM 076056 = DSM 19796GCA_000775595contigncbi1385510
66792Pontibacillus halophilus JSM 076056 = DSM 19796GCA_000425205scaffoldncbi1385510
66792Pontibacillus halophilus DSM 197961122964.4wgspatric1385510
66792Pontibacillus halophilus JSM 076056 = DSM 197961385510.3wgspatric1385510
66792Pontibacillus halophilus DSM 197962524023244draftimg1385510

GC content

@refGC-contentmethod
832445.5high performance liquid chromatography (HPLC)
6777145.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes89.474yes
flagellatedyes88.057yes
gram-positiveyes91.149yes
anaerobicno99.084yes
aerobicyes96.413yes
halophileyes90.609no
spore-formingyes94.683no
thermophileno92.855yes
glucose-utilyes86.656no
glucose-fermentno91.855yes

External links

@ref: 8324

culture collection no.: DSM 19796, CCTCC AA 207029, KCTC 13190, JSM 076056, CIP 110065

straininfo link

  • @ref: 71039
  • straininfo: 379418

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny20112668[Diversity of culturable bacteria associated with the sea urchin Hemicentrotus pulcherrimus from Naozhou Island].Huang K, Zhang L, Liu Z, Chen Q, Peng Q, Li W, Cui X, Chen YWei Sheng Wu Xue Bao2009Animals, Bacteria/classification/genetics/*isolation & purification, *Biodiversity, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Oceans and Seas, Phylogeny, RNA, Ribosomal, 16S/genetics, Sea Urchins/*microbiology, Seawater/*microbiologyGenetics
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
8324Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19796)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19796
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
23019Yi-Guang Chen,Yu-Qin Zhang,Huai-Dong Xiao,Zhu-Xiang Liu,Lang-Bo Yi,Jin-Xiao Shi,Xiao-Yang Zhi,Xiao-Long Cui,Wen-Jun Li10.1099/ijs.0.002469-0Pontibacillus halophilus sp. nov., a moderately halophilic bacterium isolated from a sea urchinIJSEM 59: 1635-1639 200919542115
36868Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7881
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71039Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID379418.1StrainInfo: A central database for resolving microbial strain identifiers
119817Curators of the CIPCollection of Institut Pasteur (CIP 110065)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110065