Strain identifier

BacDive ID: 1302

Type strain: Yes

Species: Bacillus siamensis

Strain Designation: PD-A10

Strain history: CIP <- 2010, KCTC

NCBI tax ID(s): 1177185 (strain), 659243 (species)

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General

@ref: 17960

BacDive-ID: 1302

DSM-Number: 25261

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped

description: Bacillus siamensis PD-A10 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from salted crab.

NCBI tax id

NCBI tax idMatching level
659243species
1177185strain

strain history

@refhistory
404332010, KCTC
17960<- KCTC <- S. Tanasupawat, Chulalongkorn Univ., Thailand
67771<- S Tanasupawat, Chulalongkorn Univ., Thailand
122594CIP <- 2010, KCTC

doi: 10.13145/bacdive1302.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Bacillus
  • species: Bacillus siamensis
  • full scientific name: Bacillus siamensis Sumpavapol et al. 2010

@ref: 17960

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Bacillus

species: Bacillus siamensis

full scientific name: Bacillus siamensis Sumpavapol et al. 2010 emend. Dunlap 2015

strain designation: PD-A10

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
29694positive1.5-3.5 µm0.3-0.6 µmrod-shapedyes
67771rod-shapedyesperitrichous
67771positive
122594positiverod-shapedyes

pigmentation

  • @ref: 29694
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17960BACTO 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 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 MnSO4 0.01 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
40433MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122594CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
17960positivegrowth30mesophilic
29694positivegrowth04-55
29694positiveoptimum37mesophilic
40433positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
29694positivegrowth4.5-9alkaliphile
29694positiveoptimum06-07

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29694facultative anaerobe
67771aerobe
122594facultative anaerobe

spore formation

@refspore formationtype of spore
29694yes
67771yesendospore
122594yes

halophily

  • @ref: 29694
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-14 %

observation

@refobservation
29694aggregates in chains
67771quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2969422599arabinose+carbon source
2969417057cellobiose+carbon source
2969428757fructose+carbon source
2969417234glucose+carbon source
2969417754glycerol+carbon source
2969428087glycogen+carbon source
2969417716lactose+carbon source
2969417306maltose+carbon source
2969429864mannitol+carbon source
2969416634raffinose+carbon source
2969433942ribose+carbon source
2969417814salicin+carbon source
2969430911sorbitol+carbon source
2969417992sucrose+carbon source
2969418222xylose+carbon source
296944853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol+builds acid from
6837116899D-mannitol+builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
12259417632nitrate+reduction
12259416301nitrite-reduction

metabolite production

  • @ref: 122594
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29694catalase+1.11.1.6
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
122594oxidase-
122594catalase+1.11.1.6
122594urease-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
122594-+++------++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122594+--+++---+/-++----+/-++-++++++++++++/-+/--+++-+----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
17960salted crabThailandTHAAsia
67771From fermented crab (`Poo-Dong`)ThailandTHAAsiaNakornpathom Province
122594Salted crab, poo-khemThailandTHAAsia

isolation source categories

Cat1Cat2Cat3
#Host#Arthropoda#Crustacea
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_21.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_17;97_17;98_20;99_21&stattab=map
  • Last taxonomy: Bacillus
  • 16S sequence: GQ281299
  • Sequence Identity:
  • Total samples: 18201
  • soil counts: 3768
  • aquatic counts: 2854
  • animal counts: 9674
  • plant counts: 1905

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
179601Risk group (German classification)
1225941Risk group (French classification)

Sequence information

16S sequences

  • @ref: 17960
  • description: Bacillus siamensis strain PD-A10 16S ribosomal RNA gene, partial sequence
  • accession: GQ281299
  • length: 1525
  • database: ena
  • NCBI tax ID: 1177185

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus siamensis KCTC 13613 KCTC 13613(T)GCA_000262045contigncbi1177185
66792Bacillus siamensis KCTC 136131177185.3wgspatric1177185
66792Bacillus siamensis KCTC 136132548877022draftimg1177185

GC content

@refGC-contentmethod
1796041.4high performance liquid chromatography (HPLC)
2969441.4
1796046.3sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.434yes
gram-positiveyes92.034yes
anaerobicno99.384yes
aerobicyes91.236no
halophileyes88.524no
spore-formingyes96.247no
flagellatedyes86.218no
thermophileno97.268yes
glucose-utilyes88.96yes
glucose-fermentno91.422no

External links

@ref: 17960

culture collection no.: DSM 25261, BCC 22614, KACC 16244, KCTC 13613, CIP 110217

straininfo link

  • @ref: 70953
  • straininfo: 371008

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19933584Bacillus siamensis sp. nov., isolated from salted crab (poo-khem) in Thailand.Sumpavapol P, Tongyonk L, Tanasupawat S, Chokesajjawatee N, Luxananil P, Visessanguan WInt J Syst Evol Microbiol10.1099/ijs.0.018879-02009Bacillus/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, *Food Microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Spores, Bacterial/cytology, Temperature, ThailandBiotechnology
Genetics22815459Draft genome sequence of the plant growth-promoting bacterium Bacillus siamensis KCTC 13613T.Jeong H, Jeong DE, Kim SH, Song GC, Park SY, Ryu CM, Park SH, Choi SKJ Bacteriol10.1128/JB.00805-122012Antibiosis, Bacillus/*genetics/isolation & purification/physiology, DNA, Bacterial/*chemistry/*genetics, *Food Microbiology, *Genome, Bacterial, Molecular Sequence Data, *Plant Development, *Sequence Analysis, DNABiotechnology
Phylogeny26296875Phylogenomic analysis shows that 'Bacillus vanillea' is a later heterotypic synonym of Bacillus siamensis.Dunlap CAInt J Syst Evol Microbiol10.1099/ijsem.0.0004442015Bacillus/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Genome, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vanilla/*microbiologyGenetics
33243655Biofilm development of Bacillus siamensis ATKU1 on pristine short chain low-density polyethylene: A case study on microbe-microplastics interaction.Tarafdar A, Lee JU, Jeong JE, Lee H, Jung Y, Oh HB, Woo HY, Kwon JHJ Hazard Mater10.1016/j.jhazmat.2020.1245162020Bacillus, Biofilms, Microplastics, *Plastics, *Polyethylene
Cultivation34897250Control Efficacy of Bacillus velezensis AFB2-2 against Potato Late Blight Caused by Phytophthora infestans in Organic Potato Cultivation.Kim MJ, Shim CK, Park JHPlant Pathol J10.5423/PPJ.FT.09.2021.01382021

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17960Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25261)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25261
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
29694Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2607928776041
40433Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8052
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
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
70953Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID371008.1StrainInfo: A central database for resolving microbial strain identifiers
122594Curators of the CIPCollection of Institut Pasteur (CIP 110217)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110217