Name: Bacillus siamensis PD-A10
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1302

Type strain:

Species: Bacillus siamensis

Strain Designation: PD-A10

Culture col. no.: DSM 25261, BCC 22614, KACC 16244, KCTC 13613, CIP 110217

Strain history: CIP <- 2010, KCTC

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

SI-ID 371008

BCC 22614, KCTC 13613, LMG 27594, CIP 110217

Special Collections

Section

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

Gram-positive
motile
rod-shaped
spore-forming
facultative anaerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Bacillaceae*
	Genus	*Bacillus*
	Species	**Bacillus siamensis**
	Full Scientific Name (LPSN)	Bacillus siamensis Sumpavapol et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29694]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #122594]	Gram stain	positive

[Ref.: #29694]	Cell length	1.5-3.5 µm

[Ref.: #29694]	Cell width	0.3-0.6 µm

[Ref.: #29694]	Cell shape	rod-shaped
[Ref.: #122594]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #29694]	Motility	yes
[Ref.: #122594]	Motility	yes
[Ref.: #67771]	Motility	yes

[Ref.: #67771]	Flagellum arrangement	peritrichous

[Ref.: #29694]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17960]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #17960]

Culture medium growth

[Ref.: #17960]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17960]

Culture medium composition

expand / minimize

[Ref.: #40433]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #40433]

Culture medium growth

[Ref.: #40433]

Culture medium composition

expand / minimize

[Ref.: #122594]

Culture medium

CIP Medium 72

[Ref.: #122594]

Culture medium growth

[Ref.: #122594]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #17960]	growth	30 °C
[Ref.: #29694]	growth	04-55 °C
[Ref.: #29694]	optimum	37 °C
[Ref.: #40433]	growth	37 °C
[Ref.: #67771]	growth	37 °C

	pH	Kind of pH		pH
[Ref.: #29694]			optimum	06-07
[Ref.: #29694]			growth	4.5-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29694]	Oxygen tolerance	facultative anaerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #122594]	Oxygen tolerance	facultative anaerobe

[Ref.: #67771]	Type of spore	endospore
[Ref.: #67771]	Ability of spore formation	yes
[Ref.: #29694]	Ability of spore formation	yes
[Ref.: #122594]	Ability of spore formation	yes
[Ref.: #69480]	Ability of spore formation	yes Confidence in %96.125

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29694]		NaCl		growth	0-14	%

[Ref.: #29694]	Observation	aggregates in chains
[Ref.: #67771]	Observation	quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #29694]	arabinose ChEBI	+	carbon source
[Ref.: #68371]	arbutin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #29694]	cellobiose ChEBI	+	carbon source
[Ref.: #68371]	cellobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #29694]	esculin ChEBI	+	hydrolysis
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #29694]	fructose ChEBI	+	carbon source
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #29694]	glucose ChEBI	+	carbon source
[Ref.: #29694]	glycerol ChEBI	+	carbon source
[Ref.: #68371]	glycerol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #29694]	glycogen ChEBI	+	carbon source
[Ref.: #68371]	glycogen ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #29694]	lactose ChEBI	+	carbon source
[Ref.: #68371]	lactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #29694]	maltose ChEBI	+	carbon source
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #29694]	mannitol ChEBI	+	carbon source
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #122594]	nitrate ChEBI	+	reduction
[Ref.: #122594]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #29694]	raffinose ChEBI	+	carbon source
[Ref.: #68371]	raffinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #29694]	ribose ChEBI	+	carbon source
[Ref.: #29694]	salicin ChEBI	+	carbon source
[Ref.: #68371]	salicin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #29694]	sorbitol ChEBI	+	carbon source
[Ref.: #68371]	starch ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #29694]	sucrose ChEBI	+	carbon source
[Ref.: #68371]	sucrose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #29694]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #122594]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #29694]	catalase	+	1.11.1.6
[Ref.: #122594]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122594]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #122594]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #122594]	11733	not determinedn.d.	+	-	-	+	+	+	-	-	-	+/-	+	+	-	-	-	-	+/-	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+/-	+/-	-	+	+	+	-	+	-	-	-	-	-	-	-	-	-	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #122594]	12444	-	+	+	+	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #17960]	Sample type/isolated from	salted crab
[Ref.: #17960]	Country	Thailand
[Ref.: #17960]	Country ISO 3 Code	THA
[Ref.: #17960]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From fermented crab (`Poo-Dong`)
[Ref.: #67771]	Geographic location (country and/or sea, region)	Nakornpathom Province
[Ref.: #67771]	Country	Thailand
[Ref.: #67771]	Country ISO 3 Code	THA
[Ref.: #67771]	Continent	Asia

[Ref.: #122594]	Sample type/isolated from	Salted crab, poo-khem
[Ref.: #122594]	Country	Thailand
[Ref.: #122594]	Country ISO 3 Code	THA
[Ref.: #122594]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Arthropoda	#Crustacea
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence GQ281299 (>99% sequence identity) for Bacillus from Microbeatlas

Aquatic Samples	2854
Soil Samples	3768
Animal Samples	9674
Plant Samples	1905
Total Samples	18201

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #17960]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122594]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #17960]	Bacillus siamensis strain PD-A10 16S ribosomal RNA gene, partial sequence	GQ281299	1525	GenBank ENA	1177185 tax ID
[Ref.: #124043]	Bacillus siamensis KCTC 13613 16S ribosomal RNA gene, partial sequence.	OM995809	1394	GenBank ENA	1177185 tax ID	*
[Ref.: #124043]	Bacillus siamensis KCTC 13613 16S ribosomal RNA gene, partial sequence.	KT781674	1419	GenBank ENA	1177185 tax ID	*
[Ref.: #124043]	Bacillus siamensis KCTC 13613 16S ribosomal RNA gene, partial sequence.	KT781675	1448	GenBank ENA	672 tax ID	*
[Ref.: #124043]	Bacillus siamensis KCTC 13613 16S ribosomal RNA gene, partial sequence.	KT781677	1404	GenBank ENA	1803213 tax ID	*
[Ref.: #124043]	Bacillus siamensis KCTC 13613 16S ribosomal RNA gene, partial sequence.	KT781678	1402	GenBank ENA	1803214 tax ID	*
[Ref.: #124043]	Bacillus siamensis KCTC 13613 16S ribosomal RNA gene, partial sequence.	KT781679	1398	GenBank ENA	1803215 tax ID	*
[Ref.: #124043]	Bacillus siamensis KCTC 13613 16S ribosomal RNA gene, partial sequence.	OQ618961	1374	GenBank ENA	1177185 tax ID	*
[Ref.: #124043]	Bacillus siamensis KCTC 13613 16S ribosomal RNA gene, partial sequence.	OQ625908	1374	GenBank ENA	1177185 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Bacillus siamensis KCTC 13613 KCTC 13613(T)	GCA_000262045	contig	GenBank ENA	1177185 tax ID	*
[Ref.: #66792]	Bacillus siamensis KCTC 13613	1177185.3	wgs	PATRIC	1177185 tax ID	*
[Ref.: #66792]	Bacillus siamensis KCTC 13613	2548877022	draft	JGI IMG/M	1177185 tax ID	*

[Ref.: #17960]	GC-content	41.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29694]	GC-content	41.4 mol%
[Ref.: #17960]	GC-content	46.3 mol%	sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Bacillus siamensis KCTC 13613 PATRIC: 1177185.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	81.091	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	90.95	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	96.125	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	73.18	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	87.302	yes

Availability in culture collections External links

[Ref.: #17960]

Culture collection no.

DSM 25261, BCC 22614, KACC 16244, KCTC 13613, CIP 110217

[Ref.: #70953]

SI-ID 371008

Literature:

Topic	Title	Authors	Journal	DOI	Year
Cultivation	Control Efficacy of Bacillus velezensis AFB2-2 against Potato Late Blight Caused by Phytophthora infestans in Organic Potato Cultivation.	Kim MJ, Shim CK, Park JH	Plant Pathol J	10.5423/PPJ.FT.09.2021.0138	2021	*
Phylogeny	Phylogenomic analysis shows that 'Bacillus vanillea' is a later heterotypic synonym of Bacillus siamensis.	Dunlap CA	Int J Syst Evol Microbiol	10.1099/ijsem.0.000444	2015	*
Genetics	Draft 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 SK	J Bacteriol	10.1128/JB.00805-12	2012	*
Phylogeny	Bacillus siamensis sp. nov., isolated from salted crab (poo-khem) in Thailand.	Sumpavapol P, Tongyonk L, Tanasupawat S, Chokesajjawatee N, Luxananil P, Visessanguan W	Int J Syst Evol Microbiol	10.1099/ijs.0.018879-0	2009	*
	Biofilm 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 JH	J Hazard Mater	10.1016/j.jhazmat.2020.124516	2020	*

References

#17960

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25261

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#29694

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26079 (see below)

#40433 ; Curators of the CIP;

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68371

Automatically annotated from API 50CH acid .

#68382

Automatically annotated from API zym .

#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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#70953

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID371008.1 )

#122594 Collection of Institut Pasteur ; Curators of the CIP; CIP 110217

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#26079

IJSEM 2364 2010 ( DOI 10.1099/ijs.0.018879-0 , PubMed 19933584 )

* These data were automatically processed and therefore are not curated

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Bacillus siamensis KCTC 13613

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