Name: Alicyclobacillus shizuokensis 4A-336
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 433

Type strain:

Species: Alicyclobacillus shizuokensis

Strain Designation: 4A-336

Culture col. no.: DSM 17981, IAM 15226, JCM 21680, NBRC 103103

Strain history: IAM 15226 <-- K. Goto 4-A336.

NCBI tax ID(s): 1220573 (strain), 392014 (species)

SI-ID 309423

DSM 17981, IAM 15226, JCM 21680, NBRC 103103

Special Collections

Section

When using BacDive for research please cite our paper

Alicyclobacillus shizuokensis 4A-336 is an aerobe, spore-forming, thermophilic bacterium that was isolated from soil, crop field.

Gram-positive
motile
rod-shaped
spore-forming
aerobe
thermophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Alicyclobacillaceae*
	Genus	*Alicyclobacillus*
	Species	**Alicyclobacillus shizuokensis**
	Full Scientific Name (LPSN)	Alicyclobacillus shizuokensis Goto et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31943]	Gram stain	positive

[Ref.: #31943]	Cell length	04-05 µm

[Ref.: #31943]	Cell width	0.7-0.8 µm

[Ref.: #31943]	Cell shape	rod-shaped

[Ref.: #31943]	Motility	yes

[Ref.: #31943]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7313]

Culture medium

BACILLUS ACIDOCALDARIUS MEDIUM (DSMZ Medium 13)

[Ref.: #7313]

Culture medium growth

[Ref.: #7313]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7313]

Culture medium composition

expand / minimize

[Ref.: #7313]

Culture medium

ALICYCLOBACILLUS MEDIUM (DSMZ Medium 402)

[Ref.: #7313]

Culture medium growth

[Ref.: #7313]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7313]	growth	50 °C
[Ref.: #31943]	growth	35-60 °C
[Ref.: #31943]	optimum	45-50 °C
[Ref.: #67770]	growth	50 °C

	pH	Kind of pH		pH
[Ref.: #31943]			optimum	4.25
[Ref.: #31943]			growth	4.0-4.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31943]

Oxygen tolerance

aerobe

[Ref.: #31943]	Ability of spore formation	yes
[Ref.: #125438]	Ability of spore formation	yes Confidence in %93.237

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31943]		NaCl		growth	0-5	%
[Ref.: #31943]		NaCl		optimum	2.5	%

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31943]	arabinose ChEBI	+	carbon source
[Ref.: #31943]	cellobiose ChEBI	+	carbon source
[Ref.: #31943]	galactose ChEBI	+	carbon source
[Ref.: #31943]	maltose ChEBI	+	carbon source
[Ref.: #31943]	mannitol ChEBI	+	carbon source
[Ref.: #31943]	melibiose ChEBI	+	carbon source
[Ref.: #31943]	salicin ChEBI	+	carbon source
[Ref.: #31943]	sucrose ChEBI	+	carbon source
[Ref.: #31943]	trehalose ChEBI	+	carbon source
[Ref.: #31943]	xylose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31943]		catalase	+	1.11.1.6

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

[Ref.: #7313]	Sample type/isolated from	soil, crop field
[Ref.: #7313]	Geographic location (country and/or sea, region)	Shizuoka city
[Ref.: #7313]	Country	Japan
[Ref.: #7313]	Country ISO 3 Code	JPN
[Ref.: #7313]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil of a crop field in Shizuoka City
[Ref.: #67770]	Geographic location (country and/or sea, region)	Shizuoka Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB264024 (>99% sequence identity) for Alicyclobacillus shizuokensis from Microbeatlas

Aquatic Samples	17
Soil Samples	122
Animal Samples	176
Plant Samples	33
Total Samples	348

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

[Ref.: #7313]

Biosafety level

Risk group (German classification)
According to TRBA 466

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

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #7313]	Alicyclobacillus shizuokensis gene for 16S ribosomal RNA, partial sequence	AB264024	1519	GenBank ENA	392014 tax ID
[Ref.: #124043]	Alicyclobacillus shizuokensis gene for 16S rRNA, partial sequence, strain: NBRC 103103.	AB681942	1471	GenBank ENA	392014 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Alicyclobacillus shizuokensis NBRC 103103	GCA_001552255	contig	GenBank ENA	1220573 tax ID
[Ref.: #66792]	Alicyclobacillus shizuokensis NBRC 103103	1220573.3	wgs	PATRIC	1220573 tax ID	*
[Ref.: #66792]	Alicyclobacillus shizuokensis NBRC 103103	2731957577	draft	JGI IMG/M	1220573 tax ID	*

[Ref.: #7313]	GC-content	60.5 mol%
[Ref.: #67770]	GC-content	60.5 mol%	high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Alicyclobacillus shizuokensis NBRC 103103 PATRIC: 1220573.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	65.617	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	93.469	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	93.237	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	75.033	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	yes	65.437	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	71.198	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Alicyclobacillus shizuokensis NBRC 103103 NCBI: GCA_001552255
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	facultative aerobe	64.5
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	81.6
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	52.8
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	74

Availability in culture collections External links

[Ref.: #7313]

Culture collection no.

DSM 17981, IAM 15226, JCM 21680, NBRC 103103

[Ref.: #70112]

SI-ID 309423

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Proposal of six species of moderately thermophilic, acidophilic, endospore-forming bacteria: Alicyclobacillus contaminans sp. nov., Alicyclobacillus fastidiosus sp. nov., Alicyclobacillus kakegawensis sp. nov., Alicyclobacillus macrosporangiidus sp. nov., Alicyclobacillus sacchari sp. nov. and Alicyclobacillus shizuokensis sp. nov.	Goto K, Mochida K, Kato Y, Asahara M, Fujita R, An SY, Kasai H, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.64692-0	2007	*

References

#7313

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17981

#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 )

#31943

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 #28199 (see below)

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#70112

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-ID309423.1 )

#124043

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

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

#28199

IJSEM 1276 2007 ( DOI 10.1099/ijs.0.64692-0 , PubMed 17551043 )

* These data were automatically processed and therefore are not curated

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Alicyclobacillus shizuokensis NBRC 103103

Alicyclobacillus shizuokensis NBRC 103103

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