Amphibacillus sediminis (DSM 21624, IAM 15428, JCM 23213)

Name: Amphibacillus sediminis (DSM 21624, IAM 15428, JCM 23213)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1406

Type strain

Strain Designation Shu-P-Ggiii25-2

Culture col. no. DSM 21624 IAM 15428 JCM 23213 KCTC 13120 MBIC 08269 2 more

NCBI tax ID(s) 1220586 360185

Special Collections DSMZ JCM KCTC Literature strains

Links

Amphibacillus sediminis Shu-P-Ggiii25-2 is a facultative anaerobe, spore-forming, mesophilic prokaryote that forms circular colonies and was isolated from Sediment.

spore-forming Gram-positive rod-shaped colony-forming facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 319362

IAM 15428,KCTC 13120,NBRC 103570,JCM 23213,DSM 21624

@ref 20215

Last LPSN update 2025-12-16 09:47:06

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Amphibacillus

Species Amphibacillus sediminis

Full scientific name Amphibacillus sediminis An et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell shape
23032	positive	rod-shaped
67771		rod-shaped
67771	positive

Colony morphology

@ref	Colony color	Colony shape	Medium used
23032	white	circular	trypticase soy agar

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15844	CASO AGAR (MERCK 105458) (DSMZ Medium 220)		Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
23032	trypticase soy agar			trypticase soy agar containing 50 % Herbst’s artificial seawater (l 21 distilled water): 30 g NaCl, 0.7 g KCl, 5.3 g MgSO 4 . 7H 2 O, 1.3 g CaCl 2 . 2H 2 O and 10.8 g MgCl 2 . 6H 2 O.)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15844	positive	growth	30	mesophilic
23032	positive	growth	17.0-55.0
23032	negative	growth	10.0
23032	negative	growth	60.0
23032	positive	optimum	27.0	mesophilic
67770	positive	growth	30	mesophilic
67771	positive	growth	27	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
23032	positive	optimum	8.5	alkaliphile
23032	positive	growth	7.0-9.0
23032		growth	6.5
23032		growth	9.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
23032	facultative anaerobe
67771	aerobe
125439	obligate aerobe	98

Spore formation

@ref	Spore description	Type of spore	Spore formation
23032	spherical,terminal	endospore
67771		endospore

Halophily

@ref	Salt	Growth	Tested relation	Concentration
23032	NaCl	positive	growth	<6.0 %(w/v)

Murein

@ref	Murein short key	Type
23032	A31	A1gamma m-Dpm-direct

Observation

67771

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23032	16808 ChEBI	2-dehydro-D-gluconate	-	builds acid from
23032	17426 ChEBI	5-dehydro-D-gluconate	-	builds acid from
23032	27613 ChEBI	amygdalin	-	builds acid from
23032	18305 ChEBI	arbutin	-	builds acid from
23032	17057 ChEBI	cellobiose	-	builds acid from
23032	16947 ChEBI	citrate	-	carbon source
23032	17108 ChEBI	D-arabinose	-	builds acid from
23032	18333 ChEBI	D-arabitol	-	builds acid from
23032	28847 ChEBI	D-fucose	-	builds acid from
23032	62318 ChEBI	D-lyxose	-	builds acid from
23032	16443 ChEBI	D-tagatose	-	builds acid from
23032	65327 ChEBI	D-xylose	-	builds acid from
23032	17113 ChEBI	erythritol	-	builds acid from
23032	4853 ChEBI	esculin	+	builds acid from
23032	28757 ChEBI	fructose	+	builds acid from
23032	16813 ChEBI	galactitol	-	builds acid from
23032	28260 ChEBI	galactose	-	builds acid from
23032	28066 ChEBI	gentiobiose	-	builds acid from
23032	24265 ChEBI	gluconate	-	builds acid from
23032	17234 ChEBI	glucose	+	builds acid from
23032	17754 ChEBI	glycerol	+	builds acid from
23032	28087 ChEBI	glycogen	-	builds acid from
23032	15443 ChEBI	inulin	-	builds acid from
23032	30849 ChEBI	L-arabinose	-	builds acid from
23032	18403 ChEBI	L-arabitol	-	builds acid from
23032	18287 ChEBI	L-fucose	-	builds acid from
23032	65328 ChEBI	L-xylose	-	builds acid from
23032	17716 ChEBI	lactose	-	builds acid from
23032	17306 ChEBI	maltose	+	builds acid from
23032	29864 ChEBI	mannitol	-	builds acid from
23032	37684 ChEBI	mannose	+	builds acid from
23032	6731 ChEBI	melezitose	-	builds acid from
23032	28053 ChEBI	melibiose	-	builds acid from
23032	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
23032	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
23032	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
23032	17268 ChEBI	myo-inositol	-	builds acid from
23032	506227 ChEBI	N-acetylglucosamine	-	builds acid from
23032	17632 ChEBI	nitrate	-	reduction
23032	16634 ChEBI	raffinose	-	builds acid from
23032	26546 ChEBI	rhamnose	-	builds acid from
23032	15963 ChEBI	ribitol	-	builds acid from
23032	33942 ChEBI	ribose	-	builds acid from
23032	17814 ChEBI	salicin	-	builds acid from
23032	30911 ChEBI	sorbitol	-	builds acid from
23032	27922 ChEBI	sorbose	-	builds acid from
23032	28017 ChEBI	starch	-	builds acid from
23032	17992 ChEBI	sucrose	+	builds acid from
23032	27082 ChEBI	trehalose	-	builds acid from
23032	32528 ChEBI	turanose	-	builds acid from
23032	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite
23032	15688 ChEBI	acetoin
23032	16136 ChEBI	hydrogen sulfide
23032	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Citrate test
23032	16947 ChEBI	citrate	-

Enzymes

@ref	Value	Activity	Ec
23032	arginine dihydrolase	+	3.5.3.6
23032	beta-galactosidase	+	3.2.1.23
23032	catalase	-	1.11.1.6
23032	cytochrome oxidase	-	1.9.3.1
23032	gelatinase	+
23032	lysine decarboxylase	-	4.1.1.18
23032	ornithine decarboxylase	-	4.1.1.17
23032	tryptophan deaminase	-	4.1.99.1
23032	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature
15844	Sediment	Lake Hamana, Shizuoka	Japan	JPN	Asia
23032						GYPiii medium	5 g Bacto yeast extract (BD), 1 g Polypepton (soybean, Nihon Pharma), 1 g casein Polypepton (Nihon Pharma), 1 g fish meat extract, 2 g CaCO3 , 1.5 g Na2CO3 , 10 g glucose, 70 g NaCl, 1 mg sodium pyruvate, 20 mg MgSO4.7H2O, 1 mg MnSO4.4H2O, 1 mg FeSO4.7H2O, 10 mg colistin, 10 mg sodium azide, 10 mg cycloheximide, 30 mg bromothymol blue (BTB), 5 mg Tween 80, 900 ml seawater for 1 l medium, pH 10	3 days	25.0
67770	Sediment from Lake Hamana	Shizuoka	Japan	JPN	Asia
67771	From sediment	Hamana Lake, Shizuoka City	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB243866 (>99% sequence identity) for Amphibacillus sediminis subclade from Microbeatlas

Aquatic Samples	9
Soil Samples	48
Animal Samples	61
Plant Samples	23
Total Samples	141

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15844	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM155227v1 assembly for Amphibacillus sediminis NBRC 103570	contig	GCA_001552275	1220586.4	2731957578	1220586	59.35

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Amphibacillus sediminis gene for 16S rRNA, partial sequence, strain: NBRC 103570	AB682134	1493		360185
15844	Amphibacillus sediminis rrs gene for 16S rRNA, partial sequence	AB243866	1520		360185

GC content

@ref	GC-content (mol%)	Method
15844	42.3	high performance liquid chromatography (HPLC)
67771	42.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Amphibacillus sediminis NBRC 103570
NCBI: GCA_001552275

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.00	no
125439	gram_stain	BacteriaNetⓘ	variable	76.80	no
125439	motility	BacteriaNetⓘ	yes	83.10	no
125439	spore_formation	BacteriaNetⓘ	yes	89.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Amphibacillus sediminis NBRC 103570
PATRIC: 1220586.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	82.50	no
125438	anaerobic	anaerobicⓘ	no	86.81	yes
125438	spore-forming	spore-formingⓘ	yes	86.42	yes
125438	aerobic	aerobicⓘ	no	87.16	no
125438	thermophilic	thermophileⓘ	no	86.57	no
125438	flagellated	motile2+ⓘ	yes	82.37	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amphibacillus jilinensis sp. nov., a facultatively anaerobic, alkaliphilic bacillus from a soda lake.	Wu XY, Zheng G, Zhang WW, Xu XW, Wu M, Zhu XF	Int J Syst Evol Microbiol	10.1099/ijs.0.018259-0	2009
Phylogeny	Amphibacillus sediminis sp. nov., an endospore-forming bacterium isolated from lake sediment in Japan.	An SY, Ishikawa S, Kasai H, Goto K, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.64926-0	2007

References

#15844	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21624
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#23032	Sun-Young An,Shu Ishikawa,Hiroaki Kasai,Keiichi Goto,Akira Yokota: Amphibacillus sediminis sp. nov., an endospore-forming bacterium isolated from lake sediment in Japan. IJSEM 57: 2489 - 2492 2007 ( DOI 10.1099/ijs.0.64926-0 , PubMed 17978206 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Rate our new design

Content

About us

Amphibacillus sediminis (DSM 21624, IAM 15428, JCM 23213)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001552275

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media