Amphibacillus marinus (DSM 27991, CGMCC 1.10434, JCM 17099)

Name: Amphibacillus marinus (DSM 27991, CGMCC 1.10434, JCM 17099)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23742

Type strain

Strain Designation J1

Culture col. no. DSM 27991 CGMCC 1.10434 JCM 17099 J1

NCBI tax ID(s) 872970

Special Collections DSMZ JCM Literature strains

History DSMZ <- JCM RIKEN BioResource Center, Tsukuba, Japan <- L. Zhang, Chinese Acad. Sci. (CAS), Beijing; J1 JCM <-- L. Zhang J1.

Links

Amphibacillus marinus J1 is a facultative aerobe, spore-forming, Gram-positive bacterium that was isolated from deep sea mud.

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

Name and taxonomic classification

SI-ID 406293

JCM 17099,DSM 27991

@ref 20215

Last LPSN update 2026-05-29 08:30:29

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Amphibacillus

Species Amphibacillus marinus

Full scientific name Amphibacillus marinus Ren et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
30846	positive	2.5 µm	0.35 µm	rod-shaped

Pigmentation

30846

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20924	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)		Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
20924	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

Culture temp

@ref	Growth	Type	Temperature (°C)
20924	positive	growth	30
30846	positive	growth	07-55
30846	positive	optimum	28
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
30846	positive	optimum	9
30846	positive	growth	7.5-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30846	facultative aerobe
125439	obligate aerobe	99.479

Spore formation

30846

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30846	NaCl	positive	growth	0-12 %

Observation

30846

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30846	22599 ChEBI	arabinose	+	carbon source
30846	17057 ChEBI	cellobiose	+	carbon source
30846	28757 ChEBI	fructose	+	carbon source
30846	28260 ChEBI	galactose	+	carbon source
30846	17754 ChEBI	glycerol	+	carbon source
30846	17716 ChEBI	lactose	+	carbon source
30846	17306 ChEBI	maltose	+	carbon source
30846	29864 ChEBI	mannitol	+	carbon source
30846	26546 ChEBI	rhamnose	+	carbon source
30846	30911 ChEBI	sorbitol	+	carbon source
30846	27082 ChEBI	trehalose	+	carbon source
30846	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30846	catalase	+	1.11.1.6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	chorismate metabolism	100	9 of 9
66794	L-lactaldehyde degradation	100	3 of 3
66794	ribulose monophosphate pathway	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	aerobactin biosynthesis	100	1 of 1
66794	teichoic acid biosynthesis	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ceramide biosynthesis	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	cardiolipin biosynthesis	100	7 of 7
66794	aspartate and asparagine metabolism	100	9 of 9
66794	palmitate biosynthesis	95.45	21 of 22
66794	pentose phosphate pathway	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	valine metabolism	88.89	8 of 9
66794	degradation of sugar alcohols	87.5	14 of 16
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	peptidoglycan biosynthesis	80	12 of 15
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	acetate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	propanol degradation	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	Entner Doudoroff pathway	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	phenylalanine metabolism	69.23	9 of 13
66794	purine metabolism	69.15	65 of 94
66794	pyrimidine metabolism	68.89	31 of 45
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	arginine metabolism	66.67	16 of 24
66794	degradation of hexoses	66.67	12 of 18
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	cyanate degradation	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	octane oxidation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	oxidative phosphorylation	64.84	59 of 91
66794	glycolysis	64.71	11 of 17
66794	d-xylose degradation	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	leucine metabolism	61.54	8 of 13
66794	methionine metabolism	61.54	16 of 26
66794	methylglyoxal degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	degradation of sugar acids	60	15 of 25
66794	factor 420 biosynthesis	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	non-pathway related	57.89	22 of 38
66794	glutathione metabolism	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	degradation of pentoses	53.57	15 of 28
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	starch degradation	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	vitamin E metabolism	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	butanoate fermentation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	glycogen biosynthesis	50	2 of 4
66794	tryptophan metabolism	47.37	18 of 38
66794	proline metabolism	45.45	5 of 11
66794	vitamin B6 metabolism	45.45	5 of 11
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	lysine metabolism	42.86	18 of 42
66794	citric acid cycle	42.86	6 of 14
66794	mevalonate metabolism	42.86	3 of 7
66794	lipid metabolism	38.71	12 of 31
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	cholesterol biosynthesis	36.36	4 of 11
66794	metabolism of disaccharids	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	enterobactin biosynthesis	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	lipid A biosynthesis	33.33	3 of 9
66794	ascorbate metabolism	31.82	7 of 22
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	propionate fermentation	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	carnitine metabolism	25	2 of 8
66794	sulfate reduction	23.08	3 of 13
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9
66794	arachidonic acid metabolism	22.22	4 of 18
66794	heme metabolism	21.43	3 of 14

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Mud (Sludge)

Isolation

@ref	Sample type	Geographic location	Continent
20924	deep sea mud	South China Sea	Asia
67770	Deep sea mud from South China Sea

Taxonmaps

69479

Global distribution of 16S sequence GU213062 (>99% sequence identity) for Amphibacillus marinus subclade from Microbeatlas

Aquatic Samples	11
Soil Samples	41
Animal Samples	17
Plant Samples	19
Total Samples	88

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20924	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2617270769 annotated assembly for Amphibacillus marinus CGMCC 1.10434	scaffold	GCA_900110345	872970.3	2617270769	872970	66.96

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20924	Amphibacillus marinus strain J1 16S ribosomal RNA gene, partial sequence	GU213062	1490		872970

GC content

@ref	GC-content (mol%)	Method
20924	36.7	thermal denaturation, midpoint method (Tm)
30846	36.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2617270769 annotated assembly for Amphibacillus marinus CGMCC 1.10434
BV-BRC: 872970.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.48	no
125439	motility	BacteriaNetⓘ	yes	72.35	no
125439	gram_stain	BacteriaNetⓘ	variable	49.44	no
125439	spore_formation	BacteriaNetⓘ	yes	82.36	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Amphibacillus marinus strain CGMCC 1.10434
PATRIC: 872970.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	83.12	yes
125438	anaerobic	anaerobicⓘ	no	87.77	yes
125438	aerobic	aerobicⓘ	no	87.65	no
125438	spore-forming	spore-formingⓘ	yes	86.45	yes
125438	thermophilic	thermophileⓘ	no	88.81	yes
125438	flagellated	motile2+ⓘ	yes	85.95	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amphibacillus marinus sp. nov., a member of the genus Amphibacillus isolated from marine mud.	Ren B, Yang N, Wang J, Ma XL, Wang Q, Xie F, Guo H, Liu ZH, Pugin B, Zhang LX	Int J Syst Evol Microbiol	10.1099/ijs.0.045807-0	2012

References

#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 )
#20924	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27991
#27176	IJSEM 1485 2013 ( DOI 10.1099/ijs.0.045807-0 , PubMed 22863987 )
#30846	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 #27176
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 .
#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 )

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Amphibacillus marinus (DSM 27991, CGMCC 1.10434, JCM 17099)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900110345

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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