Name: Amphibacillus xylanus Ep01
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1403

Type strain:

Species: Amphibacillus xylanus

Strain Designation: Ep01

Culture col. no.: DSM 6626, ATCC 51415, IFO 15112, JCM 7361, NBRC 15112, LMG 17667

Strain history: Y. Niimura Ep01.

NCBI tax ID(s): 698758 (strain), 1449 (species)

SI-ID 9966

LMG 17436, ATCC 51415, DSM 6626, IFO 15112, JCM 7361, LMG 17667, NBRC 15112, KCTC 3882

Other strains from Amphibacillus xylanus

A. xylanus JCM 7362
A. xylanus JCM 7363

Section

Amphibacillus xylanus Ep01 is a facultative anaerobe, chemoorganotroph, spore-forming bacterium that forms circular colonies and was isolated from alcaline compost of manure with grass and rice straw.

colony-forming
Gram-positive
rod-shaped
spore-forming
chemoorganotroph
facultative anaerobe
mesophilic
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	*Amphibacillus*
	Species	**Amphibacillus xylanus**
	Full Scientific Name (LPSN)	Amphibacillus xylanus Niimura et al. 1990

Information on morphological and physiological properties Morphology

[Ref.: #23029]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #23029]	Cell length	0.9-1.9 µm

[Ref.: #23029]	Cell width	0.3-0.5 µm

[Ref.: #23029]	Cell shape	rod-shaped

[Ref.: #23029]	Motility	no

[Ref.: #23029]	Colony color	white
[Ref.: #23029]	Colony shape	circular
[Ref.: #23029]	Incubation period	1 day
[Ref.: #23029]	Cultivation medium used	glucose agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2759]

Culture medium

AMPHIBACILLUS MEDIUM (DSMZ Medium 529)

[Ref.: #2759]

Culture medium growth

[Ref.: #2759]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2759]

Culture medium composition

expand / minimize

[Ref.: #23029]

Culture medium

glucose agar

[Ref.: #23029]

Culture medium growth

	Kind of temperature		Temperature
[Ref.: #2759]		growth	37 °C
[Ref.: #23029]		growth	25.0-44.0 °C
[Ref.: #23029]	no	growth	50.0 °C
[Ref.: #67770]		growth	39 °C

[Ref.: #2759]	Temperature range	mesophilic
[Ref.: #23029]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #23029]			growth	8.0-10.0
[Ref.: #23029]		no	growth	7.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23029]

Oxygen tolerance

facultative anaerobe

[Ref.: #23029]

Nutrition type

chemoorganotroph

[Ref.: #23029]	Spore description	oval,heat-resistant
[Ref.: #23029]	Type of spore	endospore
[Ref.: #23029]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %98
[Ref.: #69480]	Ability of spore formation	yes Confidence in %97.65

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23029]		NaCl		growth	3.0	%
[Ref.: #23029]		NaCl	no	growth	6.0	%

[Ref.: #23029]	Murein short key	A31
[Ref.: #23029]	Murein types	A1gamma m-Dpm-direct

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23029]	citrate ChEBI	-	carbon source
[Ref.: #23029]	D-mannose ChEBI	+	carbon source
[Ref.: #23029]	gelatin ChEBI	-	hydrolysis
[Ref.: #23029]	inulin ChEBI	-	carbon source
[Ref.: #23029]	melibiose ChEBI	+	carbon source
[Ref.: #23029]	nitrate ChEBI	-	reduction
[Ref.: #23029]	xylan ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #23029]		hydrogen sulfide ChEBI	no
[Ref.: #23029]		indole ChEBI	no

	Physiological tests	Metabolite	Citrate test
[Ref.: #23029]		citrate ChEBI	-

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #23029]		catalase	-	1.11.1.6
[Ref.: #23029]		cytochrome oxidase	-	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	chorismate metabolism	100	9 of 9
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	purine metabolism	69.15	65 of 94
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	oxidative phosphorylation	57.14	52 of 91
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	alanine metabolism	48.28	14 of 29
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	glutamate and glutamine metabolism	46.43	13 of 28
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	d-mannose degradation	44.44	4 of 9
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	citric acid cycle	42.86	6 of 14
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	arginine metabolism	41.67	10 of 24
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	methylglyoxal degradation	40	2 of 5
[Ref.: #66794]	lipid metabolism	38.71	12 of 31
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	lysine metabolism	35.71	15 of 42
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	glycine metabolism	30	3 of 10
[Ref.: #66794]	tyrosine metabolism	28.57	4 of 14
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #2759]	Sample type/isolated from	alcaline compost of manure with grass and rice straw

[Ref.: #67770]	Sample type/isolated from	Alkaliphilic compost
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	#Composting
#Engineered	#Waste	#Solid plant waste
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Condition	#Alkaline	-

What are isolation sources categories?

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

[Ref.: #2759]

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.: #20218]	Amphibacillus xylanus 16S rRNA gene, strain DSM 6626	AJ496807	1505	ENA	698758 tax ID	*
[Ref.: #20218]	Amphibacillus xylanus isolate Ax79 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	EU723603	725	ENA	698758 tax ID	*
[Ref.: #20218]	Amphibacillus xylanus isolate Ax85 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	EU723604	630	ENA	698758 tax ID	*
[Ref.: #20218]	Amphibacillus xylanus DNA for 16S ribosomal RNA	D82065	1450	ENA	698758 tax ID	*
[Ref.: #20218]	Amphibacillus xylanus gene for 16S rRNA, partial sequence, strain: NBRC 15112	AB680770	1495	ENA	1449 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Amphibacillus xylanus NBRC 15112	GCA_000307165	complete	GenBank	698758 tax ID	*
[Ref.: #66792]	Amphibacillus xylanus NBRC 15112	698758.3	complete	PATRIC	698758 tax ID	*
[Ref.: #66792]	Amphibacillus xylanus NBRC 15112	2524023219	complete	JGI IMG/M	698758 tax ID	*

[Ref.: #23029]	GC-content	36 mol%
[Ref.: #67770]	GC-content	36 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Amphibacillus xylanus NBRC 15112 NBRC 15112 NCBI: GCA_000307165.1
[Ref.: #69481]	spore-forming	yes	98	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Amphibacillus xylanus NBRC 15112 NBRC 15112 NCBI: GCA_000307165.1
[Ref.: #69480]	motile	yes	79.432	no
[Ref.: #69480]	flagellated	no	50.686	no
[Ref.: #69480]	gram-positive	yes	90.534	no
[Ref.: #69480]	anaerobic	no	94.307	yes
[Ref.: #69480]	aerobic	no	93.119	yes
[Ref.: #69480]	halophile	yes	80.204	no
[Ref.: #69480]	spore-forming	yes	88.334	yes
[Ref.: #69480]	glucose-util	yes	88.082	no
[Ref.: #69480]	thermophile	no	70.403	no
[Ref.: #69480]	glucose-ferment	no	52.486	no

Availability in culture collections External links

[Ref.: #2759]

Culture collection no.

DSM 6626, ATCC 51415, IFO 15112, JCM 7361, NBRC 15112, LMG 17667

[Ref.: #71054]

SI-ID 9966

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pelagirhabdus alkalitolerans gen. nov., sp. nov., an alkali-tolerant and thermotolerant bacterium isolated from beach sediment, and reclassification of Amphibacillus fermentum as Pelagirhabdus fermentum comb. nov.	Sultanpuram VR, Mothe T, Chintalapati S, Chintalapati VR	Int J Syst Evol Microbiol	10.1099/ijsem.0.000678	2015	*
Phylogeny	Amphibacillus indicireducens sp. nov., an alkaliphile that reduces an indigo dye.	Hirota K, Aino K, Nodasaka Y, Morita N, Yumoto I	Int J Syst Evol Microbiol	10.1099/ijs.0.037622-0	2012	*
Enzymology	Unusually stable NAD-specific glutamate dehydrogenase from the alkaliphile Amphibacillus xylanus.	Jahns T	Antonie Van Leeuwenhoek	10.1007/BF00393573	1996	*

References

#2759

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6626

#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 )

#23029

Youichi Niimura,Enki Koh,Fujitoshi Yanagida,Ken-Ichiro Suzuki,Kazuo Komagata,Michio Kozaki: Amphibacillus xylanus gen. nov., sp. nov., a Facultatively Anaerobic Sporeforming Xylan-Digesting Bacterium Which Lacks Cytochrome, Quinone, and Catalase. IJSEM 40: 297 - 301 1990 ( DOI 10.1099/00207713-40-3-297 )

#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) .

#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;

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#71054

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-ID9966.1 )

* These data were automatically processed and therefore are not curated

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Amphibacillus xylanus NBRC 15112 NBRC 15112

Amphibacillus xylanus NBRC 15112 NBRC 15112

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