Amphibacillus xylanus (DSM 6626, ATCC 51415, IFO 15112)

Name: Amphibacillus xylanus (DSM 6626, ATCC 51415, IFO 15112)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1403

Type strain

Strain Designation Ep01

Culture col. no. DSM 6626 ATCC 51415 IFO 15112 JCM 7361 NBRC 15112 2 more

NCBI tax ID(s) 698758 1449

Special Collections DSMZ JCM Literature strains

History <- JCM <- Y. Niimura, Tokyo Univ. of Agriculture (Ep01) Y. Niimura Ep01.

Links

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.

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

Name and taxonomic classification

SI-ID 9966

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

@ref 20215

Last LPSN update 2026-02-09 11:18:06

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Amphibacillus

Species Amphibacillus xylanus

Full scientific name Amphibacillus xylanus Niimura et al. 1990

BacDive ID	Other strains from **Amphibacillus xylanus** (2)	Type strain
165528	A. xylanus JCM 7362
165529	A. xylanus JCM 7363

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
23029	positive	0.9-1.9 µm	0.3-0.5 µm	rod-shaped

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
23029	white	circular	1 day	glucose agar

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2759	AMPHIBACILLUS MEDIUM (DSMZ Medium 529)		Medium recipe at MediaDive	Name: AMPHIBACILLUS MEDIUM (DSMZ Medium 529) Composition: Agar 15.0 g/l Glucose 10.0 g/l Na2CO3 anhydrous 5.3 g/l NaHCO3 4.2 g/l Yeast extract 3.0 g/l NH4NO3 2.0 g/l K2HPO4 1.0 g/l Polypeptone 0.3 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.1 g/l MnSO4 x 7 H2O 0.005 g/l FeSO4 x 7 H2O 0.005 g/l Distilled water
23029	glucose agar

Culture temp

@ref	Growth	Type	Temperature (°C)
2759	positive	growth	37
23029	positive	growth	25.0-44.0
23029	negative	growth	50.0
67770	positive	growth	39

Culture pH

@ref	Ability	Type	PH	PH range
23029	positive	growth	8.0-10.0	alkaliphile
23029		growth	7.0

Physiology and metabolism

Oxygen tolerance

23029

Oxygen tolerancefacultative anaerobe

Nutrition type

23029

Typechemoorganotroph

Spore formation

@ref	Spore description	Type of spore	Spore formation
23029	oval,heat-resistant	endospore

Halophily

@ref	Salt	Growth	Tested relation	Concentration
23029	NaCl	positive	growth	3.0 %
23029	NaCl		growth	6.0 %

Murein

@ref	Murein short key	Type
23029	A31	A1gamma m-Dpm-direct

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23029	16947 ChEBI	citrate	-	carbon source
23029	16024 ChEBI	D-mannose	+	carbon source
23029	5291 ChEBI	gelatin	-	hydrolysis
23029	15443 ChEBI	inulin	-	carbon source
23029	28053 ChEBI	melibiose	+	carbon source
23029	17632 ChEBI	nitrate	-	reduction
23029	37166 ChEBI	xylan	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
23029	16136 ChEBI	hydrogen sulfide
23029	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Citrate test
23029	16947 ChEBI	citrate	-

Enzymes

@ref	Value	Activity	Ec
23029	catalase	-	1.11.1.6
23029	cytochrome oxidase	-	1.9.3.1

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Composting
#Engineered	#Waste	#Solid plant waste
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Condition	#Alkaline	-

Isolation

@ref	Sample type
2759	alcaline compost of manure with grass and rice straw
67770	Alkaliphilic compost

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2759	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
66792	ASM30716v1 assembly for Amphibacillus xylanus NBRC 15112	complete	GCA_000307165	698758.3	2524023219	698758	90.99

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Amphibacillus xylanus 16S rRNA gene, strain DSM 6626	AJ496807	1505	698758
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	698758
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	698758
20218	Amphibacillus xylanus DNA for 16S ribosomal RNA	D82065	1450	698758
20218	Amphibacillus xylanus gene for 16S rRNA, partial sequence, strain: NBRC 15112	AB680770	1495	1449

GC content

@ref	GC-content (mol%)	Method
23029	36
67770	36	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Amphibacillus xylanus NBRC 15112
NCBI: GCA_000307165

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	62.10	no
125439	motility	BacteriaNetⓘ	yes	63.50	no
125439	gram_stain	BacteriaNetⓘ	variable	67.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	88.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Amphibacillus xylanus NBRC 15112 NBRC 15112
NCBI: GCA_000307165.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	84.58	yes
125438	anaerobic	anaerobicⓘ	no	86.46	yes
125438	aerobic	aerobicⓘ	no	93.51	yes
125438	spore-forming	spore-formingⓘ	yes	64.61	no
125438	thermophilic	thermophileⓘ	no	85.34	no
125438	flagellated	motile2+ⓘ	yes	75.28	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations.	Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SV.	OMICS	10.1089/omi.2009.0100	2010
	Nucleotide sequence of 5S ribosomal RNAs of 'Amphibacillus xylanus' and Clostridium carnis.	Yanagida F, Niimura Y, Koh E, Suzuki K, Kozaki M, Komagata K.	Nucleic Acids Res	10.1093/nar/17.1.443	1989
	Compilation of 5S rRNA and 5S rRNA gene sequences.	Specht T, Wolters J, Erdmann VA.	Nucleic Acids Res	10.1093/nar/18.suppl.2215	1990
Genetics	Identification of Genome Sequences of Polyphosphate-Accumulating Organisms by Machine Learning.	Liu B, Nan J, Zu X, Zhang X, Xiao Q.	Front Cell Dev Biol	10.3389/fcell.2020.626221	2020
	Functional exploration of the glycoside hydrolase family GH113.	Couturier M, Touvrey-Loiodice M, Terrapon N, Drula E, Buon L, Chirat C, Henrissat B, Helbert W.	PLoS One	10.1371/journal.pone.0267509	2022
Enzymology	Intracellular free flavin and its associated enzymes participate in oxygen and iron metabolism in Amphibacillus xylanus lacking a respiratory chain.	Kimata S, Mochizuki D, Satoh J, Kitano K, Kanesaki Y, Takeda K, Abe A, Kawasaki S, Niimura Y.	FEBS Open Bio	10.1002/2211-5463.12425	2018
Enzymology	Structural insights into the catalytic mechanism of a novel glycoside hydrolase family 113 beta-1,4-mannanase from Amphibacillus xylanus.	You X, Qin Z, Yan Q, Yang S, Li Y, Jiang Z.	J Biol Chem	10.1074/jbc.ra118.002363	2018
Genetics	Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes.	Maus I, Bremges A, Stolze Y, Hahnke S, Cibis KG, Koeck DE, Kim YS, Kreubel J, Hassa J, Wibberg D, Weimann A, Off S, Stantscheff R, Zverlov VV, Schwarz WH, Konig H, Liebl W, Scherer P, McHardy AC, Sczyrba A, Klocke M, Puhler A, Schluter A.	Biotechnol Biofuels	10.1186/s13068-017-0947-1	2017
Genetics	Metagenomic analysis of soybean endosphere microbiome to reveal signatures of microbes for health and disease.	Chouhan U, Gamad U, Choudhari JK.	J Genet Eng Biotechnol	10.1186/s43141-023-00535-4	2023
	Draft Genome Sequence of Amphibacillus jilinensis Y1(T), a Facultatively Anaerobic, Alkaliphilic and Halotolerant Bacterium.	Cheng H, Fang MX, Jiang XW, Wu M, Zhu XF, Zheng G, Yang ZJ.	Stand Genomic Sci	10.4056/sigs.4107829	2013
Metabolism	A noncellulosomal mannanase26E contains a CBM59 in Clostridium cellulovorans.	Yamamoto K, Tamaru Y.	Biomed Res Int	10.1155/2014/438787	2014
	An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding.	Drory Retwitzer M, Kifer I, Sengupta S, Yakhini Z, Barash D.	PLoS One	10.1371/journal.pone.0134262	2015
Metabolism	Molecular cloning and sequence analysis of the gene encoding the H2O2-forming NADH oxidase from Streptococcus mutans.	Higuchi M, Shimada M, Matsumoto J, Yamamoto Y, Rhaman A, Kamio Y.	Biosci Biotechnol Biochem	10.1271/bbb.58.1603	1994
Metabolism	Hydrogen peroxide-forming NADH oxidase belonging to the peroxiredoxin oxidoreductase family: existence and physiological role in bacteria.	Nishiyama Y, Massey V, Takeda K, Kawasaki S, Sato J, Watanabe T, Niimura Y.	J Bacteriol	10.1128/jb.183.8.2431-2438.2001	2001
	Dissemination of 6S RNA among bacteria.	Wehner S, Damm K, Hartmann RK, Marz M.	RNA Biol	10.4161/rna.29894	2014
	Analysis of anoxybacillus genomes from the aspects of lifestyle adaptations, prophage diversity, and carbohydrate metabolism.	Goh KM, Gan HM, Chan KG, Chan GF, Shahar S, Chong CS, Kahar UM, Chai KP.	PLoS One	10.1371/journal.pone.0090549	2014
Metabolism	A flavoprotein functional as NADH oxidase from Amphibacillus xylanus Ep01: purification and characterization of the enzyme and structural analysis of its gene.	Niimura Y, Ohnishi K, Yarita Y, Hidaka M, Masaki H, Uchimura T, Suzuki H, Kozaki M, Uozumi T.	J Bacteriol	10.1128/jb.175.24.7945-7950.1993	1993
Enzymology	Unusually stable NAD-specific glutamate dehydrogenase from the alkaliphile Amphibacillus xylanus.	Jahns T	Antonie Van Leeuwenhoek	10.1007/BF00393573	1996
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

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;
#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 xylanus (DSM 6626, ATCC 51415, IFO 15112)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Nutrition type

Spore formation

Halophily

Murein

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000307165

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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