Xylanimonas cellulosilytica (DSM 15894, CECT 5975, LMG 20990)

Name: Xylanimonas cellulosilytica (DSM 15894, CECT 5975, LMG 20990)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 12611

Type strain

Strain Designation XIL07

Culture col. no. DSM 15894 CECT 5975 LMG 20990 XIL07 NBRC 107835 3 more

NCBI tax ID(s) 446471 186189

Special Collections DSMZ JCM KCTC Wink compendium CIP

History <- D. Janssens, LMG; XIL07 <- E. Velázquez <- P. Rivas 2003, E. Velazquez, Salamanca, Spain: strain XIL07 CECT 5975 <-- E. Velázquez XIL07 <-- R. Rivas. CIP <- 2003, E. Velazquez, Salamanca, Spain: strain XIL07

Links

Xylanimonas cellulosilytica XIL07 is a facultative anaerobe, Gram-positive, oval-shaped bacterium that was isolated from decayed tree , sawdust.

Gram-positive oval-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 85151

LMG 20990,CECT 5975,DSM 15894,JCM 12276,KCTC 9989,CIP 108193,NBRC 107835

@ref 20215

Last LPSN update 2026-02-09 11:20:53

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Promicromonosporaceae

Genus Xylanimonas

Species Xylanimonas cellulosilytica

Full scientific name Xylanimonas cellulosilytica Rivas et al. 2003

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
117239	positive	oval-shaped
125439	positive		100
125438			96.5
125438	positive		92.478

Colony morphology

@ref	Colony color	Incubation period	Medium used
18398	Ivory (1014)	10-14 days	ISP 2
18398	Ivory (1014)	10-14 days	ISP 3
18398	Ivory (1014)	10-14 days	ISP 4
18398	Beige (1001)	10-14 days	ISP 5
18398	Ivory (1014)	10-14 days	ISP 6
18398	Beige (1001)	10-14 days	ISP 7
117239

Multicellular morphology

@ref	Forms multicellular complex	Medium name
18398		ISP 2
18398		ISP 3
18398		ISP 4
18398		ISP 5
18398		ISP 6
18398		ISP 7

Multimedia

@ref:	66793
multimedia content:	EM_DSM_15894_1.jpg
multimedia.multimedia content:	EM_DSM_15894_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6172	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18398	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18398	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18398	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18398	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18398	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18398	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
38260	MEDIUM 567 - for Xylanimonas cellulosilytica		Distilled water make up to (1000.000 ml);Agar (20.000 g);Yeast extract (3.000 g);Xylan (7.000 g)
117239	CIP Medium 567	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6172	positive	growth	28
18398	positive	optimum	28
38260	positive	growth	30
67770	positive	growth	28
117239	positive	growth	10-37
117239	negative	growth	41
117239	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
117239	facultative anaerobe
125439	obligate aerobe	98.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
117239	NaCl	positive	growth	0-4 %
117239	NaCl		growth	6 %
117239	NaCl		growth	8 %
117239	NaCl		growth	10 %

Murein

@ref	Murein short key	Type
6172	A11.37	A4alpha L-Lys-D-Ser-D-Asp

Observation

67770

Observationquinones: MK-9(H₄), MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
18398	22599 ChEBI	arabinose	-
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
18398	62968 ChEBI	cellulose	+
117239	16947 ChEBI	citrate	-	carbon source
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68379	17634 ChEBI	D-glucose	+	fermentation	from API Coryne
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68379	65327 ChEBI	D-xylose	+	fermentation	from API Coryne
68371	65327 ChEBI	D-xylose	+	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
117239	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
18398	28757 ChEBI	fructose	+
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
18398	17234 ChEBI	glucose	+
68379	28087 ChEBI	glycogen	+	fermentation	from API Coryne
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
117239	606565 ChEBI	hippurate	-	hydrolysis
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68379	17716 ChEBI	lactose	+	fermentation	from API Coryne
68371	17716 ChEBI	lactose	+	builds acid from	from API 50CH acid
68379	17306 ChEBI	maltose	+	fermentation	from API Coryne
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
18398	29864 ChEBI	mannitol	+
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
18398	17268 ChEBI	myo-inositol	-
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
68379	17632 ChEBI	nitrate	+	reduction	from API Coryne
117239	17632 ChEBI	nitrate	+	reduction
117239	17632 ChEBI	nitrate	+	respiration
117239	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
18398	16634 ChEBI	raffinose	-
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
18398	26546 ChEBI	rhamnose	+
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
18398	17992 ChEBI	sucrose	+
68379	17992 ChEBI	sucrose	+	fermentation	from API Coryne
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid
68379	16199 ChEBI	urea	+	hydrolysis	from API Coryne
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
18398	18222 ChEBI	xylose	-

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
117239	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
117239	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
117239	15688 ChEBI	acetoin	+
117239	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
117239	alcohol dehydrogenase	-	1.1.1.1
68379	alkaline phosphatase	-	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
117239	amylase	+
117239	beta-galactosidase	+	3.2.1.23
68379	beta-galactosidase	+	3.2.1.23	from API Coryne
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
117239	caseinase	-	3.4.21.50
117239	catalase	-	1.11.1.6
117239	cellulase	-	3.2.1.4
68382	cystine arylamidase	-	3.4.11.3	from API zym
117239	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
117239	gamma-glutamyltransferase	+	2.3.2.2
117239	gelatinase	+/-
68379	gelatinase	-		from API Coryne
117239	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
117239	lipase	-
68382	lipase (C 14)	-		from API zym
117239	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API Coryne
117239	ornithine decarboxylase	-	4.1.1.17
117239	oxidase	+
117239	phenylalanine ammonia-lyase	-	4.3.1.24
68379	pyrazinamidase	+	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	+	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
117239	tryptophan deaminase	-
117239	tween esterase	-
117239	urease	-	3.5.1.5
68379	urease	+	3.5.1.5	from API Coryne
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	formaldehyde oxidation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ethanol fermentation	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	kanosamine biosynthesis II	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	teichoic acid biosynthesis	100	1 of 1
66794	denitrification	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	aerobactin biosynthesis	100	1 of 1
66794	starch degradation	100	10 of 10
66794	adipate degradation	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	cellulose degradation	100	5 of 5
66794	chorismate metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	pentose phosphate pathway	81.82	9 of 11
66794	methylglyoxal degradation	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	lipoate biosynthesis	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	citric acid cycle	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	purine metabolism	74.47	70 of 94
66794	pyrimidine metabolism	73.33	33 of 45
66794	proline metabolism	72.73	8 of 11
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	sphingosine metabolism	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	oxidative phosphorylation	65.93	60 of 91
66794	alanine metabolism	65.52	19 of 29
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	metabolism of disaccharids	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	degradation of sugar alcohols	62.5	10 of 16
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	urea cycle	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of pentoses	60.71	17 of 28
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	lipid metabolism	58.06	18 of 31
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	degradation of hexoses	55.56	10 of 18
66794	nitrate assimilation	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	arginine metabolism	54.17	13 of 24
66794	tryptophan metabolism	52.63	20 of 38
66794	phenylmercury acetate degradation	50	1 of 2
66794	lysine metabolism	50	21 of 42
66794	pantothenate biosynthesis	50	3 of 6
66794	butanoate fermentation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	glutathione metabolism	50	7 of 14
66794	degradation of sugar acids	48	12 of 25
66794	lipid A biosynthesis	44.44	4 of 9
66794	propanol degradation	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	coenzyme M biosynthesis	40	4 of 10
66794	sulfate reduction	38.46	5 of 13
66794	vitamin B6 metabolism	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	cyanate degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenol degradation	30	6 of 20
66794	ascorbate metabolism	27.27	6 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	CMP-KDO biosynthesis	25	1 of 4
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	carotenoid biosynthesis	22.73	5 of 22
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	arachidonic acid metabolism	22.22	4 of 18
66794	chlorophyll metabolism	22.22	4 of 18

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
18398	+	+	+	-	-	+	+	+	+	+	-	not determinedn.d.	+	-	+	-	+	+	+	+	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
18398	not determinedn.d.	-	+	+	-	+	-	-	-	-	-	-	+	+	+	+	+	+	-	-
117239	-	+	+	+	-	+	-	-	-	-	+	+	+	-	-	+	-	+	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
117239	not determinedn.d.	+/-	-	-	+	-	+	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	-	+/-	-	+	+/-	+	+	+	-	+	+	-	-	-	+	+	-	+	+	+/-	-	-	-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
117239	not determinedn.d.	+	+	+	+	+	-	-	-	-	+	+	+	-	-	-	-	+	-	+	-	+	+	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Decomposing plant
#Host	#Plants	#Tree

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
6172	decayed tree (Ulmus nigra), sawdust	Ulmus nigra	Salamanca	Spain	ESP	Europe
67770	Decayed tree (Ulmus nigra)	Ulmus nigra	Salamanca	Spain	ESP	Europe
117239	Sawdust of Ulmus nigra			Spain	ESP	Europe	2001

Taxonmaps

69479

Global distribution of 16S sequence AF403541 (>99% sequence identity) for Xylanimonas cellulosilytica subclade from Microbeatlas

Aquatic Samples	14
Soil Samples	73
Animal Samples	30
Plant Samples	20
Total Samples	137

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18398	1	German classification According to TRBA 466
6172	1	Risk group (German classification) According to TRBA 466
117239	1	Risk group (French 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	ASM2496v1 assembly for Xylanimonas cellulosilytica DSM 15894	complete	GCA_000024965	446471.6	646311968	446471	98.93

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6172	Xylanomonas cellulosilytica 16S ribosomal RNA gene, partial sequence	AF403541	1518		446471

GC content

@ref	GC-content (mol%)	Method
6172	73
67770	73	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: Xylanimonas cellulosilytica DSM 15894
PATRIC: 446471.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	74.10	no
125439	motility	BacteriaNetⓘ	no	87.90	no
125439	gram_stain	BacteriaNetⓘ	positive	100.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Xylanimonas cellulosilytica DSM 15894 DSM 15894
NCBI: GCA_000024965.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.48	no
125438	anaerobic	anaerobicⓘ	no	94.70	no
125438	aerobic	aerobicⓘ	yes	67.87	yes
125438	spore-forming	spore-formingⓘ	no	61.73	no
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	96.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Disseminated Scytalidium philadelphianum infection in a Belgian Malinois.	Ringhofer JD, HIrsch EM, Michalak SR, Wiederhold N, Canete-Gibas C, Dear JD.	Med Mycol Case Rep	10.1016/j.mmcr.2025.100692	2025
	Draft Genome Sequence of Scytalidium lignicola DSM 105466, a Ubiquitous Saprotrophic Fungus.	Buttner E, Gebauer AM, Hofrichter M, Liers C, Kellner H.	Microbiol Resour Announc	10.1128/mra.01208-18	2018
Genetics	(Meta)genomic insights into the pathogenome of Cellulosimicrobium cellulans.	Sharma A, Gilbert JA, Lal R.	Sci Rep	10.1038/srep25527	2016
	Proteomic Analysis of the Xanthan-Degrading Pathway of Microbacterium sp. XT11.	Sun Z, Liu H, Wang X, Yang F, Li X.	ACS Omega	10.1021/acsomega.9b02313	2019
	Analysis of EAWAG-BBD pathway prediction system for the identification of malathion degrading microbes.	Sivakumar S, Anitha P, Ramesh B, Suresh G.	Bioinformation	10.6026/97320630013073	2017
Metabolism	Genomics of aerobic cellulose utilization systems in actinobacteria.	Anderson I, Abt B, Lykidis A, Klenk HP, Kyrpides N, Ivanova N.	PLoS One	10.1371/journal.pone.0039331	2012
Enzymology	Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria.	Selengut JD, Haft DH.	J Bacteriol	10.1128/jb.00425-10	2010
	De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes.	Weimann A, Trukhina Y, Pope PB, Konietzny SG, McHardy AC.	Biotechnol Biofuels	10.1186/1754-6834-6-24	2013
Metabolism	Deletion of a fur-like gene affects iron homeostasis and magnetosome formation in Magnetospirillum gryphiswaldense.	Uebe R, Voigt B, Schweder T, Albrecht D, Katzmann E, Lang C, Bottger L, Matzanke B, Schuler D.	J Bacteriol	10.1128/jb.00319-10	2010
Enzymology	Evolution of DNA ligases of nucleo-cytoplasmic large DNA viruses of eukaryotes: a case of hidden complexity.	Yutin N, Koonin EV.	Biol Direct	10.1186/1745-6150-4-51	2009
Metabolism	Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: implications for pathogenesis, stress responses, and evolution.	Ramage HR, Connolly LE, Cox JS.	PLoS Genet	10.1371/journal.pgen.1000767	2009
	Genomic sequencing of single microbial cells from environmental samples.	Ishoey T, Woyke T, Stepanauskas R, Novotny M, Lasken RS.	Curr Opin Microbiol	10.1016/j.mib.2008.05.006	2008
Genetics	Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.	Ricaldi JN, Fouts DE, Selengut JD, Harkins DM, Patra KP, Moreno A, Lehmann JS, Purushe J, Sanka R, Torres M, Webster NJ, Vinetz JM, Matthias MA.	PLoS Negl Trop Dis	10.1371/journal.pntd.0001853	2012
	Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
Phylogeny	Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria.	Gao B, Gupta RS.	Microbiol Mol Biol Rev	10.1128/mmbr.05011-11	2012
Genetics	Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences.	Chandra G, Chater KF.	FEMS Microbiol Rev	10.1111/1574-6976.12047	2014
Genetics	Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07).	Foster B, Pukall R, Abt B, Nolan M, Glavina Del Rio T, Chen F, Lucas S, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, Detter JC, Bruce D, Goodwin L, Ivanova N, Mavromatis K, Pati A, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A	Stand Genomic Sci	10.4056/sigs.571102	2010
Phylogeny	Reclassification of Cellulosimicrobium variabile Bakalidou et al. 2002 as Isoptericola variabilis gen. nov., comb. nov.	Stackebrandt E, Schumann P, Cui XL	Int J Syst Evol Microbiol	10.1099/ijs.0.02878-0	2004
Phylogeny	Lactococcus protaetiae sp. nov. and Xylanimonas protaetiae sp. nov., isolated from gut of larvae of Protaetia brevitarsis seulensis.	Heo J, Kim SJ, Kim MA, Tamura T, Saitou S, Hamada M, Kim JS, Hong SB, Kwon SW	Antonie Van Leeuwenhoek	10.1007/s10482-020-01413-6	2020
Phylogeny	Xylanimonas allomyrinae sp. nov. isolated from the gut of larva of Allomyrina dichotoma, reclassification of Xylanibacterium ulmi as Xylanimonas ulmi comb. nov. and Xylanimicrobium pachnodae as Xylanimonas pachnodae comb. nov., and emendation of the genus Xylanimonas.	Heo J, Cho H, Hamada M, Kim JS, Hong SB, Kim SJ, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijsem.0.004001	2020
Phylogeny	Xylanimonas cellulosilytica gen. nov., sp. nov., a xylanolytic bacterium isolated from a decayed tree (Ulmus nigra).	Rivas R, Sanchez M, Trujillo ME, Zurdo-Pineiro JL, Mateos PF, Martinez-Molina E, Velazquez E	Int J Syst Evol Microbiol	10.1099/ijs.0.02207-0	2003

References

#6172	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15894
#18398	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )
#38260	; Curators of the CIP;
#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) .
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#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;
#68371	Automatically annotated from API 50CH acid .
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#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 .
#117239	Collection of Institut Pasteur ; Curators of the CIP; CIP 108193
#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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Xylanimonas cellulosilytica (DSM 15894, CECT 5975, LMG 20990)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Murein

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API coryne

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000024965

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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