Xylanimonas pachnodae (DSM 12657, JCM 13526, NBRC 107786)

Name: Xylanimonas pachnodae (DSM 12657, JCM 13526, NBRC 107786)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 12610

Type strain

Strain Designation VPCX2

Culture col. no. DSM 12657 JCM 13526 NBRC 107786 VPCX2 NCCB 100020 3 more

NCBI tax ID(s) 101489

Special Collections DSMZ JCM Wink compendium JMRC

History DSMZ <- A.E. Cazemier; VPCX2 JCM <-- DSM 12657 <-- A. E. Cazemier VPCX2.

Links

Xylanimonas pachnodae VPCX2 is a bacterium that was isolated from hindgut of Pachnoda marginata larvae.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 49336

DSM 12657,NCCB 100020,JCM 13526

@ref 20215

Last LPSN update 2026-05-29 08:27:50

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Promicromonosporaceae

Genus Xylanimonas

Species Xylanimonas pachnodae

Full scientific name Xylanimonas pachnodae (Cazemier et al. 2004) Heo et al. 2020

Synonyms (3)

Xylanimicrobium pachnodae
Promicromonospora pachnodae
"Cellulomonas pachnodae"

Morphology

Cell morphology

@ref	Confidence	Gram stain
125439	92.058
125439	99.303	positive
125438	96

Colony morphology

@ref	Colony color	Incubation period	Medium used
18502	Ivory (1014)	10-14 days	ISP 2
18502	Ivory (1014)	10-14 days	ISP 3
18502	Ivory (1014)	10-14 days	ISP 4
18502	Ivory (1014)	10-14 days	ISP 5
18502	Ivory (1014)	10-14 days	ISP 6
18502	Ivory (1014)	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
18502		ISP 2
18502		ISP 3
18502		ISP 4
18502		ISP 5
18502		ISP 6
18502		ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
4785	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
18502	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
18502	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:
18502	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
18502	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
18502	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
18502	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

Culture temp

@ref	Growth	Type	Temperature (°C)
4785	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.031

Murein

@ref	Murein short key	Type
4785	A11.48	A4alpha L-Lys-L-Ser-D-Glu

Observation

67770

Observationquinones: MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
18502	22599 ChEBI	arabinose	+
18502	62968 ChEBI	cellulose	+
68379	17634 ChEBI	D-glucose	+	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	+	fermentation	from API Coryne
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
18502	28757 ChEBI	fructose	+
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
18502	17234 ChEBI	glucose	+
68379	28087 ChEBI	glycogen	+	fermentation	from API Coryne
68379	17716 ChEBI	lactose	+	fermentation	from API Coryne
68379	17306 ChEBI	maltose	+	fermentation	from API Coryne
18502	29864 ChEBI	mannitol	+
18502	17268 ChEBI	myo-inositol	+
68379	17632 ChEBI	nitrate	+	reduction	from API Coryne
18502	16634 ChEBI	raffinose	+
18502	26546 ChEBI	rhamnose	+
18502	17992 ChEBI	sucrose	+
68379	17992 ChEBI	sucrose	+	fermentation	from API Coryne
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
18502	18222 ChEBI	xylose	+

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	-	3.1.3.1	from API zym
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
68382	beta-galactosidase	+	3.2.1.23	from API zym
68379	beta-galactosidase	+	3.2.1.23	from API Coryne
68382	beta-glucosidase	+	3.2.1.21	from API zym
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	+		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
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
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	+		from API zym

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
18502	+	-	-	-	-	+	+	+	+	-	+	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
18502	not determinedn.d.	-	+	+	-	+	+	-	-	-	+	-	+	+	-	+	+	+	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Arthropoda	#Insecta
#Host Body-Site	#Gastrointestinal tract	-

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent
4785	hindgut of Pachnoda marginata larvae	Pachnoda marginata	Netherlands	NLD	Europe
67770	Hindgut of larvae of the scarab beetle (Pachnoda marginata)	Pachnoda marginata

Taxonmaps

69479

Global distribution of 16S sequence AF105422 (>99% sequence identity) for Xylanimicrobium pachnodae from Microbeatlas

Aquatic Samples	29
Soil Samples	95
Animal Samples	29
Plant Samples	20
Total Samples	173

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18502	1	German classification According to TRBA 466
4785	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	ASM159214v1 assembly for Xylanimicrobium pachnodae JCM 13526 = NBRC 107786	contig	GCA_001592145	1305855.5	2731957681	1305855	36.17
66792	ASM131400v1 assembly for Xylanimicrobium pachnodae JCM 13526 = NBRC 107786	contig	GCA_001314005	1305855.6	2734481968	1305855	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4785	Promicromonospora pachnodae 16S ribosomal RNA gene, partial sequence	AF105422	1467		101489

GC content

@ref	GC-content (mol%)	Method
67770	71.9	genome sequence analysis
67770	70

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM159214v1 assembly for Xylanimicrobium pachnodae JCM 13526 = NBRC 107786
NCBI: GCA_001592145

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.03	no
125439	gram_stain	BacteriaNetⓘ	positive	99.30	no
125439	spore_formation	BacteriaNetⓘ	yes	54.66	no
125439	motility	BacteriaNetⓘ	no	92.06	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Xylanimicrobium pachnodae JCM 13526 = NBRC 107786
PATRIC: 1305855.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	82.25	no
125438	anaerobic	anaerobicⓘ	no	80.41	no
125438	spore-forming	spore-formingⓘ	no	84.08	no
125438	aerobic	aerobicⓘ	no	52.10	no
125438	thermophilic	thermophileⓘ	no	93.22	no
125438	flagellated	motile2+ⓘ	no	96.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Molecular and biochemical characterization of two xylanase-encoding genes from Cellulomonas pachnodae.	Cazemier AE, Verdoes JC, van Ooyen AJ, Op den Camp HJ.	Appl Environ Microbiol	10.1128/aem.65.9.4099-4107.1999	1999
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	Antribacter gilvus gen. nov., sp. nov., a new member of the family Promicromonosporaceae from a karstic cavern.	Zhang LY, Fang BZ, Jiao JY, Zhang XT, Liu L, Meng XL, Ming H, Nie GX, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003682	2019

References

#4785	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12657
#18502	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 )
#20216	Curators of the JMRC: Jena Microbial Resource Collection (JMRC):
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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 )

Content

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Xylanimonas pachnodae (DSM 12657, JCM 13526, NBRC 107786)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Murein

Observation

Metabolite utilization

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001592145

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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