Xenorhabdus beddingii (DSM 4764, ATCC 49542, CCM 7079)

Name: Xenorhabdus beddingii (DSM 4764, ATCC 49542, CCM 7079)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5187

Status isotype of 5188

Type strain

Strain Designation Q 58, Q58

Culture col. no. DSM 4764 ATCC 49542 CCM 7079 Q 58 UQM 2871 2 more

NCBI tax ID(s) 40578

Special Collections DSMZ CIP

History DSMZ <- UQM CIP <- 2006, P. Tailliez, INRA, Montpellier, France: strain Q58 <- Boemare <- R. J. Akhurst

Links

Xenorhabdus beddingii Q 58 is a facultative anaerobe, Gram-negative, rod-shaped animal pathogen that was isolated from nematode Steinernema sp. M.

Gram-negative rod-shaped facultative anaerobe animal pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 42541

ATCC 49542,ACM 2871,DSM 4764,CCM 7079,CIP 109145

@ref 20215

Last LPSN update 2026-05-29 08:26:06

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Morganellaceae

Genus Xenorhabdus

Species Xenorhabdus beddingii

Full scientific name Xenorhabdus beddingii (Akhurst 1986) Akhurst and Boemare 1993

Synonyms (2)

Xenorhabdus nematophila subsp. beddingii
Xenorhabdus nematophilus subsp. beddingii

BacDive ID	Other strains from **Xenorhabdus beddingii** (1)	Type strain
5188	X. beddingii Q 58, DSM 4765, UQM 2872

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
116770	negative	rod-shaped
125438	negative			99.5

Colony morphology

116770

Hemolysis ability0

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
1759	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
1759	XENORHABDUS MEDIUM (DSMZ Medium 423)	Medium recipe at MediaDive	Name: XENORHABDUS MEDIUM (DSMZ Medium 423) Composition: Agar 15.0 g/l Peptone 10.0 g/l NaCl 5.0 g/l Yeast extract 5.0 g/l Distilled water
34356	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116770	CIP Medium 72	Medium recipe at CIP
116770	CIP Medium 669	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
1759	positive	growth	28
34356	positive	growth	30

Physiology and metabolism

Oxygen tolerance

116770

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125438		90.545
125439		99.005

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
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
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
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
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68369	5291 ChEBI	gelatin	+	hydrolysis	from API 20NE
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	+	builds acid from	from API 50CH acid
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68371	17754 ChEBI	glycerol	+	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
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
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
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
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
116770	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
116770	16301 ChEBI	nitrite	-	reduction
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
116770	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
116770	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
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
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
116770	catalase	-	1.11.1.6
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
68369	gelatinase	+		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
116770	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
116770	ornithine decarboxylase	-	4.1.1.17
116770	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
116770	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	+		from API zym

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
116770	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	+	+	+	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
1759	-	-	-	-	-	+	+	-	+	-	+	-	+	+	+	-	-	+/-	-	-	+/-

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
116770	not determinedn.d.	+	-	-	-	-	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	+	-	+/-	+/-	+/-	-	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Nematoda

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
1759	nematode Steinernema sp. M	Steinernema	Queensland	Australia	AUS	Australia and Oceania
116770	Animal, Nematode, Steinernema sp.	Steinernema sp.	Mackay	Australia	AUS	Australia and Oceania	1985

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
1759		1	Risk group (German classification) According to TRBA 466
116770		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	ASM212754v1 assembly for Xenorhabdus beddingii DSM 4764	scaffold	GCA_002127545	40578.4	2897667629	40578	32.18

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Xenorhabdus beddingii 16S ribosomal RNA gene, partial sequence	AY278675	1497	40578
20218	Xenorhabdus beddingii gene for 16S rRNA, partial sequence, strain: DSM 4764	D78006	1479	40578
20218	X.beddingii 16S rRNA gene (DSM 4764)	X82254	1497	40578

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM212754v1 assembly for Xenorhabdus beddingii DSM 4764
NCBI: GCA_002127545

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	72.17	no
125439	gram_stain	BacteriaNetⓘ	negative	82.38	no
125439	motility	BacteriaNetⓘ	no	72.69	no
125439	spore_formation	BacteriaNetⓘ	no	99.01	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Xenorhabdus beddingii DSM 4764
NCBI: GCA_002127545.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	99.00	yes
125438	aerobic	aerobicⓘ	no	69.70	yes
125438	spore-forming	spore-formingⓘ	no	90.55	no
125438	thermophilic	thermophileⓘ	no	98.63	yes
125438	flagellated	motile2+ⓘ	yes	75.13	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Pleiotropic role of PAX cyclolipopeptides in the Xenorhabdus bacterium mutualistically associated with entomopathogenic nematodes.	Claveyroles N, Lanois-Nouri A, El Fannassi I, Ogier J-C, Pages S, Chouchou A, Cazals G, Valette G, Carre-Mlouka A, Givaudan A.	Appl Environ Microbiol	10.1128/aem.00760-25	2025
	Antiprotozoal activity of different Xenorhabdus and Photorhabdus bacterial secondary metabolites and identification of bioactive compounds using the easyPACId approach.	Gulsen SH, Tileklioglu E, Bode E, Cimen H, Ertabaklar H, Ulug D, Ertug S, Wenski SL, Touray M, Hazir C, Bilecenoglu DK, Yildiz I, Bode HB, Hazir S.	Sci Rep	10.1038/s41598-022-13722-z	2022
Genetics	Genome announcement of Steinernema khuongi and its associated symbiont from Florida.	Baniya A, DiGennaro P.	G3 (Bethesda)	10.1093/g3journal/jkab053	2021
Metabolism	LuxS-dependent AI-2 production is not involved in global regulation of natural product biosynthesis in Photorhabdus and Xenorhabdus.	Heinrich AK, Hirschmann M, Neubacher N, Bode HB.	PeerJ	10.7717/peerj.3471	2017
Enzymology	Proteolytic enzyme production by strains of the insect pathogen xenorhabdus and characterization of an early-log-phase-secreted protease as a potential virulence factor.	Massaoud MK, Marokhazi J, Fodor A, Venekei I.	Appl Environ Microbiol	10.1128/aem.01567-10	2010
	The Xenorhabdus nematophila nilABC genes confer the ability of Xenorhabdus spp. to colonize Steinernema carpocapsae nematodes.	Cowles CE, Goodrich-Blair H.	J Bacteriol	10.1128/jb.00123-08	2008
Metabolism	The xnp1 P2-like tail synthesis gene cluster encodes xenorhabdicin and is required for interspecies competition.	Morales-Soto N, Forst SA.	J Bacteriol	10.1128/jb.00092-11	2011

References

#1759	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4764
#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 )
#34356	; 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) .
#68369	Automatically annotated from API 20NE .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#116770	Collection of Institut Pasteur ; Curators of the CIP; CIP 109145
#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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Xenorhabdus beddingii (DSM 4764, ATCC 49542, CCM 7079)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002127545

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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