Xenorhabdus cabanillasii (DSM 17905, CIP 109066, USTX62)

Name: Xenorhabdus cabanillasii (DSM 17905, CIP 109066, USTX62)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5201

Type strain

Strain Designation USTX62

Culture col. no. DSM 17905 CIP 109066 USTX62

NCBI tax ID(s) 351673

Special Collections DSMZ CIP

History <- P. Tailliez; USTX62 <- N. E. Boemare <- S. Pagès CIP <- 2005, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain USTX62

Links

Xenorhabdus cabanillasii USTX62 is a facultative anaerobe, Gram-negative, rod-shaped animal pathogen that was isolated from Steinernema riobrave.

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

Name and taxonomic classification

SI-ID 297365

CIP 109066,DSM 17905

@ref 20215

Last LPSN update 2026-02-09 11:18:54

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Morganellaceae

Genus Xenorhabdus

Species Xenorhabdus cabanillasii

Full scientific name Xenorhabdus cabanillasii Tailliez et al. 2006

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
117085	negative	rod-shaped
125438	negative		100
125439	negative		92.6

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7236	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
117085	CIP Medium 72		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7236	positive	growth	30

Physiology and metabolism

Oxygen tolerance

117085

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125438		93.042
125439		91.1

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
117085	17632 ChEBI	nitrate	-	reduction
117085	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
117085	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
117085	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
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
117085	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
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
117085	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
117085	ornithine decarboxylase	-	4.1.1.17
117085	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
117085	tryptophan deaminase	-
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
117085	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	+	-	+	-	-

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
7236	Steinernema riobrave	Steinernema riobrave	Texas	USA	USA	North America
117085	Animal, Nematode Steinernema riobrave SE62		Texas	United States of America	USA	North America	1999

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
7236		1	Risk group (German classification) According to TRBA 466
117085		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	ASM338666v1 assembly for Xenorhabdus cabanillasii DSM 17905	contig	GCA_003386665	351673.4	2778260932	351673	73.46

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7236	Xenorhabdus cabanillasii strain USTX62 16S ribosomal RNA gene, partial sequence	AY521244	1485		351673

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Xenorhabdus cabanillasii DSM 17905
NCBI: GCA_003386665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	91.10	no
125439	motility	BacteriaNetⓘ	yes	51.40	no
125439	gram_stain	BacteriaNetⓘ	negative	92.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	59.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Xenorhabdus cabanillasii strain DSM 17905
PATRIC: 351673.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	98.25	yes
125438	spore-forming	spore-formingⓘ	no	93.04	no
125438	aerobic	aerobicⓘ	no	67.95	no
125438	thermophilic	thermophileⓘ	no	99.00	yes
125438	flagellated	motile2+ⓘ	yes	75.62	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome announcement of Steinernema khuongi and its associated symbiont from Florida.	Baniya A, DiGennaro P.	G3 (Bethesda)	10.1093/g3journal/jkab053	2021
Enzymology	The Odilorhabdin Antibiotic Biosynthetic Cluster and Acetyltransferase Self-Resistance Locus Are Niche and Species Specific.	Lanois-Nouri A, Pantel L, Fu J, Houard J, Ogier JC, Polikanov YS, Racine E, Wang H, Gaudriault S, Givaudan A, Gualtieri M.	mBio	10.1128/mbio.02826-21	2022
Phylogeny	New insight into diversity in the genus Xenorhabdus, including the description of ten novel species.	Tailliez P, Pages S, Ginibre N, Boemare N	Int J Syst Evol Microbiol	10.1099/ijs.0.64287-0	2006

References

#7236	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17905
#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 )
#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) .
#68382	Automatically annotated from API zym .
#117085	Collection of Institut Pasteur ; Curators of the CIP; CIP 109066
#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 cabanillasii (DSM 17905, CIP 109066, USTX62)

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

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003386665

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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