Name: Xenorhabdus ishibashii GDh7
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 23011

Type strain:

Species: Xenorhabdus ishibashii

Strain Designation: GDh7

Culture col. no.: DSM 22670, CGMCC 1.9166

Strain history: <- L. Qiu, State Key Lab. for Biocontrol, Sun Yat-sen Univ., Guangzhou, People's Republic of China; GDh7

NCBI tax ID(s): 1034471 (species)

SI-ID 388284

DSM 22670, CGMCC 1.9166, LMG 28560

Special Collections

Other strains from Xenorhabdus ishibashii

Section

Xenorhabdus ishibashii GDh7 is a facultative anaerobe, Gram-negative, motile animal pathogen that was isolated from infective nematode juveniles of Steinernema aciari.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Morganellaceae*
	Genus	*Xenorhabdus*
	Species	**Xenorhabdus ishibashii**
	Full Scientific Name (LPSN)	Xenorhabdus ishibashii Kuwata et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30650]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #30650]	Cell length	3.1 µm

[Ref.: #30650]	Cell width	0.75 µm

[Ref.: #30650]	Cell shape	rod-shaped

[Ref.: #30650]	Motility	yes

[Ref.: #30650]

Pigment production

yes

Multimedia content

[Ref.: #19311]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19311]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #19311]

Culture medium growth

[Ref.: #19311]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19311]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #19311]			growth	28 °C
[Ref.: #30650]			growth	37-42 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30650]

Oxygen tolerance

facultative anaerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %91.282
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

[Ref.: #30650]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30650]	acetate ChEBI	+	carbon source
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68368]	amygdalin ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	+	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68368]	D-mannitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30650]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #30650]	ethanol ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE, API 20E
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #30650]	glucosamine ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68368]	L-arabinose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	L-rhamnose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	lysine ChEBI	+	degradation	* from API 20E
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #30650]	malonate ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68368]	melibiose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68368]	ornithine ChEBI	+	degradation	* from API 20E
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	sucrose ChEBI	-	fermentation	* from API 20E
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE, API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #68368]	acetoin ChEBI	yes	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68369]	indole ChEBI	no	* from API 20NE, API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	+		* from API 20E
[Ref.: #68369]		indole ChEBI		-	* from API 20NE, API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68368]	arginine dihydrolase	+	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	-	3.2.1.23	* from API 20E
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #68369]	cytochrome oxidase	-	1.9.3.1	* from API 20NE, API 20E
[Ref.: #30650]	gelatinase	+
[Ref.: #68369]	gelatinase	+		* from API 20NE, API 20E
[Ref.: #68368]	lysine decarboxylase	+	4.1.1.18	* from API 20E
[Ref.: #68368]	ornithine decarboxylase	+	4.1.1.17	* from API 20E
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #19311]	17707	-	+	+	+	+	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #19311]	24547	-	-	-	+	+	+	+	-	+	-	+	-	+	+	+	-	-	+	+	-	-
[Ref.: #19311]	23319	-	-	+	-	-	+	+	-	+	-	+	-	+	+	+	-	-	+	+	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #19311]	Sample type/isolated from	infective nematode juveniles of Steinernema aciari
[Ref.: #19311]	Host species	Steinernema aciari
[Ref.: #19311]	Geographic location (country and/or sea, region)	Guangdong Province
[Ref.: #19311]	Country	China
[Ref.: #19311]	Country ISO 3 Code	CHN
[Ref.: #19311]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Infection	#Disease	-
#Host	#Invertebrates (Other)	#Nematoda

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #19311]	Pathogenicity (animal)	yes
[Ref.: #19311]	Biosafety level	1	Risk group (German classification) According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #19311]	Xenorhabdus ishibashii strain GDh7 16S ribosomal RNA gene, partial sequence	GQ149086	1480	GenBank ENA	1034471 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Xenorhabdus ishibashii DSM 22670	GCA_002632755	scaffold	GenBank ENA	1034471 tax ID	*
[Ref.: #66792]	Xenorhabdus ishibashii strain DSM 22670	1034471.3	wgs	PATRIC	1034471 tax ID	*
[Ref.: #66792]	Xenorhabdus ishibashii DSM 22670	2839585306	draft	JGI IMG/M	1034471 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Xenorhabdus ishibashii DSM 22670 NCBI: GCA_002632755.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Xenorhabdus ishibashii DSM 22670 NCBI: GCA_002632755.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	100	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.635	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	67.78	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	91.282	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	99	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	77.031	no

Availability in culture collections External links

[Ref.: #19311]

Culture collection no.

DSM 22670, CGMCC 1.9166

[Ref.: #87251]

SI-ID 388284

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Xenorhabdus ishibashii sp. nov., isolated from the entomopathogenic nematode Steinernema aciari.	Kuwata R, Qiu LH, Wang W, Harada Y, Yoshida M, Kondo E, Yoshiga T	Int J Syst Evol Microbiol	10.1099/ijs.0.041145-0	2012	*

References

#19311

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22670

#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 )

#30650

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26981 (see below)

#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) .

#68368

Automatically annotated from API 20E .

#68369

Automatically annotated from API 20NE .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#87251

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID388284.1 )

#26981

IJSEM 1690 2013 ( DOI 10.1099/ijs.0.041145-0 , PubMed 22922533 )

* These data were automatically processed and therefore are not curated

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Xenorhabdus ishibashii DSM 22670

Xenorhabdus ishibashii DSM 22670

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