Xenorhabdus miraniensis (DSM 17902, CIP 109069, Q1)

Name: Xenorhabdus miraniensis (DSM 17902, CIP 109069, Q1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5198

Type strain

Strain Designation Q1

Culture col. no. DSM 17902 CIP 109069 Q1

NCBI tax ID(s) 351674

Special Collections DSMZ CIP

History <- P. Tailliez; Q1 <- N. E. Boemare <- R. Akhurst

Links

Xenorhabdus miraniensis Q1 is an animal pathogen that was isolated from Steinernema species.

animal pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 297373

CIP 109069,DSM 17902

@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 miraniensis

Full scientific name Xenorhabdus miraniensis Tailliez et al. 2006

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	100

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7233	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
7233	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

Culture temp

@ref	Growth	Type	Temperature (°C)
7233	positive	growth	30
7233	positive	growth	28

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		96.2

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	+	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	+	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	+	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	+	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE

Metabolite production

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

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	+	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68369	cytochrome oxidase	-	1.9.3.1	from API 20NE
68369	gelatinase	+		from API 20NE
68369	urease	+	3.5.1.5	from API 20NE

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
7233	-	+	+	+	+	+	+	+	+	-	+	-	+	+	+	-	-	+	+	-	-

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
7233	Steinernema species	Steinernema	Queensland, Mirani	Australia	AUS	Australia and Oceania

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
7233		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
66792	ASM263261v1 assembly for Xenorhabdus miraniensis DSM 17902	scaffold	GCA_002632615	351674.5	2995678834	351674	33.09

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7233	Xenorhabdus miraniensis strain Q1 16S ribosomal RNA gene, partial sequence	DQ211713	1481		351674

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Xenorhabdus miraniensis DSM 17902
NCBI: GCA_002632615

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.20	no
125439	motility	BacteriaNetⓘ	no	62.30	no
125439	gram_stain	BacteriaNetⓘ	negative	87.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	75.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Xenorhabdus miraniensis DSM 17902
NCBI: GCA_002632615.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	98.06	no
125438	aerobic	aerobicⓘ	no	66.94	no
125438	spore-forming	spore-formingⓘ	no	89.92	no
125438	thermophilic	thermophileⓘ	no	99.50	yes
125438	flagellated	motile2+ⓘ	yes	75.58	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genomic Characterization of Probiotic Purple Nonsulfur Bacteria Cereibacter sphaeroides Strains S3W10 and SS15: Implications for Enhanced Shrimp Aquaculture.	Klaysubun C, Chaichana N, Suwannasin S, Singkhamanan K, Yaikhan T, Kantachote D, Pomwised R, Wonglapsuwan M, Surachat K.	Life (Basel)	10.3390/life14121691	2024
	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
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
Phylogeny	Description of Xenorhabdus khoisanae sp. nov., the symbiont of the entomopathogenic nematode Steinernema khoisanae.	Ferreira T, van Reenen CA, Endo A, Sproer C, Malan AP, Dicks LMT	Int J Syst Evol Microbiol	10.1099/ijs.0.049049-0	2013

References

#7233	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17902
#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) .
#68369	Automatically annotated from API 20NE .
#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 miraniensis (DSM 17902, CIP 109069, Q1)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002632615

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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