Name: Xenorhabdus thuongxuanensis 30TX1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 140466

Type strain:

Species: Xenorhabdus thuongxuanensis

Strain Designation: 30TX1

Culture col. no.: CCM 8727, LMG 29916, DSM 104078, CIP 111194

Strain history: CIP <- 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain 30TX1

NCBI tax ID(s): 1873484 (species)

SI-ID 407361

DSM 104078

Special Collections

Section

When using BacDive for research please cite our paper

Xenorhabdus thuongxuanensis 30TX1 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from nematodes from soil samples from primary forest habitats.

colony-forming
Gram-negative
motile
rod-shaped
aerobe
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Morganellaceae*
	Genus	*Xenorhabdus*
	Species	**Xenorhabdus thuongxuanensis**
	Full Scientific Name (LPSN)	Xenorhabdus thuongxuanensis Kämpfer et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43220]	Gram stain	negative
[Ref.: #123536]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %96.9
[Ref.: #125438]	Gram stain	negative Confidence in %100

[Ref.: #43220]	Cell length	2 µm

[Ref.: #43220]	Cell width	1 µm

[Ref.: #43220]	Cell shape	rod-shaped
[Ref.: #123536]	Cell shape	rod-shaped

[Ref.: #43220]	Motility	yes
[Ref.: #123536]	Motility	yes

[Ref.: #43220]	Colony size	2 mm
[Ref.: #43220]	Colony color	yellow
[Ref.: #43220]	Colony shape	circular
[Ref.: #43220]	Cultivation medium used	tryptic soy agar (TSA)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #68997]

Culture medium

REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b)

[Ref.: #68997]

Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

[Ref.: #43220]

Culture medium

tryptic soy agar (TSA)

[Ref.: #43220]

Culture medium growth

[Ref.: #43220]

Culture medium

nutritient agar (NA)

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Culture medium growth

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Culture medium

brain heart infusion agar

[Ref.: #43220]

Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #43220]

Culture medium growth

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Culture medium

MacConkey agar

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Culture medium growth

[Ref.: #123536]

Culture medium

CIP Medium 29

[Ref.: #123536]

Culture medium growth

[Ref.: #123536]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #43220]	negative	growth	39 °C
[Ref.: #43220]		growth	10-37 °C
[Ref.: #68997]		growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43220]

Oxygen tolerance

aerobe

[Ref.: #43220]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %97.6
[Ref.: #125438]	Ability of spore formation	no Confidence in %91.306

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43220]	2-oxoglutarate ChEBI	-	carbon source
[Ref.: #43220]	3-hydroxybenzoate ChEBI	-	carbon source
[Ref.: #43220]	3-hydroxybutyrate ChEBI	-	carbon source
[Ref.: #43220]	4-hydroxybenzoate ChEBI	-	carbon source
[Ref.: #43220]	acetate ChEBI	+	carbon source
[Ref.: #43220]	adipate ChEBI	-	carbon source
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #43220]	arbutin ChEBI	-	carbon source
[Ref.: #68369]	arginine ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #43220]	azelaate ChEBI	-	carbon source
[Ref.: #43220]	beta-alanine ChEBI	-	carbon source
[Ref.: #43220]	cellobiose ChEBI	-	builds acid from
[Ref.: #43220]	cellobiose ChEBI	-	carbon source
[Ref.: #43220]	cis-aconitate ChEBI	-	carbon source
[Ref.: #43220]	citrate ChEBI	-	carbon source
[Ref.: #43220]	D-arabitol ChEBI	-	builds acid from
[Ref.: #43220]	D-fructose ChEBI	+	carbon source
[Ref.: #43220]	D-galactose ChEBI	-	carbon source
[Ref.: #43220]	D-glucose ChEBI	+	builds acid from
[Ref.: #43220]	D-glucose ChEBI	+	carbon source
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	fermentation	* from API 20NE
[Ref.: #43220]	D-mannitol ChEBI	-	builds acid from
[Ref.: #43220]	D-mannitol ChEBI	-	carbon source
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #43220]	D-mannose ChEBI	-	builds acid from
[Ref.: #43220]	D-mannose ChEBI	+	carbon source
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #43220]	D-ribose ChEBI	-	carbon source
[Ref.: #43220]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #43220]	D-sorbitol ChEBI	-	carbon source
[Ref.: #43220]	D-xylose ChEBI	-	builds acid from
[Ref.: #43220]	D-xylose ChEBI	-	carbon source
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #43220]	erythritol ChEBI	-	builds acid from
[Ref.: #43220]	esculin ChEBI	-	hydrolysis
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #43220]	fumarate ChEBI	+	carbon source
[Ref.: #43220]	galactitol ChEBI	-	builds acid from
[Ref.: #43220]	gamma-aminobutyric acid ChEBI	-	carbon source
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #43220]	gluconate ChEBI	+	carbon source
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #43220]	glutarate ChEBI	-	carbon source
[Ref.: #43220]	glycerol ChEBI	-	carbon source
[Ref.: #43220]	itaconate ChEBI	-	carbon source
[Ref.: #43220]	L-alanine ChEBI	-	carbon source
[Ref.: #43220]	L-arabinose ChEBI	-	builds acid from
[Ref.: #43220]	L-arabinose ChEBI	-	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #43220]	L-aspartate ChEBI	-	carbon source
[Ref.: #43220]	L-histidine ChEBI	+	carbon source
[Ref.: #43220]	L-leucine ChEBI	-	carbon source
[Ref.: #43220]	L-ornithine ChEBI	-	carbon source
[Ref.: #43220]	L-phenylalanine ChEBI	-	carbon source
[Ref.: #43220]	L-proline ChEBI	-	carbon source
[Ref.: #43220]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #43220]	L-rhamnose ChEBI	-	carbon source
[Ref.: #43220]	L-serine ChEBI	-	carbon source
[Ref.: #43220]	L-tryptophan ChEBI	-	carbon source
[Ref.: #43220]	lactate ChEBI	+	carbon source
[Ref.: #43220]	lactose ChEBI	-	builds acid from
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #43220]	maltitol ChEBI	-	carbon source
[Ref.: #43220]	maltose ChEBI	-	builds acid from
[Ref.: #43220]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #43220]	melibiose ChEBI	-	builds acid from
[Ref.: #43220]	melibiose ChEBI	-	carbon source
[Ref.: #43220]	mesaconate ChEBI	-	carbon source
[Ref.: #43220]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #43220]	myo-inositol ChEBI	-	builds acid from
[Ref.: #43220]	myo-inositol ChEBI	-	carbon source
[Ref.: #43220]	N-acetylgalactosamine ChEBI	-	carbon source
[Ref.: #43220]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #43220]	phenylacetate ChEBI	-	carbon source
[Ref.: #43220]	propionate ChEBI	-	carbon source
[Ref.: #43220]	putrescine ChEBI	-	carbon source
[Ref.: #43220]	pyruvate ChEBI	+	carbon source
[Ref.: #43220]	raffinose ChEBI	-	builds acid from
[Ref.: #43220]	ribitol ChEBI	-	builds acid from
[Ref.: #43220]	ribitol ChEBI	-	carbon source
[Ref.: #43220]	salicin ChEBI	-	builds acid from
[Ref.: #43220]	salicin ChEBI	-	carbon source
[Ref.: #43220]	suberic acid ChEBI	-	carbon source
[Ref.: #43220]	sucrose ChEBI	-	builds acid from
[Ref.: #43220]	sucrose ChEBI	-	carbon source
[Ref.: #43220]	trans-aconitate ChEBI	-	carbon source
[Ref.: #43220]	trehalose ChEBI	-	builds acid from
[Ref.: #43220]	trehalose ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	+	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43220]	hydrogen sulfide ChEBI	no
[Ref.: #43220]	indole ChEBI	no
[Ref.: #68369]	indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test	Citrate test
[Ref.: #43220]		citrate ChEBI		-
[Ref.: #68369]		indole ChEBI	-		* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #43220]	arginine dihydrolase	-	3.5.3.6
[Ref.: #68369]	arginine dihydrolase	+	3.5.3.6	* from API 20NE
[Ref.: #43220]	beta-galactosidase	-	3.2.1.23
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #43220]	catalase	-	1.11.1.6
[Ref.: #43220]	cytochrome oxidase	-	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	-	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #43220]	lysine decarboxylase	-	4.1.1.18
[Ref.: #43220]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #43220]	urease	-	3.5.1.5
[Ref.: #68369]	urease	+	3.5.1.5	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43220]

Fatty acid	Percentage	ECL
C16:0	23.5
C14:0	14.5
C18:1ω7c	13.9
C16:1ω7c / C15:0 iso 2OH	12.3
C17:0 cyclo	11.6
C16:1 iso I / C14:0 3OH	10.6
C19:0 cyclo ω8c	4.4
C15:0	1.9
C12:0 3OH	1.5
C15:0 iso 3OH	1.3
C12:0	1.3
C15:0 iso	1.2
Unknown	1.1	14502
C16:0 3OH	0.9

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.: #43220]	27205	-	-	+	+	+	-	+	-	+	-	+	-	+	+	+	-	-	+	+	-	-

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

[Ref.: #43220]	Sample type/isolated from	nematodes from soil samples from primary forest habitats
[Ref.: #43220]	Geographic location (country and/or sea, region)	Thuong Xuan and EaPok
[Ref.: #43220]	Country	Vietnam
[Ref.: #43220]	Country ISO 3 Code	VNM
[Ref.: #43220]	Continent	Asia

[Ref.: #123536]	Sample type/isolated from	Animal, Steinernema sangi
[Ref.: #123536]	Geographic location (country and/or sea, region)	Thuong Xuan, Thanh Hoa
[Ref.: #123536]	Country	Vietnam
[Ref.: #123536]	Country ISO 3 Code	VNM
[Ref.: #123536]	Continent	Asia
[Ref.: #123536]	Isolation date	1998-01-05

[Ref.: #68997]	Sample type/isolated from	nematode (Steinernema sangi) obtained from soil of a primary forest habitat
[Ref.: #68997]	Geographic location (country and/or sea, region)	Thanh Hoa province, Thuong Xuan
[Ref.: #68997]	Country	Vietnam
[Ref.: #68997]	Country ISO 3 Code	VNM
[Ref.: #68997]	Continent	Asia
[Ref.: #68997]	Geographic location	19.9500°/105.2330°
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil
#Host	#Invertebrates (Other)	#Nematoda

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX602193 (>99% sequence identity) for Xenorhabdus thuongxuanensis from Microbeatlas

Aquatic Samples	16
Soil Samples	4
Animal Samples	83
Plant Samples	4
Total Samples	107

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

[Ref.: #123536]

Biosafety level

Risk group (French classification)

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.: #43220]	Xenorhabdus thuongxuanensis strain 30TX1 16S ribosomal RNA gene, complete sequence	KX602193	1526	GenBank ENA	1873484 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Xenorhabdus thuongxuanensis 30TX1	GCA_001908095	scaffold	GenBank ENA	1873484 tax ID	*
[Ref.: #66792]	Xenorhabdus thuongxuanensis 30TX1	2791355039	draft	JGI IMG/M	1873484 tax ID	*

[Ref.: #43220]	GC-content	43.1 mol%
[Ref.: #68997]	GC-content	43.1 mol%	sequence analysis

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Xenorhabdus thuongxuanensis 30TX1 NCBI: GCA_001908095.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	100	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	98.842	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	57.425	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	91.306	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98.659	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	77.482	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Xenorhabdus thuongxuanensis 30TX1 NCBI: GCA_001908095
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	97.6
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	51.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	96.9
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	55.4

Availability in culture collections External links

[Ref.: #43220]

Culture collection no.

CCM 8727, LMG 29916, DSM 104078, CIP 111194

[Ref.: #96725]

SI-ID 407361

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Xenorhabdus thuongxuanensis sp. nov. and Xenorhabdus eapokensis sp. nov., isolated from Steinernema species.	Kampfer P, Tobias NJ, Ke LP, Bode HB, Glaeser SP	Int J Syst Evol Microbiol	10.1099/ijsem.0.001770	2017	*

References

#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 )

#43220

Peter Kämpfer, Nicholas J. Tobias, Long Phan Ke, Helge B. Bode, Stefanie P. Glaeser: Xenorhabdus thuongxuanensis sp. nov. and Xenorhabdus eapokensis sp. nov., isolated from Steinernema species. IJSEM 67: 1107 - 1114 2017 ( DOI 10.1099/ijsem.0.001770 , PubMed 28056225 )

#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 .

#68997

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104078

#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 .

#96725

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-ID407361.1 )

#123536 Collection of Institut Pasteur ; Curators of the CIP; CIP 111194

#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 .

* These data were automatically processed and therefore are not curated

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