Name: Xenorhabdus doucetiae FRM16
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5204

Type strain:

Species: Xenorhabdus doucetiae

Strain Designation: FRM16

Culture col. no.: DSM 17909, CIP 109074

Strain history: CIP <- 2005, N. Boemare, INRA, Montpellier Univ., Montpellier, France: strain FRM16

NCBI tax ID(s): 1123505 (strain), 351671 (species)

SI-ID 297366

CIP 109074, DSM 17909

Section

Xenorhabdus doucetiae FRM16 is a facultative anaerobe, mesophilic, motile animal pathogen that was isolated from Steinernema diaprepesi.

motile
animal pathogen
facultative anaerobe
mesophilic
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 doucetiae**
	Full Scientific Name (LPSN)	Xenorhabdus doucetiae Tailliez et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #118968]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.926

[Ref.: #118968]	Cell shape	rod-shaped

[Ref.: #118968]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %98.961

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7240]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #7240]

Culture medium growth

[Ref.: #7240]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7240]

Culture medium composition

expand / minimize

[Ref.: #118968]

Culture medium

CIP Medium 72

[Ref.: #118968]

Culture medium growth

[Ref.: #118968]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #7240]			growth	28 °C

[Ref.: #7240]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #118968]

Oxygen tolerance

facultative anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %98.967

[Ref.: #7240]

Name of produced compound

xenoamicins

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #118968]		nitrate ChEBI	-	reduction
[Ref.: #118968]		nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #118968]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #118968]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #118968]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #118968]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #118968]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #118968]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #118968]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #118968]	11653	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	+	-	+	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	vitamin B6 metabolism	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	pyrimidine metabolism	80	36 of 45
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	purine metabolism	79.79	75 of 94
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	daunorubicin biosynthesis	44.44	4 of 9
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #7240]	Sample type/isolated from	Steinernema diaprepesi
[Ref.: #7240]	Host species	Steinernema diaprepesi
[Ref.: #7240]	Geographic location (country and/or sea, region)	Martinique Island
[Ref.: #7240]	Country	France
[Ref.: #7240]	Country ISO 3 Code	FRA
[Ref.: #7240]	Continent	Europe

[Ref.: #118968]	Sample type/isolated from	Animal, Nematode Steinernema diaprepesi
[Ref.: #118968]	Geographic location (country and/or sea, region)	Martinique
[Ref.: #118968]	Country	France
[Ref.: #118968]	Country ISO 3 Code	FRA
[Ref.: #118968]	Continent	Europe
[Ref.: #118968]	Isolation date	1994
* marker position based on {}

Isolation sources categories

#Host

#Invertebrates (Other)

#Nematoda

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ211709 (>99% sequence identity) for Xenorhabdus doucetiae from Microbeatlas

Aquatic Samples	9
Soil Samples	19
Animal Samples	76
Plant Samples	8
Total Samples	112

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

[Ref.: #7240]	Pathogenicity (animal)	yes
[Ref.: #7240]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118968]	Biosafety level	1	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.: #7240]	Xenorhabdus doucetiae strain FRM16 16S ribosomal RNA gene, partial sequence	DQ211709	1487	ENA	1123505 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Xenorhabdus doucetiae FRM16	GCA_000968195	complete	GenBank	351671 tax ID	*
[Ref.: #66792]	Xenorhabdus doucetiae DSM 17909	GCA_008124675	scaffold	GenBank	351671 tax ID	*
[Ref.: #66792]	Xenorhabdus doucetiae strain DSM 17909	351671.8	wgs	PATRIC	351671 tax ID	*
[Ref.: #66792]	Xenorhabdus doucetiae strain FRM16 = DSM 17909	351671.5	complete	PATRIC	351671 tax ID	*
[Ref.: #66792]	Xenorhabdus doucetiae DSM 17909	2599185204	draft	JGI IMG/M	351671 tax ID	*
[Ref.: #66792]	Xenorhabdus doucetiae DSM 17909	2630968576	complete	JGI IMG/M	351671 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Xenorhabdus doucetiae FRM16 NCBI: GCA_000968195.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Xenorhabdus doucetiae FRM16 NCBI: GCA_000968195.1
[Ref.: #69480]	motile	yes	89.594	no
[Ref.: #69480]	flagellated	yes	62.634	no
[Ref.: #69480]	gram-positive	no	98.062	no
[Ref.: #69480]	anaerobic	no	98.224	no
[Ref.: #69480]	aerobic	yes	76.87	no
[Ref.: #69480]	halophile	no	85.252	no
[Ref.: #69480]	spore-forming	no	94.928	no
[Ref.: #69480]	thermophile	no	98.493	yes
[Ref.: #69480]	glucose-util	yes	88.547	no
[Ref.: #69480]	glucose-ferment	yes	84.637	no

Availability in culture collections External links

[Ref.: #7240]

Culture collection no.

DSM 17909, CIP 109074

[Ref.: #74696]

SI-ID 297366

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	A New Member of the Growing Family of Contact-Dependent Growth Inhibition Systems in Xenorhabdus doucetiae.	Ogier JC, Duvic B, Lanois A, Givaudan A, Gaudriault S	PLoS One	10.1371/journal.pone.0167443	2016	*
Metabolism	Structure and biosynthesis of xenoamicins from entomopathogenic Xenorhabdus.	Zhou Q, Grundmann F, Kaiser M, Schiell M, Gaudriault S, Batzer A, Kurz M, Bode HB	Chemistry	10.1002/chem.201302481	2013	*
Phylogeny	Description of Xenorhabdus magdalenensis sp. nov., the symbiotic bacterium associated with Steinernema australe.	Tailliez P, Pages S, Edgington S, Tymo LM, Buddie AG	Int J Syst Evol Microbiol	10.1099/ijs.0.034322-0	2011	*
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

#7240

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17909

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#68382

Automatically annotated from API zym .

#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 .

#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 )

#74696

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-ID297366.1 )

#118968 Collection of Institut Pasteur ; Curators of the CIP; CIP 109074
* These data were automatically processed and therefore are not curated

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