Xenorhabdus nematophila (DSM 3370, ATCC 19061, CCM 7081)

Name: Xenorhabdus nematophila (DSM 3370, ATCC 19061, CCM 7081)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5185

Type strain

Culture col. no. DSM 3370 ATCC 19061 CCM 7081 CCUG 14189 CIP 108994 2 more

NCBI tax ID(s) 406817 628

Special Collections DSMZ CCUG CIP

History <- E. Stackebrandt <- ATCC <- G.O. Poinar, Jr. and G.M.Thomas ("Achromobacter nematophilus") CIP <- 2005, CCUG <- 1983, F. Gavini, INSERM, Villeneuve d'Ascq, France <- G.O. Poinar, Jr <- G. M. Thomas

Links

Xenorhabdus nematophila DSM 3370 is an aerobe, Gram-negative, motile animal pathogen that was isolated from intestinal lumen of Neoplectana sp..

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

Name and taxonomic classification

SI-ID 6427

LMG 1036,ATCC 19061,CCUG 14189,DSM 3370,LMG 7801,LMG 8289,NCIB 9965,NCIMB 9965,CECT 4841,CCRC 13945,CCM 7081,BCRC 13945,CIP 108994

@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 nematophila

Full scientific name Xenorhabdus nematophila corrig. (Poinar and Thomas 1965) Thomas and Poinar 1979 (Approved Lists 1980)

Synonyms (2)

Xenorhabdus nematophilus
"Achromobacter nematophilus"

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
121262	negative	rod-shaped
125438	negative			99.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
121262	CIP Medium 72		Medium recipe at CIP
1363	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

Culture temp

@ref	Growth	Type	Temperature (°C)
1363	positive	growth	28
46042	positive	growth	30
46042	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
46042	aerobe
46042	microaerophile
121262	facultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.5
125438		93.244

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	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	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
121262	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
121262	16301 ChEBI	nitrite	-	reduction
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
121262	35581 ChEBI	indole

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121262	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
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
121262	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
68369	gelatinase	+		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
121262	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
121262	ornithine decarboxylase	-	4.1.1.17
121262	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
121262	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	kanosamine biosynthesis II	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	lipoate biosynthesis	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	sulfopterin metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	L-lactaldehyde degradation	100	3 of 3
66794	cyanate degradation	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	CMP-KDO biosynthesis	100	4 of 4
66794	aerobactin biosynthesis	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	taurine degradation	100	1 of 1
66794	gluconeogenesis	100	8 of 8
66794	ubiquinone biosynthesis	100	7 of 7
66794	photosynthesis	92.86	13 of 14
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	vitamin B6 metabolism	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	vitamin B12 metabolism	88.24	30 of 34
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	heme metabolism	85.71	12 of 14
66794	glutathione metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	NAD metabolism	83.33	15 of 18
66794	pyrimidine metabolism	82.22	37 of 45
66794	pentose phosphate pathway	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	gallate degradation	80	4 of 5
66794	purine metabolism	79.79	75 of 94
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	lactate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	alanine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	histidine metabolism	68.97	20 of 29
66794	octane oxidation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	methionine metabolism	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	lipid metabolism	64.52	20 of 31
66794	citric acid cycle	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	oxidative phosphorylation	62.64	57 of 91
66794	degradation of sugar alcohols	62.5	10 of 16
66794	lysine metabolism	61.9	26 of 42
66794	leucine metabolism	61.54	8 of 13
66794	urea cycle	61.54	8 of 13
66794	non-pathway related	60.53	23 of 38
66794	myo-inositol biosynthesis	60	6 of 10
66794	phenol degradation	60	12 of 20
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	tyrosine metabolism	57.14	8 of 14
66794	d-mannose degradation	55.56	5 of 9
66794	pantothenate biosynthesis	50	3 of 6
66794	arginine metabolism	50	12 of 24
66794	ethanol fermentation	50	1 of 2
66794	starch degradation	50	5 of 10
66794	glycine metabolism	50	5 of 10
66794	propionate fermentation	50	5 of 10
66794	butanoate fermentation	50	2 of 4
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	degradation of pentoses	46.43	13 of 28
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	propanol degradation	42.86	3 of 7
66794	arachidonate biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	sulfate reduction	38.46	5 of 13
66794	methane metabolism	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	polyamine pathway	30.43	7 of 23
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	d-xylose degradation	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	carnitine metabolism	25	2 of 8
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	catecholamine biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	arachidonic acid metabolism	22.22	4 of 18

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
121262	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	+	-	+	-	-

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
1363	-	-	+	-	-	-	+	-	+	-	+	-	+	-	-	-	-	-	-	-	-
1363	-	-	-	-	-	-	+	-	+	-	+	-	+	-	-	-	-	+	-	+	+/-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Nematoda
#Host Body-Site	#Gastrointestinal tract	-

Isolation

@ref	Sample type	Host species	Isolation date
1363	intestinal lumen of Neoplectana sp.	Neoplectana
46042	Intestinal lumen of Neoaplectana sp.
121262	Intestinal lumen DD 136 strain of Neoaplectana carpocapsae Weiser		1964

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
1363		1	Risk group (German classification) According to TRBA 466
121262		1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
66792	ASM25295v1 assembly for Xenorhabdus nematophila ATCC 19061	chromosome	GCA_000252955	649633108	406817	86.88

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Xenorhabdus nematophila gene for 16S rRNA, partial sequence, strain: ATCC 19061	D78009	1479	628
20218	Xenorhabdus nematophila 16S ribosomal RNA gene, partial sequence	AY278674	1496	628
20218	X.nematophilus 16S rRNA gene (DSM 3370)	X82251	1497	628
124043	Xenorhabdus nematophila strain ATCC 19061 16S ribosomal RNA gene, partial sequence 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence and 23S ribosomal RNA gene, partial sequence.	FJ515824	2160	628

GC content

1363

GC-content (mol%)43.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Xenorhabdus nematophila ATCC 19061
PATRIC: 406817.27

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.50	no
125439	motility	BacteriaNetⓘ	no	55.20	no
125439	gram_stain	BacteriaNetⓘ	negative	87.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	66.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Xenorhabdus nematophila ATCC 19061
PATRIC: 406817.27

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	98.06	yes
125438	spore-forming	spore-formingⓘ	no	93.24	no
125438	aerobic	aerobicⓘ	no	67.50	no
125438	thermophilic	thermophileⓘ	no	96.66	yes
125438	flagellated	motile2+ⓘ	yes	76.93	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Substrate Promiscuity of the Triceptide Maturase XncB Leads to Incorporation of Various Amino Acids and Detection of Oxygenated Products.	Phan CS, Chang L, Nguyen TQN, Suarez AFL, Ho XH, Chen H, Koh IYF, Morinaka BI.	ACS Chem Biol	10.1021/acschembio.3c00782	2024
Enzymology	Proteolytic enzyme production by strains of the insect pathogen xenorhabdus and characterization of an early-log-phase-secreted protease as a potential virulence factor.	Massaoud MK, Marokhazi J, Fodor A, Venekei I.	Appl Environ Microbiol	10.1128/aem.01567-10	2010
Phylogeny	Phylogenetic profiling: how much input data is enough?	Skunca N, Dessimoz C.	PLoS One	10.1371/journal.pone.0114701	2015
	Pleiotropic role of PAX cyclolipopeptides in the Xenorhabdus bacterium mutualistically associated with entomopathogenic nematodes.	Claveyroles N, Lanois-Nouri A, El Fannassi I, Ogier J-C, Pages S, Chouchou A, Cazals G, Valette G, Carre-Mlouka A, Givaudan A.	Appl Environ Microbiol	10.1128/aem.00760-25	2025
Genetics	Genetic toolbox for Photorhabdus and Xenorhabdus: pSEVA based heterologous expression systems and CRISPR/Cpf1 based genome editing for rapid natural product profiling.	Rill A, Zhao L, Bode HB.	Microb Cell Fact	10.1186/s12934-024-02363-8	2024
Pathogenicity	Txp40, an insecticidal toxin protein from Xenorhabdus nematophila: Purification, toxicity assessment and biophysical characterization.	Kinkar OU, Prashar A, Kumar A, Hadapad AB, Hire RS, Makde RD.	Toxicon	10.1016/j.toxicon.2022.09.003	2022
	The Xenorhabdus nematophila LrhA transcriptional regulator modulates production of gamma-keto-N-acyl amides with inhibitory activity against mutualistic host nematode egg hatching.	Lam YC, Hamchand R, Mucci NC, Kauffman SJ, Dudkina N, Reagle EV, Casanova-Torres AM, DeCuyper J, Chen H, Song D, Thomas MG, Palm NW, Goodrich-Blair H, Crawford JM.	Appl Environ Microbiol	10.1128/aem.00528-24	2024
	HETERORHABDITIS BACTERIOPHORA NEMATODES ARE SENSITIVE TO THE BACTERIAL PATHOGEN PHOTORHABDUS ASYMBIOTICA.	Kim I, Heryanto C, Eleftherianos I.	J Parasitol	10.1645/22-55	2023
	Quorum sensing regulators and non-ribosomal peptide synthetases govern antibacterial secretions in Xenorhabdus szentirmaii.	Dey R, Valle DO, Chakraborty A, Mayer KA, Uppala JK, Chakraborty A, Mirza S, Skwor T, Forst S, Dey M.	Front Microbiol	10.3389/fmicb.2025.1560663	2025
	The plasmid-borne hipBA operon of Klebsiella michiganensis encodes a potent plasmid stabilization system.	Shutt-McCabe J, Shaik KB, Hoyles L, McVicker G.	J Appl Microbiol	10.1093/jambio/lxae246	2024
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
	Antagonistic Efficacy of Symbiotic Bacterium Xenorhabdus sp. SCG against Meloidogyne spp.	Kim JH, Lee BM, Lee HC, Choi IS, Koo KB, Son KH.	J Microbiol Biotechnol	10.4014/jmb.2404.04003	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
	Draft Genome Sequence and Annotation of the Insect Pathogenic Bacterium Xenorhabdus nematophila Strain C2-3, Isolated from Nematode Steinernema carpocapsae in the Republic of Korea.	Hong SJ, Ullah I, Park GS, Jung BK, Choi J, Khan AR, Kim MC, Shin JH.	Genome Announc	10.1128/genomea.01521-14	2015
Metabolism	Effects of cpxR on the growth characteristics and antibiotic production of Xenorhabdus nematophila.	Guo S, Wang Z, Liu B, Gao J, Fang X, Tang Q, Bilal M, Wang Y, Zhang X.	Microb Biotechnol	10.1111/1751-7915.13362	2019
	Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus nematophila Strain F1.	Lanois A, Ogier JC, Gouzy J, Laroui C, Rouy Z, Givaudan A, Gaudriault S.	Genome Announc	10.1128/genomea.00342-13	2013
	A Surface Exposed, Two-Domain Lipoprotein Cargo of a Type XI Secretion System Promotes Colonization of Host Intestinal Epithelia Expressing Glycans.	Grossman AS, Escobar CA, Mans EJ, Mucci NC, Mauer TJ, Jones KA, Moore CC, Abraham PE, Hettich RL, Schneider L, Campagna SR, Forest KT, Goodrich-Blair H.	Front Microbiol	10.3389/fmicb.2022.800366	2022
Metabolism	A Widespread Bacterial Secretion System with Diverse Substrates.	Grossman AS, Mauer TJ, Forest KT, Goodrich-Blair H.	mBio	10.1128/mbio.01956-21	2021
Metabolism	CpxR negatively regulates the production of xenocoumacin 1, a dihydroisocoumarin derivative produced by Xenorhabdus nematophila.	Zhang S, Fang X, Tang Q, Ge J, Wang Y, Zhang X.	Microbiologyopen	10.1002/mbo3.674	2019
Metabolism	The Global Transcription Factor Lrp Controls Virulence Modulation in Xenorhabdus nematophila.	Hussa EA, Casanova-Torres AM, Goodrich-Blair H.	J Bacteriol	10.1128/jb.00272-15	2015
Genetics	Anti-Foc RT4 Activity of a Newly Isolated Streptomyces sp. 5-10 From a Medicinal Plant (Curculigo capitulata).	Yun T, Zhang M, Zhou D, Jing T, Zang X, Qi D, Chen Y, Li K, Zhao Y, Tang W, Huang J, Wang W, Xie J.	Front Microbiol	10.3389/fmicb.2020.610698	2020
	Type S Non-Ribosomal Peptide Synthetases for the Rapid Generation of Tailormade Peptide Libraries.	Abbood N, Duy Vo T, Watzel J, Bozhueyuek KAJ, Bode HB.	Chemistry	10.1002/chem.202103963	2022
Metabolism	Discovery of Lysine Hydroxylases in the Clavaminic Acid Synthase-Like Superfamily for Efficient Hydroxylysine Bioproduction.	Hara R, Yamagata K, Miyake R, Kawabata H, Uehara H, Kino K.	Appl Environ Microbiol	10.1128/aem.00693-17	2017
Genetics	Comparative Genomic Analyses of the Genus Photobacterium Illuminate Biosynthetic Gene Clusters Associated with Antagonism.	Lau NS, Heng WL, Miswan N, Azami NA, Furusawa G.	Int J Mol Sci	10.3390/ijms23179712	2022
Metabolism	High Levels of the Xenorhabdus nematophila Transcription Factor Lrp Promote Mutualism with the Steinernema carpocapsae Nematode Host.	Cao M, Patel T, Rickman T, Goodrich-Blair H, Hussa EA.	Appl Environ Microbiol	10.1128/aem.00276-17	2017
Metabolism	Analysis of the PixA inclusion body protein of Xenorhabdus nematophila.	Goetsch M, Owen H, Goldman B, Forst S.	J Bacteriol	10.1128/jb.188.7.2706-2710.2006	2006
Genetics	Genome announcement of Steinernema khuongi and its associated symbiont from Florida.	Baniya A, DiGennaro P.	G3 (Bethesda)	10.1093/g3journal/jkab053	2021
Metabolism	LuxS-dependent AI-2 production is not involved in global regulation of natural product biosynthesis in Photorhabdus and Xenorhabdus.	Heinrich AK, Hirschmann M, Neubacher N, Bode HB.	PeerJ	10.7717/peerj.3471	2017
	Assessing computational tools for the discovery of small RNA genes in bacteria.	Lu X, Goodrich-Blair H, Tjaden B.	RNA	10.1261/rna.2689811	2011
Genetics	Antimicrobial activity screening of rhizosphere soil bacteria from tomato and genome-based analysis of their antimicrobial biosynthetic potential.	Zhou L, Song C, Li Z, Kuipers OP.	BMC Genomics	10.1186/s12864-020-07346-8	2021
	The hmsHFRS operon of Xenorhabdus nematophila is required for biofilm attachment to Caenorhabditis elegans.	Drace K, Darby C.	Appl Environ Microbiol	10.1128/aem.00336-08	2008
Metabolism	NilD CRISPR RNA contributes to Xenorhabdus nematophila colonization of symbiotic host nematodes.	Veesenmeyer JL, Andersen AW, Lu X, Hussa EA, Murfin KE, Chaston JM, Dillman AR, Wassarman KM, Sternberg PW, Goodrich-Blair H.	Mol Microbiol	10.1111/mmi.12715	2014
	The Global Regulators Lrp, LeuO, and HexA Control Secondary Metabolism in Entomopathogenic Bacteria.	Engel Y, Windhorst C, Lu X, Goodrich-Blair H, Bode HB.	Front Microbiol	10.3389/fmicb.2017.00209	2017
Genetics	Activating and Attenuating the Amicoumacin Antibiotics.	Park HB, Perez CE, Perry EK, Crawford JM.	Molecules	10.3390/molecules21070824	2016
Metabolism	Examination of Xenorhabdus nematophila lipases in pathogenic and mutualistic host interactions reveals a role for xlpA in nematode progeny production.	Richards GR, Goodrich-Blair H.	Appl Environ Microbiol	10.1128/aem.01715-09	2010
Metabolism	Evolutionary patchwork of an insecticidal toxin shared between plant-associated pseudomonads and the insect pathogens Photorhabdus and Xenorhabdus.	Ruffner B, Pechy-Tarr M, Hofte M, Bloemberg G, Grunder J, Keel C, Maurhofer M.	BMC Genomics	10.1186/s12864-015-1763-2	2015
Metabolism	The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle.	Rougon-Cardoso A, Flores-Ponce M, Ramos-Aboites HE, Martinez-Guerrero CE, Hao YJ, Cunha L, Rodriguez-Martinez JA, Ovando-Vazquez C, Bermudez-Barrientos JR, Abreu-Goodger C, Chavarria-Hernandez N, Simoes N, Montiel R.	Sci Rep	10.1038/srep37536	2016
	CpxRA influences Xenorhabdus nematophila colonization initiation and outgrowth in Steinernema carpocapsae nematodes through regulation of the nil locus.	Herbert Tran EE, Andersen AW, Goodrich-Blair H.	Appl Environ Microbiol	10.1128/aem.02658-08	2009
Metabolism	Xenocin export by the flagellar type III pathway in Xenorhabdus nematophila.	Singh P, Park D, Forst S, Banerjee N.	J Bacteriol	10.1128/jb.01532-12	2013
	New insights into the colonization and release processes of Xenorhabdus nematophila and the morphology and ultrastructure of the bacterial receptacle of its nematode host, Steinernema carpocapsae.	Snyder H, Stock SP, Kim SK, Flores-Lara Y, Forst S.	Appl Environ Microbiol	10.1128/aem.02947-06	2007
Metabolism	Pyrimidine nucleoside salvage confers an advantage to Xenorhabdus nematophila in its host interactions.	Orchard SS, Goodrich-Blair H.	Appl Environ Microbiol	10.1128/aem.71.10.6254-6259.2005	2005
Enzymology	Isolation and characterization of Xenorhabdus nematophila transposon insertion mutants defective in lipase activity against Tween.	Richards GR, Vivas EI, Andersen AW, Rivera-Santos D, Gilmore S, Suen G, Goodrich-Blair H.	J Bacteriol	10.1128/jb.00173-09	2009
	Prioritizing bona fide bacterial small RNAs with machine learning classifiers.	Eppenhof EJJ, Pena-Castillo L.	PeerJ	10.7717/peerj.6304	2019
	Molecular Characterization of SehB, a Type II Antitoxin of Salmonella enterica Serotype Typhimurium: Amino Acid Residues Involved in DNA-Binding, Homodimerization, Toxin Interaction, and Virulence.	Chimal-Cazares F, Hernandez-Martinez G, Pacheco S, Ares MA, Soria-Bustos J, Sanchez-Gutierrez M, Izquierdo-Vega JA, Ibarra JA, Gonzalez-Y-Merchand JA, Gorvel JP, Meresse S, De la Cruz MA.	Front Microbiol	10.3389/fmicb.2020.00614	2020
	OpnS, an outer membrane porin of Xenorhabdus nematophila, confers a competitive advantage for growth in the insect host.	van der Hoeven R, van der Hoeven R, Forst S.	J Bacteriol	10.1128/jb.00148-09	2009
	Xenorhabdus nematophila requires an intact iscRSUA-hscBA-fdx operon to colonize Steinernema carpocapsae nematodes.	Martens EC, Gawronski-Salerno J, Vokal DL, Pellitteri MC, Menard ML, Goodrich-Blair H.	J Bacteriol	10.1128/jb.185.12.3678-3682.2003	2003
	Delineation of the Ancestral Tus-Dependent Replication Fork Trap.	Toft CJ, Moreau MJJ, Perutka J, Mandapati S, Enyeart P, Sorenson AE, Ellington AD, Schaeffer PM.	Int J Mol Sci	10.3390/ijms222413533	2021
Metabolism	Role of Mrx fimbriae of Xenorhabdus nematophila in competitive colonization of the nematode host.	Snyder H, He H, Owen H, Hanna C, Forst S.	Appl Environ Microbiol	10.1128/aem.05328-11	2011
Genetics	Comparative Genomics between Two Xenorhabdus bovienii Strains Highlights Differential Evolutionary Scenarios within an Entomopathogenic Bacterial Species.	Bisch G, Ogier JC, Medigue C, Rouy Z, Vincent S, Tailliez P, Givaudan A, Gaudriault S.	Genome Biol Evol	10.1093/gbe/evv248	2016
	Early colonization events in the mutualistic association between Steinernema carpocapsae nematodes and Xenorhabdus nematophila bacteria.	Martens EC, Heungens K, Goodrich-Blair H.	J Bacteriol	10.1128/jb.185.10.3147-3154.2003	2003
Genetics	Unravelling the antibiotic and heavy metal resistome of a chronically polluted soil.	Salam LB.	3 Biotech	10.1007/s13205-020-02219-z	2020
	CpxRA contributes to Xenorhabdus nematophila virulence through regulation of lrhA and modulation of insect immunity.	Herbert Tran EE, Goodrich-Blair H.	Appl Environ Microbiol	10.1128/aem.02657-08	2009
Metabolism	The insect pathogenic bacterium Xenorhabdus innexi has attenuated virulence in multiple insect model hosts yet encodes a potent mosquitocidal toxin.	Kim IH, Aryal SK, Aghai DT, Casanova-Torres AM, Hillman K, Kozuch MP, Mans EJ, Mauer TJ, Ogier JC, Ensign JC, Gaudriault S, Goodman WG, Goodrich-Blair H, Dillman AR.	BMC Genomics	10.1186/s12864-017-4311-4	2017
Enzymology	Molecular characterizations of cytolethal distending toxin produced by Providencia alcalifaciens strains isolated from patients with diarrhea.	Shima A, Hinenoya A, Asakura M, Sugimoto N, Tsukamoto T, Ito H, Nagita A, Faruque SM, Yamasaki S.	Infect Immun	10.1128/iai.05831-11	2012
Metabolism	Mutational analyses reveal overall topology and functional regions of NilB, a bacterial outer membrane protein required for host association in a model of animal-microbe mutualism.	Bhasin A, Chaston JM, Goodrich-Blair H.	J Bacteriol	10.1128/jb.06711-11	2012
	CpxRA regulates mutualism and pathogenesis in Xenorhabdus nematophila.	Herbert EE, Cowles KN, Goodrich-Blair H.	Appl Environ Microbiol	10.1128/aem.01586-07	2007
	The Xenorhabdus nematophila nilABC genes confer the ability of Xenorhabdus spp. to colonize Steinernema carpocapsae nematodes.	Cowles CE, Goodrich-Blair H.	J Bacteriol	10.1128/jb.00123-08	2008
	Xenorhabdus nematophila lrhA is necessary for motility, lipase activity, toxin expression, and virulence in Manduca sexta insects.	Richards GR, Herbert EE, Park Y, Goodrich-Blair H.	J Bacteriol	10.1128/jb.00358-08	2008
Metabolism	Identification and functional characterization of a Xenorhabdus nematophila oligopeptide permease.	Orchard SS, Goodrich-Blair H.	Appl Environ Microbiol	10.1128/aem.70.9.5621-5627.2004	2004
Metabolism	The xnp1 P2-like tail synthesis gene cluster encodes xenorhabdicin and is required for interspecies competition.	Morales-Soto N, Forst SA.	J Bacteriol	10.1128/jb.00092-11	2011
	The target spectrum of SdsR small RNA in Salmonella.	Frohlich KS, Haneke K, Papenfort K, Vogel J.	Nucleic Acids Res	10.1093/nar/gkw632	2016
Pathogenicity	Txp40, a ubiquitous insecticidal toxin protein from Xenorhabdus and Photorhabdus bacteria.	Brown SE, Cao AT, Dobson P, Hines ER, Akhurst RJ, East PD.	Appl Environ Microbiol	10.1128/aem.72.2.1653-1662.2006	2006
Metabolism	A UDP-HexNAc:polyprenol-P GalNAc-1-P transferase (WecP) representing a new subgroup of the enzyme family.	Merino S, Jimenez N, Molero R, Bouamama L, Regue M, Tomas JM.	J Bacteriol	10.1128/jb.01441-10	2011
Metabolism	Comparative genomics reveals new evolutionary and ecological patterns of selenium utilization in bacteria.	Peng T, Lin J, Xu YZ, Zhang Y.	ISME J	10.1038/ismej.2015.246	2016
Pathogenicity	Response of ants to a deterrent factor(s) produced by the symbiotic bacteria of entomopathogenic nematodes.	Zhou X, Kaya HK, Heungens K, Goodrich-Blair H.	Appl Environ Microbiol	10.1128/aem.68.12.6202-6209.2002	2002
Pathogenicity	Novel conjugative transferable multiple drug resistance plasmid pAQU1 from Photobacterium damselae subsp. damselae isolated from marine aquaculture environment.	Nonaka L, Maruyama F, Miyamoto M, Miyakoshi M, Kurokawa K, Masuda M.	Microbes Environ	10.1264/jsme2.me11338	2012
Phylogeny	Phenotypic variation and host interactions of Xenorhabdus bovienii SS-2004, the entomopathogenic symbiont of Steinernema jollieti nematodes.	Sugar DR, Murfin KE, Chaston JM, Andersen AW, Richards GR, deLeon L, Baum JA, Clinton WP, Forst S, Goldman BS, Krasomil-Osterfeld KC, Slater S, Stock SP, Goodrich-Blair H.	Environ Microbiol	10.1111/j.1462-2920.2011.02663.x	2012
Metabolism	A novel l-isoleucine-4'-dioxygenase and l-isoleucine dihydroxylation cascade in Pantoea ananatis.	Smirnov SV, Sokolov PM, Kotlyarova VA, Samsonova NN, Kodera T, Sugiyama M, Torii T, Hibi M, Shimizu S, Yokozeki K, Ogawa J.	Microbiologyopen	10.1002/mbo3.87	2013
	Whole-genome comparison between Photorhabdus strains to identify genomic regions involved in the specificity of nematode interaction.	Gaudriault S, Duchaud E, Lanois A, Canoy AS, Bourot S, Derose R, Kunst F, Boemare N, Givaudan A.	J Bacteriol	10.1128/jb.188.2.809-814.2006	2006
	Global analysis of biosynthetic gene clusters reveals conserved and unique natural products in entomopathogenic nematode-symbiotic bacteria.	Shi YM, Hirschmann M, Shi YN, Ahmed S, Abebew D, Tobias NJ, Grun P, Crames JJ, Poschel L, Kuttenlochner W, Richter C, Herrmann J, Muller R, Thanwisai A, Pidot SJ, Stinear TP, Groll M, Kim Y, Bode HB.	Nat Chem	10.1038/s41557-022-00923-2	2022
Enzymology	Insecticidal pilin subunit from the insect pathogen Xenorhabdus nematophila.	Khandelwal P, Choudhury D, Birah A, Reddy MK, Gupta GP, Banerjee N.	J Bacteriol	10.1128/jb.186.19.6465-6476.2004	2004
	Genetic characterization of the HrpL regulon of the fire blight pathogen Erwinia amylovora reveals novel virulence factors.	McNally RR, Toth IK, Cock PJ, Pritchard L, Hedley PE, Morris JA, Zhao Y, Sundin GW.	Mol Plant Pathol	10.1111/j.1364-3703.2011.00738.x	2012
Phylogeny	Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks.	Dillman AR, Macchietto M, Porter CF, Rogers A, Williams B, Antoshechkin I, Lee MM, Goodwin Z, Lu X, Lewis EE, Goodrich-Blair H, Stock SP, Adams BJ, Sternberg PW, Mortazavi A.	Genome Biol	10.1186/s13059-015-0746-6	2015
Metabolism	A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD.	Frohlich KS, Papenfort K, Berger AA, Vogel J.	Nucleic Acids Res	10.1093/nar/gkr1156	2012
	Occurrence of sep insecticidal toxin complex genes in Serratia spp. and Yersinia frederiksenii.	Dodd SJ, Hurst MR, Glare TR, O'Callaghan M, Ronson CW.	Appl Environ Microbiol	10.1128/aem.00954-06	2006
	Automated design of probes for rRNA-targeted fluorescence in situ hybridization reveals the advantages of using dual probes for accurate identification.	Wright ES, Yilmaz LS, Corcoran AM, Okten HE, Noguera DR.	Appl Environ Microbiol	10.1128/aem.01685-14	2014
	MARTX, multifunctional autoprocessing repeats-in-toxin toxins.	Satchell KJ.	Infect Immun	10.1128/iai.00525-07	2007
Pathogenicity	Functional and transcriptional analysis of chromosomal encoded hipBA(Xn2) type II toxin-antitoxin (TA) module from Xenorhabdus nematophila.	Yadav M, Rathore JS	Microb Pathog	10.1016/j.micpath.2021.105309	2021
Enzymology	Novel insecticidal chitinase from the insect pathogen Xenorhabdus nematophila.	Mahmood S, Kumar M, Kumari P, Mahapatro GK, Banerjee N, Sarin NB	Int J Biol Macromol	10.1016/j.ijbiomac.2020.05.078	2020
Pathogenicity	Characteristics and Function of the Chitin Binding Protein from Xenorhabdus nematophila.	Liu J, Song P, Zhang J, Nangong Z, Liu X, Gao Y, Wang Q	Protein Pept Lett	10.2174/0929866526666190327143335	2019
Genetics	TAome analysis of type-II toxin-antitoxin system from Xenorhabdus nematophila.	Yadav M, Rathore JS	Comput Biol Chem	10.1016/j.compbiolchem.2018.07.010	2018
Phylogeny	The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes.	Chaston JM, Suen G, Tucker SL, Andersen AW, Bhasin A, Bode E, Bode HB, Brachmann AO, Cowles CE, Cowles KN, Darby C, de Leon L, Drace K, Du Z, Givaudan A, Herbert Tran EE, Jewell KA, Knack JJ, Krasomil-Osterfeld KC, Kukor R, Lanois A, Latreille P, Leimgruber NK, Lipke CM, Liu R, Lu X, Martens EC, Marri PR, Medigue C, Menard ML, Miller NM, Morales-Soto N, Norton S, Ogier JC, Orchard SS, Park D, Park Y, Qurollo BA, Sugar DR, Richards GR, Rouy Z, Slominski B, Slominski K, Snyder H, Tjaden BC, van der Hoeven R, Welch RD, Wheeler C, Xiang B, Barbazuk B, Gaudriault S, Goodner B, Slater SC, Forst S, Goldman BS, Goodrich-Blair H	PLoS One	10.1371/journal.pone.0027909	2011
	Characterization of Tn5-Induced Mutants of Xenorhabdus nematophilus ATCC 19061.	Xu J, Olson ME, Kahn ML, Hurlbert RE	Appl Environ Microbiol	10.1128/aem.57.4.1173-1180.1991	1991

References

#1363	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3370
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#46042	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 14189
#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 )
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#121262	Collection of Institut Pasteur ; Curators of the CIP; CIP 108994
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 nematophila (DSM 3370, ATCC 19061, CCM 7081)

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