Photorhabdus luminescens (DSM 3368, ATCC 29999, CCM 7077)

Name: Photorhabdus luminescens (DSM 3368, ATCC 29999, CCM 7077)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5032

Type strain

Strain Designation Hb

Culture col. no. DSM 3368 ATCC 29999 CCM 7077 Hb CIP 106429 1 more

NCBI tax ID(s) 29488 171439

Special Collections DSMZ CIP

History <- E. Stackebrandt <- ATCC <- G.M. Thomas; Hb CIP <- 2000, N. Boemare, Montpellier Univ., Montpellier, France <- 1984, CSIRO <- 1980, ATCC <- G.M. Thomas: strain Hb, Xenorhabdus luminescens

Links

Photorhabdus luminescens Hb is a facultative anaerobe, Gram-negative, motile animal pathogen that was isolated from Nematode Heterorhabditis bacteriophora.

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

Name and taxonomic classification

SI-ID 11108

LMG 8287,ATCC 29999,DSM 3368,LMG 7797,NCIB 12670,CIP 106429,NCIMB 12670,CCM 7077,BCRC 14801,CCRC 14801

@ref 20215

Last LPSN update 2026-02-09 11:18:52

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Morganellaceae

Genus Photorhabdus

Species Photorhabdus luminescens

Full scientific name Photorhabdus luminescens (Thomas and Poinar 1979) Boemare et al. 1993

Synonyms (1)

Xenorhabdus luminescens

BacDive ID	Other strains from **Photorhabdus luminescens** (3)	Type strain
5029	P. luminescens HSH1, W7.1, DSM 12189
5030	P. luminescens LN2, DSM 12191
5031	P. luminescens HB 1-3, DSM 12205

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
120673	negative	rod-shaped
125438	negative		100
125439	negative		98.5

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
1361	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
40311	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
120673	CIP Medium 13	Medium recipe at CIP
1361	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)	Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
1361	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
1361	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)
1361	positive	growth	30
1361	positive	growth	28
40311	positive	growth	30
120673	positive	growth	30-37
120673	negative	growth	5
120673	negative	growth	10
120673	negative	growth	41

Physiology and metabolism

Oxygen tolerance

120673

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125438		93.832
125439		99.2

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
120673	16947 ChEBI	citrate	+	carbon source
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	+	builds acid from	from API 50CH acid
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
120673	4853 ChEBI	esculin	-	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68369	5291 ChEBI	gelatin	+	hydrolysis	from API 20NE
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
120673	17234 ChEBI	glucose	+	fermentation
68371	17754 ChEBI	glycerol	+	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
120673	17716 ChEBI	lactose	-	fermentation
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
120673	15792 ChEBI	malonate	-	assimilation
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
120673	29864 ChEBI	mannitol	-	fermentation
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	+	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
120673	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
120673	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
120673	132112 ChEBI	sodium thiosulfate	-	builds gas from
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
120673	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120673	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
120673	15688 ChEBI	acetoin	-
120673	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120673	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
120673	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
120673	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120673	caseinase	+	3.4.21.50
120673	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	-	1.9.3.1	from API 20NE
120673	DNase	-
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
120673	gelatinase	+/-
68369	gelatinase	+		from API 20NE
120673	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
120673	lipase	+
68382	lipase (C 14)	-		from API zym
120673	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
120673	ornithine decarboxylase	-	4.1.1.17
120673	oxidase	-
120673	phenylalanine ammonia-lyase	-	4.3.1.24
120673	protease	+
68382	trypsin	+	3.4.21.4	from API zym
120673	tryptophan deaminase	-
120673	tween esterase	-
120673	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

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
120673	-	+	-	-	-	+	+	-	+	-	+	-	-	-	-	+	-	+	-	-

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
1361	-	+	+	-	-	+	+	-	+	-	+	+	+	+	+	-	-	+	+	-	-
1361	-	-	-	-	-	-	+	-	+	-	+	+	+	+	+	-	-	+	+	-	-
1361	-	-	-	+	+	+	+	-	+	-	+	+	+	+	+	-	-	+	+	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
120673	not determinedn.d.	+	-	-	-	+	-	-	-	-	-	+	+	+	-	-	-	+	+	-	-	-	+	-	-	+	-	-	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
120673	not determinedn.d.	+	+	-	+	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-	+	-	-	-	-	+	-	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	+	+	-	-	-	-	+	+	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	+	+	-	-	-	-	-	+	-	-	+	+	+	+	+	+	-	+	+	-

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	Isolation date
1361	Nematode Heterorhabditis bacteriophora	Heterorhabditis bacteriophora	Breacon	Australia	AUS	Australia and Oceania
120673	Animal, Nematode, Heterorhabditis bacteriophora			Australia	AUS	Australia and Oceania	1978

Taxonmaps

69479

Global distribution of 16S sequence X82248 (>99% sequence identity) for Photorhabdus luminescens from Microbeatlas

Aquatic Samples	13
Soil Samples	1
Animal Samples	24
Plant Samples	1
Total Samples	39

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
1361		1	Risk group (German classification) According to TRBA 466
120673		1	Risk group (French 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	ASM108380v1 assembly for Photorhabdus luminescens subsp. luminescens DSM 3368	contig	GCA_001083805	171439.3	2648501375	171439	74.74
66792	IMG-taxon 2597490348 annotated assembly for Photorhabdus luminescens ATCC 29999	scaffold	GCA_900102985	29488.49	2597490348	29488	61.57

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Photorhabdus luminescens subsp. luminescens strain ATCC 29999 16S ribosomal RNA gene, partial sequence	AY870658	1475	171439
20218	Photorhabdus luminescens gene for 16S rRNA, partial sequence, strain: ATCC 29999	D78005	1482	29488
20218	Photorhabdus luminescens subsp. luminescens 16S rRNA gene, strain (DSM 3368)	X82248	1499	171439
20218	Photorhabdus luminescens subsp. luminescens strain Hb 16S ribosomal RNA gene, partial sequence	AY278640	1499	171439
124043	Photorhabdus luminescens strain ATCC 29999 16S ribosomal RNA gene, partial sequence.	MK039082	1349	29488

GC content

1361

GC-content (mol%)44.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Photorhabdus luminescens ATCC 29999
NCBI: GCA_900102985

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.20	no
125439	motility	BacteriaNetⓘ	yes	54.00	no
125439	gram_stain	BacteriaNetⓘ	negative	98.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	69.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Photorhabdus luminescens ATCC 29999
NCBI: GCA_900102985.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	99.27	yes
125438	aerobic	aerobicⓘ	no	69.49	yes
125438	spore-forming	spore-formingⓘ	no	93.83	no
125438	thermophilic	thermophileⓘ	no	98.97	yes
125438	flagellated	motile2+ⓘ	yes	74.88	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Heterorhabditis and Photorhabdus Symbiosis: A Natural Mine of Bioactive Compounds.	Parihar RD, Dhiman U, Bhushan A, Gupta PK, Gupta P.	Front Microbiol	10.3389/fmicb.2022.790339	2022
	Draft Genome Sequence of Photorhabdus luminescens HIM3 Isolated from an Entomopathogenic Nematode in Agricultural Soils.	Salgado-Morales R, Rivera-Gomez N, Martinez-Ocampo F, Lozano-Aguirre Beltran LF, Hernandez-Mendoza A, Dantan-Gonzalez E.	Genome Announc	10.1128/genomea.00745-17	2017
	Assessing the Pathogenicity of Two Bacteria Isolated from the Entomopathogenic Nematode Heterorhabditis indica against Galleria mellonella and Some Pest Insects.	Salgado-Morales R, Martinez-Ocampo F, Obregon-Barboza V, Vilchis-Martinez K, Jimenez-Perez A, Dantan-Gonzalez E.	Insects	10.3390/insects10030083	2019
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
Phylogeny	Isolation and identification of Photobacterium phosphoreum from an unexpected niche: migrating salmon.	Budsberg KJ, Wimpee CF, Braddock JF.	Appl Environ Microbiol	10.1128/aem.69.11.6938-6942.2003	2003
	Whole-Genome Sequencing and Biosynthetic Gene Cluster Analysis of Novel Entomopathogenic Bacteria Xenorhabdus thailandensis ALN 7.1 and ALN 11.5.	Meesil W, Ardpairin J, Sharkey LKR, Pidot SJ, Vitta A, Thanwisai A.	Biology (Basel)	10.3390/biology14080905	2025
Metabolism	An integrated AI knowledge graph framework of bacterial enzymology and metabolism.	Spencer NR, Gunabalasingam M, Dial K, Di X, Malcolm T, Magarvey NA.	Proc Natl Acad Sci U S A	10.1073/pnas.2425048122	2025
	BMP signaling to pharyngeal muscle in the C. elegans response to a bacterial pathogen regulates anti-microbial peptide expression and pharyngeal pumping.	Ciccarelli EJ, Bendelstein M, Yamamoto KK, Reich H, Savage-Dunn C.	Mol Biol Cell	10.1091/mbc.e23-05-0185	2024
	Bioprospecting for polyesterase activity relevant for PET degradation in marine Enterobacterales isolates.	Galarza-Verkovitch D, Turak O, Wiese J, Rahn T, Hentschel U, Borchert E.	AIMS Microbiol	10.3934/microbiol.2023027	2023
	Epidemiological survey of serum titers from adults against various Gram-negative bacterial V-antigens.	Kinoshita M, Shimizu M, Akiyama K, Kato H, Moriyama K, Sawa T.	PLoS One	10.1371/journal.pone.0220924	2020
Pathogenicity	Quorum Sensing Inhibitory Activity of Giganteone A from Myristica cinnamomea King against Escherichia coli Biosensors.	Sivasothy Y, Krishnan T, Chan KG, Abdul Wahab SM, Othman MA, Litaudon M, Awang K.	Molecules	10.3390/molecules21030391	2016
	Phloretin, an Apple Phytoalexin, Affects the Virulence and Fitness of Pectobacterium brasiliense by Interfering With Quorum-Sensing.	Pun M, Khazanov N, Galsurker O, Weitman M, Kerem Z, Senderowitz H, Yedidia I.	Front Plant Sci	10.3389/fpls.2021.671807	2021
Pathogenicity	Anti-quorum sensing activity of the traditional Chinese herb, Phyllanthus amarus.	Priya K, Yin WF, Chan KG.	Sensors (Basel)	10.3390/s131114558	2013
Pathogenicity	Silencing quorum sensing through extracts of Melicope lunu-ankenda.	Tan LY, Yin WF, Chan KG.	Sensors (Basel)	10.3390/s120404339	2012
Pathogenicity	Piper nigrum, Piper betle and Gnetum gnemon--natural food sources with anti-quorum sensing properties.	Tan LY, Yin WF, Chan KG.	Sensors (Basel)	10.3390/s130303975	2013
Metabolism	Characterization of N-acylhomoserine lactone-degrading bacteria associated with the Zingiber officinale (ginger) rhizosphere: co-existence of quorum quenching and quorum sensing in Acinetobacter and Burkholderia.	Chan KG, Atkinson S, Mathee K, Sam CK, Chhabra SR, Camara M, Koh CL, Williams P.	BMC Microbiol	10.1186/1471-2180-11-51	2011
Metabolism	Inhibition of quorum sensing-controlled virulence factor production in Pseudomonas aeruginosa PAO1 by Ayurveda spice clove (Syzygium aromaticum) bud extract.	Krishnan T, Yin WF, Chan KG.	Sensors (Basel)	10.3390/s120404016	2012
Metabolism	A metalloprotease secreted by the insect pathogen Photorhabdus luminescens induces melanization.	Held KG, LaRock CN, D'Argenio DA, Berg CA, Collins CM.	Appl Environ Microbiol	10.1128/aem.01000-07	2007
	Escherichia coli deletion mutants illuminate trade-offs between growth rate and flux through a foreign anabolic pathway.	Falls KC, Williams AL, Bryksin AV, Matsumura I.	PLoS One	10.1371/journal.pone.0088159	2014
Enzymology	Pandoraea sp. RB-44, a novel quorum sensing soil bacterium.	Han-Jen RE, Wai-Fong Y, Kok-Gan C.	Sensors (Basel)	10.3390/s131014121	2013
	Innate immunity mediated longevity and longevity induced by germ cell removal converge on the C-type lectin domain protein IRG-7.	Yunger E, Safra M, Levi-Ferber M, Haviv-Chesner A, Henis-Korenblit S.	PLoS Genet	10.1371/journal.pgen.1006577	2017
Enzymology	Identification of a new family of enzymes with potential O-acetylpeptidoglycan esterase activity in both Gram-positive and Gram-negative bacteria.	Weadge JT, Pfeffer JM, Clarke AJ.	BMC Microbiol	10.1186/1471-2180-5-49	2005
Metabolism	Identification of a quorum-sensing signal molecule in the facultative intracellular pathogen Brucella melitensis.	Taminiau B, Daykin M, Swift S, Boschiroli ML, Tibor A, Lestrate P, De Bolle X, O'Callaghan D, Williams P, Letesson JJ.	Infect Immun	10.1128/iai.70.6.3004-3011.2002	2002
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
Phylogeny	Fast and accurate identification of Xenorhabdus and Photorhabdus species by restriction analysis of PCR-amplified 16S rRNA genes.	Brunel B, Givaudan A, Lanois A, Akhurst RJ, Boemare N.	Appl Environ Microbiol	10.1128/aem.63.2.574-580.1997	1997
	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
	Rapid methods for testing the efficacy of sterilization-grade filter membranes.	Griffiths MH, Andrew PW, Ball PR, Hall GM.	Appl Environ Microbiol	10.1128/aem.66.8.3432-3437.2000	2000
	Quorum sensing in Aeromonas hydrophila and Aeromonas salmonicida: identification of the LuxRI homologs AhyRI and AsaRI and their cognate N-acylhomoserine lactone signal molecules.	Swift S, Karlyshev AV, Fish L, Durant EL, Winson MK, Chhabra SR, Williams P, Macintyre S, Stewart GS.	J Bacteriol	10.1128/jb.179.17.5271-5281.1997	1997
	Identification of the gene encoding the major NAD(P)H-flavin oxidoreductase of the bioluminescent bacterium Vibrio fischeri ATCC 7744.	Zenno S, Saigo K, Kanoh H, Inouye S.	J Bacteriol	10.1128/jb.176.12.3536-3543.1994	1994
	Bioluminescence as a reporter of intracellular survival of Bordetella bronchiseptica in murine phagocytes.	Forde CB, Parton R, Coote JG.	Infect Immun	10.1128/iai.66.7.3198-3207.1998	1998
	Variants of smooth Salmonella enterica serovar Enteritidis that grow to higher cell density than the wild type are more virulent.	Guard-Petter J.	Appl Environ Microbiol	10.1128/aem.64.6.2166-2172.1998	1998
	Molecular biology of the symbiotic-pathogenic bacteria Xenorhabdus spp. and Photorhabdus spp.	Forst S, Nealson K.	Microbiol Rev	10.1128/mr.60.1.21-43.1996	1996
Genetics	Variation in the effectors of the type III secretion system among Photorhabdus species as revealed by genomic analysis.	Brugirard-Ricaud K, Givaudan A, Parkhill J, Boemare N, Kunst F, Zumbihl R, Duchaud E.	J Bacteriol	10.1128/jb.186.13.4376-4381.2004	2004
	The insect-killing bacterium Photorhabdus luminescens has the lowest mutation rate among bacteria.	Pan J, Williams E, Sung W, Lynch M, Long H	Mar Life Sci Technol	10.1007/s42995-020-00060-0	2020
Enzymology	Identification and Characterization of an Efficient Phenylalanine Ammonia-Lyase from Photorhabdus luminescens.	Zhang F, Ren J, Zhan J	Appl Biochem Biotechnol	10.1007/s12010-020-03477-6	2021
Pathogenicity	Survival of insect pathogenic and human clinical isolates of Photorhabdus luminescens in previously sterile soil.	Bleakley BH, Chen X	Can J Microbiol	10.1139/w98-231	1999
Enzymology	Identification of the genes encoding NAD(P)H-flavin oxidoreductases that are similar in sequence to Escherichia coli Fre in four species of luminous bacteria: Photorhabdus luminescens, Vibrio fischeri, Vibrio harveyi, and Vibrio orientalis.	Zenno S, Saigo K	J Bacteriol	10.1128/jb.176.12.3544-3551.1994	1994
Genetics	Photorhabdus aballayi sp. nov. and Photorhabdus luminescens subsp. venezuelensis subsp. nov., isolated from Heterorhabditis amazonensis entomopathogenic nematodes.	Machado RAR, Bhat AH, Castaneda-Alvarez C, Puza V, San-Blas E.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005872	2023
Phylogeny	Photorhabdus khanii subsp. guanajuatensis subsp. nov., isolated from Heterorhabditis atacamensis, and Photorhabdus luminescens subsp. mexicana subsp. nov., isolated from Heterorhabditis mexicana entomopathogenic nematodes.	Machado RAR, Bruno P, Arce CCM, Liechti N, Kohler A, Bernal J, Bruggmann R, Turlings TCJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003154	2019
Phylogeny	Polyphasic classification of the genus Photorhabdus and proposal of new taxa: P. luminescens subsp. luminescens subsp. nov., P. luminescens subsp. akhurstii subsp. nov., P. luminescens subsp. laumondii subsp. nov., P. temperata sp. nov., P. temperata subsp. temperata subsp. nov. and P. asymbiotica sp. nov.	Fischer-Le Saux M, Viallard V, Brunel B, Normand P, Boemare NE	Int J Syst Bacteriol	10.1099/00207713-49-4-1645	1999

References

#1361	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3368
#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 )
#40311	; Curators of the CIP;
#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 .
#68371	Automatically annotated from API 50CH acid .
#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 .
#120673	Collection of Institut Pasteur ; Curators of the CIP; CIP 106429
#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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Photorhabdus luminescens (DSM 3368, ATCC 29999, CCM 7077)

Name and taxonomic classification

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Physiology and metabolism

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