Photorhabdus namnaonensis (LMG 29915, CCM 8729, DSM 104082)

Name: Photorhabdus namnaonensis (LMG 29915, CCM 8729, DSM 104082)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133380

Type strain

Strain Designation PB45.5

Culture col. no. LMG 29915 CCM 8729 DSM 104082 PB45.5 CIP 111196

NCBI tax ID(s) 1851568

Special Collections DSMZ Literature strains CIP

Links

Photorhabdus namnaonensis PB45.5 is a Gram-negative, motile, rod-shaped prokaryote that has a brown pigmentation and was isolated from entomopathogenic nematodes (Heterorhabdi-; tis baujardi) from Thailand.

Gram-negative motile rod-shaped pigmented genome sequence

Name and taxonomic classification

SI-ID 404126

LMG 29915,DSM 104082

@ref 20215

Last LPSN update 2025-12-16 10:01:46

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Morganellaceae

Genus Photorhabdus

Species Photorhabdus namnaonensis

Full scientific name Photorhabdus namnaonensis (Glaeser et al. 2017) Machado et al. 2018

Synonyms (1)

Photorhabdus luminescens subsp. namnaonensis

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
25251	negative	2 µm	1 µm	rod-shaped
125439	negative
125438	negative
121229	negative			rod-shaped

Colony morphology

@ref	Colony size	Colony color	Medium used
25251	2 mm	Slightly yellowish	NA

Pigmentation

@ref	Production	Color	Name
25251		brown	brown diffusible pigments

Multimedia

@ref:	66476
multimedia content:	DSM_104082.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_104082.jpg
caption:	DSM 104082 on medium 535 at 28 °C
intellectual property rights:	Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth
25251	Nutrient agar (NA)
25251	brain heart infusion agar
25251	Trypticase Soy Agar (TSA)
25251	Reasoner's 2A agar (R2A)
25251	MacConkey
66476	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
66476	NUTRIENT AGAR (DSMZ Medium 1)
121229	CIP Medium 72

Culture temp

@ref	Growth	Type	Temperature (°C)
25251	positive	growth	10-37
25251	negative	growth	39-40
66476	positive	growth	28

Physiology and metabolism

Spore formation

@ref	Spore formation
25251
125439
125438

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25251	30916 ChEBI	2-oxoglutarate	-	carbon source
25251	16193 ChEBI	3-hydroxybenzoate	-	carbon source
25251	37054 ChEBI	3-hydroxybutyrate	-	carbon source
25251	17879 ChEBI	4-hydroxybenzoate	-	carbon source
25251	58143 ChEBI	5-dehydro-D-gluconate	-	builds acid from
25251	30089 ChEBI	acetate	+/-	carbon source
25251	17128 ChEBI	adipate	-	carbon source
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
25251	18305 ChEBI	arbutin	-	carbon source
25251	78208 ChEBI	azelaate	-	carbon source
25251	16958 ChEBI	beta-alanine	-	carbon source
25251	17968 ChEBI	butyrate	-	carbon source
25251	17057 ChEBI	cellobiose	-	builds acid from
25251	17057 ChEBI	cellobiose	-	carbon source
25251	16383 ChEBI	cis-aconitate	+/-	carbon source
25251	16947 ChEBI	citrate	+	builds base from
25251	16947 ChEBI	citrate	+/-	carbon source
25251	18333 ChEBI	D-arabitol	-	builds acid from
25251	15824 ChEBI	D-fructose	+/-	carbon source
25251	12936 ChEBI	D-galactose	-	carbon source
25251	17634 ChEBI	D-glucose	+	builds acid from
25251	17634 ChEBI	D-glucose	+/-	carbon source
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
25251	16899 ChEBI	D-mannitol	-	builds acid from
25251	16899 ChEBI	D-mannitol	-	carbon source
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
25251	16024 ChEBI	D-mannose	+	builds acid from
25251	16024 ChEBI	D-mannose	+/-	carbon source
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
25251	16988 ChEBI	D-ribose	+/-	carbon source
25251	17924 ChEBI	D-sorbitol	-	builds acid from
25251	17924 ChEBI	D-sorbitol	-	carbon source
25251	65327 ChEBI	D-xylose	-	builds acid from
25251	65327 ChEBI	D-xylose	-	carbon source
25251	17113 ChEBI	erythritol	-	builds acid from
25251	4853 ChEBI	esculin	-	hydrolysis
25251	4853 ChEBI	esculin	-	builds acid from
25251	4853 ChEBI	esculin	-	carbon source
25251	28757 ChEBI	fructose	-	builds acid from
25251	29806 ChEBI	fumarate	+/-	carbon source
25251	16813 ChEBI	galactitol	-	builds acid from
25251	16865 ChEBI	gamma-aminobutyric acid	-	carbon source
68369	5291 ChEBI	gelatin	+	hydrolysis	from API 20NE
25251	24265 ChEBI	gluconate	+/-	carbon source
25251	17859 ChEBI	glutaric acid	-	carbon source
25251	17754 ChEBI	glycerol	-	carbon source
25251	17754 ChEBI	glycerol	-	builds acid from
25251	17240 ChEBI	itaconate	-	carbon source
25251	16977 ChEBI	L-alanine	+/-	carbon source
25251	30849 ChEBI	L-arabinose	-	builds acid from
25251	30849 ChEBI	L-arabinose	-	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
25251	29991 ChEBI	L-aspartate	+/-	carbon source
25251	18287 ChEBI	L-fucose	-	builds acid from
25251	18287 ChEBI	L-fucose	-	carbon source
25251	15603 ChEBI	L-leucine	-	carbon source
25251	15589 ChEBI	L-malate	+	carbon source
25251	15729 ChEBI	L-ornithine	-	carbon source
25251	17295 ChEBI	L-phenylalanine	-	carbon source
25251	17203 ChEBI	L-proline	+/-	carbon source
25251	62345 ChEBI	L-rhamnose	-	builds acid from
25251	62345 ChEBI	L-rhamnose	-	carbon source
25251	17115 ChEBI	L-serine	+/-	carbon source
25251	16828 ChEBI	L-tryptophan	-	carbon source
25251	24996 ChEBI	lactate	+/-	carbon source
25251	17716 ChEBI	lactose	-	builds acid from
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
25251	15792 ChEBI	malonate	-	builds base from
25251	68428 ChEBI	maltitol	-	carbon source
25251	17306 ChEBI	maltose	+	builds acid from
25251	17306 ChEBI	maltose	+/-	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
25251	28053 ChEBI	melibiose	-	builds acid from
25251	28053 ChEBI	melibiose	-	carbon source
25251	36986 ChEBI	mesaconate	-	carbon source
25251	17268 ChEBI	myo-inositol	-	builds acid from
25251	17268 ChEBI	myo-inositol	+/-	carbon source
25251	28037 ChEBI	N-acetylgalactosamine	+/-	carbon source
25251	506227 ChEBI	N-acetylglucosamine	-	builds acid from
25251	506227 ChEBI	N-acetylglucosamine	+/-	carbon source
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
25251	18401 ChEBI	phenylacetate	-	carbon source
25251	17272 ChEBI	propionate	-	carbon source
25251	17148 ChEBI	putrescine	-	carbon source
25251	15361 ChEBI	pyruvate	+/-	carbon source
25251	16634 ChEBI	raffinose	-	builds acid from
25251	15963 ChEBI	ribitol	-	builds acid from
25251	15963 ChEBI	ribitol	-	carbon source
25251	33942 ChEBI	ribose	-	builds acid from
25251	17814 ChEBI	salicin	-	builds acid from
25251	17814 ChEBI	salicin	-	carbon source
25251	9300 ChEBI	suberic acid	-	carbon source
25251	17992 ChEBI	sucrose	-	builds acid from
25251	17992 ChEBI	sucrose	-	carbon source
25251	15708 ChEBI	trans-aconitate	-	carbon source
25251	27082 ChEBI	trehalose	+	builds acid from
25251	27082 ChEBI	trehalose	+/-	carbon source
25251	17151 ChEBI	xylitol	-	builds acid from
25251	17151 ChEBI	xylitol	-	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite
25251	15688 ChEBI	acetoin
25251	16136 ChEBI	hydrogen sulfide
25251	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
25251	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
25251	arginine dihydrolase	-	3.5.3.6
25251	beta-galactosidase	-	3.2.1.23
25251	catalase	-	1.11.1.6
25251	cytochrome oxidase	-	1.9.3.1
68369	cytochrome oxidase	-	1.9.3.1	from API 20NE
25251	DNase	+
25251	gelatinase	+
68369	gelatinase	+		from API 20NE
25251	lysine decarboxylase	-	4.1.1.18
25251	ornithine decarboxylase	-	4.1.1.17
25251	urease	-	3.5.1.5

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
66476	-	-	+	+	+	+	+	-	+	-	+	+	+	+	+	-	-	+	+	-	-
66476	-	+	-	-	-	-	+	-	+	-	+	+	+	+	-	+/-	-	+	+	-	-
66476	-	-	+	+	+	+	+	-	+	-	+	+	+	+	+	-	-	+	+	-	-
66476	-	+	-	-	-	-	+	-	+	-	+	+	+	+	-	-	-	+	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Nematoda

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Isolation date
25251	entomopathogenic nematodes (Heterorhabdi- tis baujardi) from Thailand	Nam Nao district of Phetchabun in central Thailand	Thailand	THA	Asia	16	101 16/101	2009-10
121229	H. Baujardi	Nam Nao, Sub District, Nam Nao District, Phetchabun	Thailand	THA	Asia			2009-01-02
66476	entomopathogenic nematode (Heterorhabditis baujardi) from soil	Phetchabun, Nam Nao district (16° 45' 07.6'' N, 101° 33' 42.2'' E)	Thailand	THA	Asia	16.7521	101.562 16.7521/101.562

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
121229	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
66792	ASM168433v1 assembly for Photorhabdus namnaonensis PB45.5	scaffold	GCA_001684335	2846550419	1851568	33.72

Genome browser: GCA_001684335

GC content

@ref	GC-content (mol%)
25251	42.5
66476	42.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Photorhabdus namnaonensis PB45.5
NCBI: GCA_001684335

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.60	no
125439	motility	BacteriaNetⓘ	no	56.20	no
125439	gram_stain	BacteriaNetⓘ	negative	99.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	69.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Photorhabdus namnaonensis PB45.5
NCBI: GCA_001684335.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	yes
125438	anaerobic	anaerobicⓘ	no	98.58	no
125438	aerobic	aerobicⓘ	no	63.00	no
125438	spore-forming	spore-formingⓘ	no	93.78	yes
125438	thermophilic	thermophileⓘ	no	98.97	no
125438	flagellated	motile2+ⓘ	yes	73.95	no

Literature

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 )
#25251	S. P. T. Glaeser, N. J.,Thanwisai, A.,Chantratita, N.,Bode, H. B.,Kämpfer, P.: Photorhabdus luminescens subsp. namnaonensis subsp. nov., isolated from Heterorhabditis baujardi nematodes. IJSEM 67: 1046 - 1051 2017 ( DOI 10.1099/ijsem.0.001761 , PubMed 28032540 )
#66476	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104082
#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 .
#121229	Collection of Institut Pasteur ; Curators of the CIP; CIP 111196
#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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