Name: Photorhabdus bodei LJ24-63
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 158410

Type strain:

Species: Photorhabdus bodei

Strain Designation: LJ24-63

Culture col. no.: DSM 105690, CCOS 1159

Strain history: <- R. Machado, Univ. Bern, Switzerland; LJ24-63 <-

NCBI tax ID(s): 2029681 (species)

SI-ID 400626

DSM 105690

Special Collections

Section

Photorhabdus bodei LJ24-63 is a Gram-negative bacterium that was isolated from entomopathogenic nematodes.

Gram-negative
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	*Photorhabdus*
	Species	**Photorhabdus bodei**
	Full Scientific Name (LPSN)	Photorhabdus bodei Machado et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #66582]	Colony color	orangey or yellowish
[Ref.: #66582]	Cultivation medium used	Nutrient agar (NA)

Multimedia content

[Ref.: #65086]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

[Ref.: #66582]

Culture medium

Nutrient agar (NA)

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Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #66582]			growth	12-37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]	Ability of spore formation	no Confidence in %92.241
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #66582]	amygdalin ChEBI	-	builds acid from
[Ref.: #66582]	amygdalin ChEBI	-	oxidation
[Ref.: #66582]	arabinose ChEBI	-	oxidation
[Ref.: #66582]	arbutin ChEBI	-	builds acid from
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #66582]	cellobiose ChEBI	-	builds acid from
[Ref.: #66582]	D-arabinose ChEBI	-	builds acid from
[Ref.: #66582]	D-arabitol ChEBI	-	builds acid from
[Ref.: #66582]	D-fructose ChEBI	+	builds acid from
[Ref.: #66582]	D-fucose ChEBI	-	builds acid from
[Ref.: #66582]	D-galactose ChEBI	-	builds acid from
[Ref.: #66582]	D-glucose ChEBI	+	builds acid from
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	fermentation	* from API 20NE
[Ref.: #66582]	D-lyxose ChEBI	-	builds acid from
[Ref.: #66582]	D-mannitol ChEBI	-	builds acid from
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #66582]	D-mannose ChEBI	+	builds acid from
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #66582]	D-ribose ChEBI	+	builds acid from
[Ref.: #66582]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #66582]	D-tagatose ChEBI	-	builds acid from
[Ref.: #66582]	D-trehalose ChEBI	+	builds acid from
[Ref.: #66582]	D-xylose ChEBI	-	builds acid from
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #66582]	erythritol ChEBI	-	builds acid from
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #66582]	esculin ferric citrate	+	builds acid from
[Ref.: #66582]	galactitol ChEBI	-	builds acid from
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #66582]	gentiobiose ChEBI	-	builds acid from
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #66582]	glucose ChEBI	+	oxidation
[Ref.: #66582]	glycerol ChEBI	+	builds acid from
[Ref.: #66582]	glycogen ChEBI	-	builds acid from
[Ref.: #66582]	inulin ChEBI	-	builds acid from
[Ref.: #66582]	L-arabinose ChEBI	-	builds acid from
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #66582]	L-arabitol ChEBI	-	builds acid from
[Ref.: #66582]	L-fucose ChEBI	-	builds acid from
[Ref.: #66582]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #66582]	L-sorbose ChEBI	-	builds acid from
[Ref.: #66582]	L-xylose ChEBI	-	builds acid from
[Ref.: #66582]	lactose ChEBI	-	builds acid from
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #66582]	maltose ChEBI	+	builds acid from
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #66582]	mannitol ChEBI	-	oxidation
[Ref.: #66582]	melezitose ChEBI	-	builds acid from
[Ref.: #66582]	melibiose ChEBI	-	builds acid from
[Ref.: #66582]	melibiose ChEBI	-	oxidation
[Ref.: #66582]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #66582]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #66582]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #66582]	myo-inositol ChEBI	+	builds acid from
[Ref.: #66582]	myo-inositol ChEBI	-	oxidation
[Ref.: #66582]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #66582]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #66582]	potassium 2-dehydro-D-gluconate	-	builds acid from
[Ref.: #66582]	potassium 5-dehydro-D-gluconate	-	builds acid from
[Ref.: #66582]	potassium gluconate ChEBI	-	builds acid from
[Ref.: #66582]	raffinose ChEBI	-	builds acid from
[Ref.: #66582]	rhamnose ChEBI	-	oxidation
[Ref.: #66582]	ribitol ChEBI	-	builds acid from
[Ref.: #66582]	salicin ChEBI	+	builds acid from
[Ref.: #66582]	sorbitol ChEBI	-	oxidation
[Ref.: #66582]	starch ChEBI	-	builds acid from
[Ref.: #66582]	sucrose ChEBI	-	builds acid from
[Ref.: #66582]	sucrose ChEBI	-	oxidation
[Ref.: #68369]	tryptophan ChEBI	+	energy source	* from API 20NE
[Ref.: #66582]	turanose ChEBI	-	builds acid from
[Ref.: #68369]	urea ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #66582]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #66582]	acetoin ChEBI	no
[Ref.: #66582]	hydrogen sulfide ChEBI	no
[Ref.: #66582]	indole ChEBI	yes
[Ref.: #68369]	indole ChEBI	yes	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	+	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #66582]	arginine dihydrolase	-	3.5.3.6
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #66582]	beta-galactosidase	-	3.2.1.23
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #66582]	catalase	+	1.11.1.6
[Ref.: #66582]	cytochrome oxidase	-	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	-	1.9.3.1	* from API 20NE
[Ref.: #66582]	gelatinase	+
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #66582]	lysine decarboxylase	-	4.1.1.18
[Ref.: #66582]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #66582]	tryptophan deaminase	+	4.1.99.1
[Ref.: #66582]	urease	-	3.5.1.5
[Ref.: #68369]	urease	+	3.5.1.5	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #65086]	24618	-	+	+	-	+	+	+	-	+	-	+	-	+	+	+	-	-	+	+	-	-

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

[Ref.: #65086]	Sample type/isolated from	entomopathogenic nematodes
[Ref.: #65086]	Geographic location (country and/or sea, region)	Liaoning, Jinzhou
[Ref.: #65086]	Country	China
[Ref.: #65086]	Country ISO 3 Code	CHN
[Ref.: #65086]	Continent	Asia

[Ref.: #66582]	Sample type/isolated from	Heterorhabditis beicherriana
[Ref.: #66582]	Geographic location (country and/or sea, region)	Liaoning Province
[Ref.: #66582]	Country	China
[Ref.: #66582]	Country ISO 3 Code	CHN
[Ref.: #66582]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host

#Invertebrates (Other)

#Nematoda

What are isolation sources categories?

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.: #66582]	Photorhabdus bodei strain LJ24-63 16S ribosomal RNA gene, partial sequence	MK039080	1349	GenBank ENA	2029681 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Photorhabdus bodei LJ24-63	GCA_003287735	scaffold	GenBank ENA	2029681 tax ID	*
[Ref.: #66792]	Photorhabdus bodei LJ24-63	2840807575	draft	JGI IMG/M	2029681 tax ID	*

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Photorhabdus bodei LJ24-63 NCBI: GCA_003287735.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Photorhabdus bodei LJ24-63 NCBI: GCA_003287735.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	100	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	98.933	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	58.264	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	92.241	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.969	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	75.118	no

Availability in culture collections External links

[Ref.: #65086]

Culture collection no.

DSM 105690, CCOS 1159

[Ref.: #111213]

SI-ID 400626

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Whole-genome-based revisit of Photorhabdus phylogeny: proposal for the elevation of most Photorhabdus subspecies to the species level and description of one novel species Photorhabdus bodei sp. nov., and one novel subspecies Photorhabdus laumondii subsp. clarkei subsp. nov.	Machado RAR, Wuthrich D, Kuhnert P, Arce CCM, Thonen L, Ruiz C, Zhang X, Robert CAM, Karimi J, Kamali S, Ma J, Bruggmann R, Erb M	Int J Syst Evol Microbiol	10.1099/ijsem.0.002820	2018	*

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 )

#65086

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105690

#66582

Ricardo A. R. Machado, Daniel Wüthrich, Peter Kuhnert, Carla C. M. Arce, Lisa Thönen, Celia Ruiz, Xi Zhang, Christelle A. M. Robert, Javad Karimi, Shokoofeh Kamali, Juan Ma, Rémy Bruggmann and Matthias Erb: Whole-genome-based revisit of Photorhabdus phylogeny: proposal for the elevation of most Photorhabdus subspecies to the species level and description of one novel species Photorhabdus bodei sp. nov., and one novel subspecies Photorhabdus laumondii subsp. clarkei subsp. nov.. IJSEM 68: 2664 - 2681 2018 ( DOI 10.1099/ijsem.0.002820 , PubMed 29877789 )

#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 .

#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 )

#111213

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-ID400626.1 )

* These data were automatically processed and therefore are not curated

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