Name: Photorhabdus laumondii subsp. clarkei BOJ-47
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158409

Type strain:

Species: Photorhabdus laumondii subsp. clarkei

Strain Designation: BOJ-47

Culture col. no.: DSM 105531, CCOS 1160

Strain history: <- R. Machado, Univ. Berne, Switzerland; BOJ-47

NCBI tax ID(s): 2029685 (subspecies)

SI-ID 403312

DSM 105531

Section

Photorhabdus laumondii subsp. clarkei BOJ-47 is a mesophilic bacterium that was isolated from Entomopathogenic nematodes.

mesophilic
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 laumondii subsp. clarkei**
	Full Scientific Name (LPSN)	Photorhabdus laumondii subsp. clarkei Machado et al. 2018

Information on morphological and physiological properties Morphology

Multimedia content

[Ref.: #65085]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65085]

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

	Temperatures	Kind of temperature		Temperature
[Ref.: #65085]			growth	28 °C

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Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	+	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	+	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #68369]	cytochrome oxidase	-	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #68369]	urease	+	3.5.1.5	* from API 20NE

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.: #65085]	24619	-	+	+	-	+	+	+	-	+	-	+	-	+	+	+	-	-	+	+	-	-

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

[Ref.: #65085]	Sample type/isolated from	Entomopathogenic nematodes
[Ref.: #65085]	Geographic location (country and/or sea, region)	Bojnourd, North Khorasan
[Ref.: #65085]	Country	Iran
[Ref.: #65085]	Country ISO 3 Code	IRN
[Ref.: #65085]	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

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Photorhabdus laumondii subsp. clarkei BOJ-47	GCA_003287575	contig	GenBank	2029685 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Photorhabdus laumondii subsp. clarkei BOJ-47 NCBI: GCA_003287575.1
[Ref.: #69480]	motile	yes	88.845	no
[Ref.: #69480]	flagellated	yes	66.178	no
[Ref.: #69480]	gram-positive	no	98.278	no
[Ref.: #69480]	anaerobic	no	98.06	no
[Ref.: #69480]	aerobic	yes	85.027	no
[Ref.: #69480]	halophile	no	86.962	no
[Ref.: #69480]	spore-forming	no	93.415	no
[Ref.: #69480]	glucose-util	yes	92.759	yes
[Ref.: #69480]	thermophile	no	98.681	yes
[Ref.: #69480]	glucose-ferment	yes	85.407	no

Availability in culture collections External links

[Ref.: #65085]

Culture collection no.

DSM 105531, CCOS 1160

[Ref.: #111212]

SI-ID 403312

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 )

#65085

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105531

#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) .

#111212

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-ID403312.1 )

* These data were automatically processed and therefore are not curated

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