Name: Photorhabdus khanii C1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5051

Type strain:

Species: Photorhabdus khanii

Strain Designation: C1, NC-19, NC19

Culture col. no.: DSM 3369, ATCC 29304, CIP 109947

Strain history: CIP <- 2009, P. Tailliez, EMIP-UMII INRA, Montpellier Univ., Montpellier, France: strain NC19

NCBI tax ID(s): 1004150 (species)

SI-ID 11109

LMG 8288, ATCC 29304, DSM 3369, CIP 109947

Section

Photorhabdus khanii C1 is a facultative anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from hemocoel of Heliothis virescens larvae.

Gram-negative
motile
rod-shaped
animal pathogen
facultative anaerobe
mesophilic
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 khanii**
	Full Scientific Name (LPSN)	Photorhabdus khanii (Tailliez et al. 2010) Machado et al. 2018

Synonym

Photorhabdus temperata subsp. khanii

Information on morphological and physiological properties Morphology

[Ref.: #120410]	Gram stain	negative

[Ref.: #120410]	Cell shape	rod-shaped

[Ref.: #120410]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #33678]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #33678]

Culture medium growth

[Ref.: #33678]

Culture medium composition

expand / minimize

[Ref.: #1362]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #1362]

Culture medium growth

[Ref.: #1362]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1362]

Culture medium composition

expand / minimize

[Ref.: #120410]

Culture medium

CIP Medium 72

[Ref.: #120410]

Culture medium growth

[Ref.: #120410]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #1362]			growth	25 °C
[Ref.: #33678]			growth	30 °C

[Ref.: #1362]	Temperature range	mesophilic
[Ref.: #33678]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #120410]

Oxygen tolerance

facultative anaerobe

	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]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #120410]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #120410]	nitrite ChEBI	-	reduction
[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.: #120410]		indole ChEBI	no
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

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

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68369]	arginine dihydrolase	+	3.5.3.6	* from API 20NE
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #120410]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68369]	cytochrome oxidase	-	1.9.3.1	* from API 20NE
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120410]	oxidase	-
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #120410]	urease	-	3.5.1.5
[Ref.: #68369]	urease	+	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	+		* from API zym
	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.: #1362]	25190	-	-	-	+	+	+	+	-	+	-	+	-	+	+	+	-	-	+/-	-	-	-

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #120410]	12243	-	+	-	+	-	+	+	-	+	-	+	+	-	-	-	+	-	+	-	-

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

[Ref.: #1362]	Sample type/isolated from	hemocoel of Heliothis virescens larvae
[Ref.: #1362]	Host species	Heliothis virescens

[Ref.: #120410]	Sample type/isolated from	Animal, Nematode, Chromonema helliothidis
[Ref.: #120410]	Geographic location (country and/or sea, region)	Clayton, North Carolina
[Ref.: #120410]	Country	United States of America
[Ref.: #120410]	Country ISO 3 Code	USA
[Ref.: #120410]	Continent	North America
[Ref.: #120410]	Isolation date	1976
* marker position based on {}

Isolation sources categories

#Host

#Arthropoda

#Insecta

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X82249 (>99% sequence identity) for Photorhabdus from Microbeatlas

Aquatic Samples	4
Soil Samples	5
Animal Samples	11
Plant Samples	2
Total Samples	22

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #1362]	Pathogenicity (animal)	yes
[Ref.: #1362]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120410]	Biosafety level	1	Risk group (French classification)

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.: #1362]	Photorhabdus temperata strain NC19 16S ribosomal RNA gene, partial sequence	AY278657	1499	ENA	1004151 tax ID
[Ref.: #20218]	Photorhabdus luminescens gene for 16S rRNA, partial sequence, strain: ATCC 29304	D78004	1483	ENA	29488 tax ID	*
[Ref.: #20218]	Photorhabdus temperata 16S rRNA gene, strain DSM 3369	X82249	1499	ENA	171441 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Photorhabdus khanii NC19	GCA_000517265	scaffold	GenBank	1004151 tax ID	*
[Ref.: #66792]	Photorhabdus khanii NC19	2518285522	draft	JGI IMG/M	1004151 tax ID	*

[Ref.: #1362]

GC-content

44.0 mol%

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 khanii NC19 NC19 NCBI: GCA_000517265.1
[Ref.: #69480]	motile	yes	87.565	no
[Ref.: #69480]	flagellated	yes	64.509	no
[Ref.: #69480]	gram-positive	no	98.511	no
[Ref.: #69480]	anaerobic	no	98.356	no
[Ref.: #69480]	halophile	no	85.622	no
[Ref.: #69480]	spore-forming	no	93.998	no
[Ref.: #69480]	thermophile	no	98.221	yes
[Ref.: #69480]	glucose-util	yes	92.052	yes
[Ref.: #69480]	aerobic	yes	85.739	no
[Ref.: #69480]	glucose-ferment	yes	86.894	no

Availability in culture collections External links

[Ref.: #1362]

Culture collection no.

DSM 3369, ATCC 29304, CIP 109947

[Ref.: #74546]

SI-ID 11109

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*

References

#1362

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3369

#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 )

#33678 ; 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 .

#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 .

#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) .

#74546

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-ID11109.1 )

#120410 Collection of Institut Pasteur ; Curators of the CIP; CIP 109947
* These data were automatically processed and therefore are not curated

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