Name: Photorhabdus cinerea 3107
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5048

Type strain:

Species: Photorhabdus cinerea

Strain Designation: 3107

Culture col. no.: DSM 19724, NCAIM B 02271

Strain history: <- T. Tóth, Research and Extension Centre for Fruit Growing, Hungary

NCBI tax ID(s): 471575 (species)

SI-ID 404858

DSM 19724

Other strains from Photorhabdus cinerea

P. cinerea 3014, DSM 19716
P. cinerea 3240, DSM 19717

Section

Photorhabdus cinerea 3107 is an aerobe, mesophilic, Gram-negative animal pathogen that was isolated from intestine of the entomopathogenic nematode Heterorhabditis downesi from a deciduous forest.

Gram-negative
rod-shaped
aerobe
animal pathogen
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 cinerea**
	Full Scientific Name (LPSN)	Photorhabdus cinerea (Tóth and Lakatos 2008) Machado et al. 2018

Synonym

Photorhabdus temperata subsp. cinerea

Information on morphological and physiological properties Morphology

[Ref.: #31185]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.806

[Ref.: #31185]	Cell length	02-07 µm

[Ref.: #31185]	Cell width	1 µm

[Ref.: #31185]	Cell shape	rod-shaped

[Ref.: #69480]	Motility	yes Confidence in %98.225

[Ref.: #31185]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8263]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #8263]

Culture medium growth

[Ref.: #8263]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8263]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8263]	growth	28 °C
[Ref.: #31185]	growth	28-35 °C
[Ref.: #31185]	optimum	28 °C

[Ref.: #8263]	Temperature range	mesophilic
[Ref.: #31185]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31185]			optimum	7
[Ref.: #31185]			growth	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31185]

Oxygen tolerance

aerobe

[Ref.: #31185]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.774

[Ref.: #31185]

Observation

aggregates in chains

	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.: #31185]	histidine ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #31185]	maltose ChEBI	+	carbon source
[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	no	* 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.: #31185]	gelatinase	+
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #31185]	urease	+	3.5.1.5
[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.: #8263]	25477	-	-	+	+	+	+	+	-	+	-	+	-	+	+	+	-	-	+/-	-	-	-

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

[Ref.: #8263]	Sample type/isolated from	intestine of the entomopathogenic nematode Heterorhabditis downesi from a deciduous forest
[Ref.: #8263]	Host species	Heterorhabditis downesi
[Ref.: #8263]	Geographic location (country and/or sea, region)	Ásotthalom
[Ref.: #8263]	Country	Hungary
[Ref.: #8263]	Country ISO 3 Code	HUN
[Ref.: #8263]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Forest
#Host	#Invertebrates (Other)	#Nematoda
#Host Body-Site	#Gastrointestinal tract	-

What are isolation sources categories?

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

[Ref.: #8263]	Pathogenicity (animal)	yes
[Ref.: #8263]	Biosafety level	1	Risk group (German classification) According to TRBA 466

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.: #8263]	Photorhabdus temperata subsp. cinerea strain 3107 16S ribosomal RNA gene, partial sequence	EU136626	1479	ENA	471575 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Photorhabdus cinerea DSM 19724	GCA_011189575	scaffold	GenBank	471575 tax ID	*
[Ref.: #66792]	Photorhabdus cinerea strain DSM 19724	471575.3	wgs	PATRIC	471575 tax ID	*
[Ref.: #66792]	Photorhabdus cinerea DSM 19724	2897721305	draft	JGI IMG/M	471575 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Photorhabdus cinerea DSM 19724 NCBI: GCA_011189575.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Photorhabdus cinerea DSM 19724 NCBI: GCA_011189575.1
[Ref.: #69480]	motile	yes	89.731	no
[Ref.: #69480]	flagellated	yes	63.082	no
[Ref.: #69480]	gram-positive	no	98.461	no
[Ref.: #69480]	anaerobic	no	98.082	yes
[Ref.: #69480]	aerobic	yes	87.143	no
[Ref.: #69480]	halophile	no	86.551	no
[Ref.: #69480]	spore-forming	no	94.206	no
[Ref.: #69480]	thermophile	no	97.49	yes
[Ref.: #69480]	glucose-util	yes	91.524	no
[Ref.: #69480]	glucose-ferment	yes	84.153	no

Availability in culture collections External links

[Ref.: #8263]

Culture collection no.

DSM 19724, NCAIM B 02271

[Ref.: #74543]

SI-ID 404858

References

#8263

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19724

#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 )

#31185

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27512 (see below)

#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 )

#74543

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-ID404858.1 )

#27512

IJSEM 2579 2008 ( DOI 10.1099/ijs.0.2008/000273-0 , PubMed 18984696 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Photorhabdus cinerea in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Photorhabdus cinerea DSM 19724

Photorhabdus cinerea DSM 19724

Change proposal

Change proposal