Photorhabdus hainanensis (DSM 22397, CIP 109946, C8404)

Name: Photorhabdus hainanensis (DSM 22397, CIP 109946, C8404)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5050

Type strain

Strain Designation C8404

Culture col. no. DSM 22397 CIP 109946 C8404 CN 8404

NCBI tax ID(s) 1004166

Special Collections DSMZ CIP

Links

Photorhabdus hainanensis C8404 is a facultative anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from Heterorhabditis species.

Gram-negative motile rod-shaped facultative anaerobe mesophilic animal pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 370406

CIP 109946,DSM 22397

@ref 20215

Last LPSN update 2025-12-16 09:47:58

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Morganellaceae

Genus Photorhabdus

Species Photorhabdus hainanensis

Full scientific name Photorhabdus hainanensis (Tailliez et al. 2010) Machado et al. 2018

Synonyms (1)

Photorhabdus luminescens subsp. hainanensis

Morphology

Cell morphology

@ref	Gram stain	Cell shape
119787	negative	rod-shaped
125439	negative
125438	negative

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16317	REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)	Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a; with strain-specific modifications) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37889	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119787	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16317	positive	growth	28	mesophilic
37889	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

119787

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.5
125438		94.241

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
119787	17632 ChEBI	nitrate	-	reduction
119787	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119787	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
119787	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119787	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
119787	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
119787	-	+	-	-	-	+	+	-	+	-	+	+	-	-	-	+	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
16317	Heterorhabditis species	Heterorhabditis	Hainan island	China	CHN	Asia
119787	Animal, Nematode, Heterorhabditis sp.		Hainan Island	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence EU930342 (>99% sequence identity) for Photorhabdus from Microbeatlas

Aquatic Samples	1
Soil Samples	1
Animal Samples	3
Plant Samples	6
Total Samples	11

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
16317		1	Risk group (German classification) According to TRBA 466
119787		1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1844896v1 assembly for Photorhabdus hainanensis DSM 22397	scaffold	GCA_018448965	1004166.3	8067870578	1004166	43.35

Genome browser: GCA_018448965

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16317	Photorhabdus luminescens strain C8404 16S ribosomal RNA gene, partial sequence	EU930342	1379		1004166
124043	Photorhabdus hainanensis strain DSM 22397 16S ribosomal RNA gene, partial sequence.	MN714265	1345		1004166

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Photorhabdus hainanensis DSM 22397
NCBI: GCA_018448965

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	no	60.90	no
125439	gram_stain	BacteriaNetⓘ	negative	98.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	79.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Photorhabdus hainanensis DSM 22397
NCBI: GCA_018448965.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	99.12	yes
125438	aerobic	aerobicⓘ	no	68.92	yes
125438	spore-forming	spore-formingⓘ	no	94.24	no
125438	thermophilic	thermophileⓘ	no	98.97	yes
125438	flagellated	motile2+ⓘ	yes	73.95	no

Literature

References

#16317	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22397
#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 )
#37889	; 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) .
#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 .
#119787	Collection of Institut Pasteur ; Curators of the CIP; CIP 109946
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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