Photobacterium aquae (DSM 100848, CGMCC 1.12159, JCM 18480)

Name: Photobacterium aquae (DSM 100848, CGMCC 1.12159, JCM 18480)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131276

Type strain

Strain Designation AE6

Culture col. no. DSM 100848 CGMCC 1.12159 JCM 18480 AE6

NCBI tax ID(s) 1195763

Special Collections DSMZ JCM

History DSMZ <- JCM <- Z.-P. Liu, State Key Lab. Microbial Resources, Inst. Microbiol., Chinese Academy of Sciences, Beijing; AE6 JCM <-- Z.-P. Liu AE6.

Links

Photobacterium aquae AE6 is a bacterium that was isolated from recirculating mariculture system.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 401457

JCM 18480,DSM 100848

@ref 20215

Last LPSN update 2026-05-29 08:37:34

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order "Vibrionales"

Family Vibrionaceae

Genus Photobacterium

Species Photobacterium aquae

Full scientific name Photobacterium aquae Liu et al. 2014

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	100
125439	negative	98.193

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22503	REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)		Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l Na2CO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
22503	positive	growth	28
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	90.413

Spore formation

@ref	Spore formation	Confidence
125439		99.897

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68368	16899 ChEBI	D-mannitol	-	fermentation	from API 20E
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
68368	30849 ChEBI	L-arabinose	-	fermentation	from API 20E
68368	62345 ChEBI	L-rhamnose	-	fermentation	from API 20E
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	-		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
68368	beta-galactosidase	-	3.2.1.23	from API 20E
68368	cytochrome oxidase	+	1.9.3.1	from API 20E
68368	gelatinase	+		from API 20E
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68368	urease	-	3.5.1.5	from API 20E

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
22503	-	+	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	-	-
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Host species
22503	recirculating mariculture system	Tianjin	China	CHN	Asia	38.8469	117.62 38.8469/117.62
67770	Water from a grouper (Epinephelus malabaricas) culture tank in the recirculating mariculture system in Tianjin		China	CHN	Asia			Epinephelus malabaricas

Taxonmaps

69479

Global distribution of 16S sequence JQ948040 (>99% sequence identity) for Photobacterium from Microbeatlas

Aquatic Samples	283
Soil Samples	33
Animal Samples	130
Plant Samples	7
Total Samples	453

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22503	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM102944v1 assembly for Photobacterium aquae CGMCC 1.12159	contig	GCA_001029445	1195763.3	2713896763	1195763	54.46

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22503	Photobacterium aquae strain AE6 16S ribosomal RNA gene, partial sequence	JQ948040	1366		1195763

GC content

22503

GC-content (mol%)47.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM102944v1 assembly for Photobacterium aquae CGMCC 1.12159
BV-BRC: 1195763.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	90.41	no
125439	gram_stain	BacteriaNetⓘ	negative	98.19	no
125439	motility	BacteriaNetⓘ	yes	73.12	no
125439	spore_formation	BacteriaNetⓘ	no	99.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Photobacterium aquae strain CGMCC 1.12159
PATRIC: 1195763.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	93.86	no
125438	spore-forming	spore-formingⓘ	no	88.32	no
125438	aerobic	aerobicⓘ	no	61.90	no
125438	thermophilic	thermophileⓘ	no	98.93	yes
125438	flagellated	motile2+ⓘ	yes	87.16	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Photobacterium aquae sp. nov., isolated from a recirculating mariculture system.	Liu Y, Liu LZ, Song L, Zhou YG, Qi FJ, Liu ZP	Int J Syst Evol Microbiol	10.1099/ijs.0.055020-0	2013

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 )
#22503	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100848
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#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 .
#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 )

Content

About us

Photobacterium aquae (DSM 100848, CGMCC 1.12159, JCM 18480)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001029445

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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