Photobacterium chitinilyticum (MCCC 1K03517, KCTC 62619, JCM 32689)

Name: Photobacterium chitinilyticum (MCCC 1K03517, KCTC 62619, JCM 32689)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 164329

Type strain

Culture col. no. MCCC 1K03517 KCTC 62619 JCM 32689 BEI 247

NCBI tax ID(s) 2485123

Special Collections JCM KCTC Literature strains

History JCM <-- M. Yu; Coll. of Mar. Life Sci., Ocean Univ. of China, China; BEI247.

Links

Photobacterium chitinilyticum JCM 32689 is a facultative aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from Sea water at the bottom of the East China Sea .

Gram-negative motile rod-shaped colony-forming facultative aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 27225

KCTC 62619,JCM 32689

@ref 20215

Last LPSN update 2026-05-29 08:45:23

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order "Vibrionales"

Family Vibrionaceae

Genus Photobacterium

Species Photobacterium chitinilyticum

Full scientific name Photobacterium chitinilyticum Wang et al. 2019

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
67911	negative	1.2-2.7 µm	0.5-0.9 µm	rod-shaped	polar
125439	negative					98.386
125438	negative					99.5

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
67911	0.5-1.0 mm	yellow	circular	1 day	Marine agar (MA)

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
67770	positive	growth	28
67911	positive	growth	10-37
67911	positive	optimum	24

Culture pH

@ref	Ability	Type	PH
67911	positive	optimum	7
67911	positive	growth	5.0-8.0

Physiology and metabolism

Oxygen tolerance

67911

Oxygen tolerancefacultative aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.917

Halophily

@ref	Salt	Growth	Tested relation	Concentration
67911	NaCl	positive	growth	1.0-5.0 %(w/v)
67911	NaCl	positive	optimum	3 %(w/v)

Observation

@ref	Observation
67911	The major respiratory quinone is Q-8
67911	The major polar lipids are phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, two phospholipids and one unknown lipid
67911	Non-luminescent is observed on MA and LM plate

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
67911		1 % sodium lactate	+	assimilation
67911	13705 ChEBI	acetoacetate	+	assimilation
67911	58187 ChEBI	alginate	-	hydrolysis
67911	27613 ChEBI	amygdalin	+	fermentation
67911	161680 ChEBI	aztreonam	+	assimilation
67911		casein	-	hydrolysis
67911	17057 ChEBI	cellobiose	+	assimilation
67911	62968 ChEBI	cellulose	-	hydrolysis
67911	16947 ChEBI	citrate	+	assimilation
67911		crab shell chitin	-	hydrolysis
67911	15824 ChEBI	D-fructose	+	respiration
67911	78697 ChEBI	D-fructose 6-phosphate	+	assimilation
67911	28847 ChEBI	D-fucose	+	builds acid from
67911	28847 ChEBI	D-fucose	+	respiration
67911	62318 ChEBI	D-lyxose	+	builds acid from
67911	16899 ChEBI	D-mannitol	+	respiration
67911	16024 ChEBI	D-mannose	+	respiration
67911	17924 ChEBI	D-sorbitol	+	assimilation
67911	16443 ChEBI	D-tagatose	+	builds acid from
67911	16991 ChEBI	dna	+	hydrolysis
67911	5291 ChEBI	gelatin	+	hydrolysis
67911	28066 ChEBI	gentiobiose	+	builds acid from
67911	28066 ChEBI	gentiobiose	+	respiration
67911	17234 ChEBI	glucose	+	fermentation
67911	17234 ChEBI	glucose	+	oxidation
67911	32323 ChEBI	glucuronamide	+	assimilation
67911	24297 ChEBI	glucuronate	+	assimilation
67911		L-alanine 4-nitroanilide	+	assimilation
67911	15971 ChEBI	L-histidine	+	assimilation
67911	62345 ChEBI	L-rhamnose	+	respiration
67911	17716 ChEBI	lactose	+	builds acid from
67911	6472 ChEBI	lincomycin	+	assimilation
67911	25115 ChEBI	malate	+	assimilation
67911	29864 ChEBI	mannitol	+	fermentation
67911	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from
67911	43943 ChEBI	methyl alpha-D-mannoside	+	builds acid from
67911	320055 ChEBI	methyl beta-D-glucopyranoside	+	assimilation
67911	17268 ChEBI	myo-inositol	+	oxidation
67911	63154 ChEBI	N-acetyl-beta-D-mannosamine	+	assimilation
67911	59640 ChEBI	N-acetylglucosamine	+	respiration
67911	100147 ChEBI	nalidixic acid	+	assimilation
67911		potassium 5-dehydro-D-gluconate	+	builds acid from
67911	26710 ChEBI	sodium chloride	+	assimilation
67911	132106 ChEBI	sodium propionate	+	assimilation
67911	28017 ChEBI	starch	-	hydrolysis
67911	17992 ChEBI	sucrose	+	fermentation
67911	17992 ChEBI	sucrose	+	oxidation
67911	45735 ChEBI	troleandomycin	+	assimilation
67911	32528 ChEBI	turanose	+	builds acid from
67911	32528 ChEBI	turanose	+	respiration
67911	53424 ChEBI	tween 20	+	hydrolysis
67911	53423 ChEBI	tween 40	+	hydrolysis
67911	53426 ChEBI	tween 80	+	hydrolysis
67911	16199 ChEBI	urea	-	hydrolysis
67911	28001 ChEBI	vancomycin	+	assimilation
67911	17151 ChEBI	xylitol	+	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
67911	16136 ChEBI	hydrogen sulfide
67911	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
67911	acid phosphatase	-	3.1.3.2
67911	alkaline phosphatase	-	3.1.3.1
67911	alpha-fucosidase	+	3.2.1.51
67911	alpha-galactosidase	+	3.2.1.22
67911	alpha-glucosidase	+	3.2.1.20
67911	alpha-mannosidase	+	3.2.1.24
67911	arginine dihydrolase	+	3.5.3.6
67911	beta-galactosidase	+	3.2.1.23
67911	beta-glucosidase	+	3.2.1.21
67911	beta-glucuronidase	+	3.2.1.31
67911	catalase	+	1.11.1.6
67911	chymotrypsin	+	3.4.4.5
67911	cystine arylamidase	+	3.4.11.3
67911	cytochrome oxidase	+	1.9.3.1
67911	esterase (C 4)	+
67911	esterase Lipase (C 8)	+
67911	gelatinase	+
67911	leucine arylamidase	-	3.4.11.1
67911	lipase (C 14)	+
67911	lysine decarboxylase	-	4.1.1.18
67911	N-acetyl-beta-glucosaminidase	+	3.2.1.52
67911	naphthol-AS-BI-phosphohydrolase	-
67911	ornithine decarboxylase	-	4.1.1.17
67911	trypsin	+	3.4.21.4
67911	tryptophan deaminase	-	4.1.99.1
67911	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

67911

Fatty acid	Percentage
C16:1 w7c /C16:1 w6c	52.5
C16:0	23.3
C18:1 w7c	6
C14:0	4.5
C12:0 3OH	4
C18:0	1.7

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Latitude	Longitude
67770	Sea water at the bottom of the East China Sea (28° N, 122° E)		28	122 28/122
67911	seawater at the bottom	East China Sea	28.588	122.24 28.588/122.24

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67911	ASM410435v1 assembly for Photobacterium chitinilyticum BEI247	contig	GCA_004104355	2485123.3	2885236679	2485123	15.18

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Photobacterium chitinilyticum 16S ribosomal RNA gene, partial sequence	MG754451	1517		2485123

GC content

@ref	GC-content (mol%)	Method
67911	46.45	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM410435v1 assembly for Photobacterium chitinilyticum BEI247
NCBI: GCA_004104355

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	98.39	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	87.57	no
125439	motility	BacteriaNetⓘ	yes	77.69	no
125439	spore_formation	BacteriaNetⓘ	no	99.92	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Photobacterium chitinilyticum BEI247
NCBI: GCA_004104355.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	yes
125438	anaerobic	anaerobicⓘ	no	94.17	yes
125438	aerobic	aerobicⓘ	no	67.98	no
125438	spore-forming	spore-formingⓘ	no	87.55	no
125438	thermophilic	thermophileⓘ	no	100.00	yes
125438	flagellated	motile2+ⓘ	yes	89.32	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Photobacterium chitinilyticum sp. nov., a marine bacterium isolated from seawater at the bottom of the East China Sea.	Wang X, Li Y, Xue CX, Li B, Zhou S, Liu L, Zhang XH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003343	2019

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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67911	Xiaolei Wang, Yuying Li, Chun-Xu Xue, Bei Li, Shun Zhou, Lijun Liu, Xiao-Hua Zhang: Photobacterium chitinilyticum sp. nov., a marine bacterium isolated from seawater at the bottom of the East China Sea. IJSEM 69: 1477 - 1483 2019 ( DOI 10.1099/ijsem.0.003343 )
#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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Photobacterium chitinilyticum (MCCC 1K03517, KCTC 62619, JCM 32689)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_004104355

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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