Aequorivita vladivostokensis (CIP 108845, KMM 3516, IFO 16718)

Name: Aequorivita vladivostokensis (CIP 108845, KMM 3516, IFO 16718)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 139663

Type strain

Culture col. no. CIP 108845 KMM 3516 IFO 16718 NBRC 16718 JCM 11732

NCBI tax ID(s) 171194

Special Collections JCM CIP

History CIP <- 2005, KMM JCM <-- M. Suzuki R3516 <-- O. I. Nedashkovskaya. CIP <- 2005, KMM

Links

Aequorivita vladivostokensis CIP 108845 is a Gram-negative, rod-shaped bacterium of the family Flavobacteriaceae.

Gram-negative rod-shaped genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 99606

NBRC 16718,JCM 11732,IFO 16718,CIP 108845

@ref 20215

Last LPSN update 2026-05-29 08:39:33

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Aequorivita

Species Aequorivita vladivostokensis

Full scientific name Aequorivita vladivostokensis (Nedashkovskaya et al. 2003) Hahnke et al. 2017

Synonyms (1)

Vitellibacter vladivostokensis

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
42261	negative	rod-shaped
125438			90.5
125438	negative		99.106
125439	negative		99.649

Colony morphology

42261

Hemolysis ability0

Pigmentation

@ref	Production	Name
42261		flexirubin type pigments

Culture and growth conditions

Culture medium

@ref	Name	Composition	Medium link
42261	Marine agar (MA)	Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
42261	CIP Medium 13		Medium recipe at CIP
42261	CIP Medium 72		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
42261	positive	growth	25
42261	positive	growth	15-37
42261	negative	growth	5
42261	negative	growth	41
42261	negative	growth	45
67770	positive	growth	25

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	95.438

Spore formation

@ref	Spore formation	Confidence
125439		99.888

Halophily

@ref	Salt	Growth	Tested relation	Concentration
42261	NaCl	positive	growth	0-10 %

Observation

67770

Observationquinones: MK-6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
42261	4853 ChEBI	esculin	-	hydrolysis
42261	606565 ChEBI	hippurate	+	hydrolysis
42261	15792 ChEBI	malonate	-	assimilation
42261	17632 ChEBI	nitrate	-	reduction
42261	17632 ChEBI	nitrate	-	respiration
42261	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
42261	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
42261	15688 ChEBI	acetoin	-
42261	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
42261	alcohol dehydrogenase	-	1.1.1.1
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
42261	amylase	-
42261	beta-galactosidase	+	3.2.1.23
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
42261	caseinase	+	3.4.21.50
42261	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
42261	gamma-glutamyltransferase	+	2.3.2.2
42261	gelatinase	+
42261	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
42261	lipase	-
68382	lipase (C 14)	-		from API zym
42261	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
42261	ornithine decarboxylase	-	4.1.1.17
42261	oxidase	-
42261	phenylalanine ammonia-lyase	+	4.3.1.24
42261	protease	+
68382	trypsin	+	3.4.21.4	from API zym
42261	tryptophan deaminase	-
42261	tween esterase	+
42261	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
42261	-	+	+	+	-	+	+	-	+	+	+	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date	Host species
42261		Troitsa bay	Sea of Japan	RUS
67770	Holothurian (Apostichopus japonicus) collected from Troitsa Bay in the Gulf of Peter the Great	Sea of Japan					Apostichopus japonicus
42261	Holothurian, Apostichopus japonicus	Troitsa bay, Sea of Japan	Russian Federation	RUS	Europe	1997

Taxonmaps

69479

Global distribution of 16S sequence AB071382 (>99% sequence identity) for Aequorivita from Microbeatlas

Aquatic Samples	702
Soil Samples	138
Animal Samples	135
Plant Samples	22
Total Samples	997

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42261	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM95285v1 assembly for Aequorivita vladivostokensis KMM 3516	contig	GCA_000952855	171194.13	2627853707	171194	67.95

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Vitellibacter vladivostokensis gene for 16S rRNA, partial sequence	AB071382	1400		171194
124043	Vitellibacter vladivostokensis gene for 16S rRNA, partial sequence, strain: NBRC 16718.	AB681115	1449		171194

GC content

@ref	GC-content (mol%)	Method
67770	41.3	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM95285v1 assembly for Aequorivita vladivostokensis KMM 3516
BV-BRC: 171194.13

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.44	no
125439	motility	BacteriaNetⓘ	no	85.82	no
125439	gram_stain	BacteriaNetⓘ	negative	99.65	no
125439	spore_formation	BacteriaNetⓘ	no	99.89	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Aequorivita vladivostokensis strain KMM 3516
PATRIC: 171194.13

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.11	no
125438	anaerobic	anaerobicⓘ	no	98.68	no
125438	spore-forming	spore-formingⓘ	no	89.33	no
125438	aerobic	aerobicⓘ	yes	86.10	no
125438	thermophilic	thermophileⓘ	no	96.39	no
125438	flagellated	motile2+ⓘ	no	90.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Genome-Based Taxonomic Classification of Bacteroidetes.	Hahnke RL, Meier-Kolthoff JP, Garcia-Lopez M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk HP, Goker M.	Front Microbiol	10.3389/fmicb.2016.02003	2016
	Marine sediments microbes degrade a limited repertoire of organic UV filters.	Fagervold SK, Rohee C, Lebaron P.	Environ Sci Pollut Res Int	10.1007/s11356-025-36772-y	2025
Genetics	Draft genome sequence of Vitellibacter vladivostokensis KMM 3516(T): a protease-producing bacterium.	Thevarajoo S, Selvaratnam C, Chan KG, Goh KM, Chong CS	Mar Genomics	10.1016/j.margen.2015.04.009	2015
Phylogeny	Aequorivita iocasae sp. nov., a halophilic bacterium isolated from sediment collected at a cold seep field in the South China Sea.	Zhang H, Wang H, Cao L, Chen H, Zhong Z, Wang M, Lian C, Liu R, Zhou L, Li C	Int J Syst Evol Microbiol	10.1099/ijsem.0.005199	2022
Phylogeny	Vitellibacter echinoideorum sp. nov., isolated from a sea urchin (Tripneustes gratilla).	Lin SY, Hameed A, Wen CZ, Liu YC, Hsu YH, Shen FT, Lai WA, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.000258	2015
Phylogeny	Vitellibacter vladivostokensis gen. nov., sp. nov., a new member of the phylum Cytophaga-Flavobacterium-Bacteroides.	Nedashkovskaya OI, Suzuki M, Vysotskii MV, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.02302-0	2003

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 )
#42261	Collection of Institut Pasteur ; Curators of the CIP; CIP 108845
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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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Aequorivita vladivostokensis (CIP 108845, KMM 3516, IFO 16718)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000952855

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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