Abyssibacter profundi (KCTC 52933, MCCC 1K03450, OUC007)

Name: Abyssibacter profundi (KCTC 52933, MCCC 1K03450, OUC007)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159837

Type strain

Strain Designation OUC007

Culture col. no. KCTC 52933 MCCC 1K03450 OUC007 JCM 32025

NCBI tax ID(s) 2182787

Special Collections JCM KCTC Literature strains

Links

Abyssibacter profundi OUC007 is an aerobe, mesophilic, Gram-negative prokaryote that forms circular colonies and was isolated from the seawater at a depth of 1000 m in the Mariana Trench at station MT1.

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

Name and taxonomic classification

SI-ID 26607

KCTC 52933

@ref 20215

Last LPSN update 2025-12-16 10:08:21

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Nevskiales

Family Salinisphaeraceae

Genus Abyssibacter

Species Abyssibacter profundi

Full scientific name Abyssibacter profundi Zhou et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement
66716	negative	1.7-1.9 µm	0.4-0.6 µm	rod-shaped	polar
125439	negative
125439

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
66716	1-2 mm	transparent	circular	3 days	Marine agar (MA)

Culture and growth conditions

Culture medium

@ref	Name	Growth
66716	Marine agar (MA)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
66716	positive	optimum	37	mesophilic
66716	positive	growth	10-45
67770	positive	growth	37	mesophilic
67771	positive	growth	37	mesophilic

Culture pH

@ref	Ability	Type	PH
66716	positive	optimum	7.0-8.0
66716	positive	growth	7.0-9.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
66716	aerobe
67771	aerobe
125439	aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.8

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66716	NaCl	positive	growth	0-7 %(w/v)
66716	NaCl	positive	optimum	2-3 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66716	28644 ChEBI	2-oxopentanoate	+	carbon source
66716	16724 ChEBI	4-hydroxybutyrate	+	carbon source
66716	17128 ChEBI	adipate	-	assimilation
66716	58187 ChEBI	alginate	-	hydrolysis
66716	40585 ChEBI	alpha-cyclodextrin	+	carbon source
66716	27613 ChEBI	amygdalin	-	builds acid from
66716	18305 ChEBI	arbutin	-	builds acid from
66716	8295 ChEBI	beta-hydroxybutyrate	+	carbon source
66716		casein	-	hydrolysis
66716	17057 ChEBI	cellobiose	-	builds acid from
66716	62968 ChEBI	cellulose	-	hydrolysis
66716	17029 ChEBI	chitin	-	hydrolysis
66716	16383 ChEBI	cis-aconitate	+	carbon source
66716	17108 ChEBI	D-arabinose	-	builds acid from
66716	18333 ChEBI	D-arabitol	-	builds acid from
66716	15824 ChEBI	D-fructose	-	builds acid from
66716	28847 ChEBI	D-fucose	-	builds acid from
66716	12936 ChEBI	D-galactose	-	builds acid from
66716	17634 ChEBI	D-glucose	-	assimilation
66716	17634 ChEBI	D-glucose	-	builds acid from
66716	62318 ChEBI	D-lyxose	-	builds acid from
66716	16899 ChEBI	D-mannitol	-	assimilation
66716	16899 ChEBI	D-mannitol	-	builds acid from
66716	16024 ChEBI	D-mannose	-	assimilation
66716	16024 ChEBI	D-mannose	-	builds acid from
66716	16988 ChEBI	D-ribose	-	builds acid from
66716	17924 ChEBI	D-sorbitol	-	builds acid from
66716	16443 ChEBI	D-tagatose	-	builds acid from
66716	65327 ChEBI	D-xylose	-	builds acid from
66716	27689 ChEBI	decanoate	-	assimilation
66716	16991 ChEBI	dna	-	hydrolysis
66716	17113 ChEBI	erythritol	-	builds acid from
66716		esculin ferric citrate	-	builds acid from
66716	16813 ChEBI	galactitol	-	builds acid from
66716	5291 ChEBI	gelatin	+	hydrolysis
66716	28066 ChEBI	gentiobiose	-	builds acid from
66716	17754 ChEBI	glycerol	+	builds acid from
66716	28087 ChEBI	glycogen	-	builds acid from
66716	15443 ChEBI	inulin	-	builds acid from
66716	21217 ChEBI	L-alaninamide	+	carbon source
66716	30849 ChEBI	L-arabinose	-	assimilation
66716	30849 ChEBI	L-arabinose	-	builds acid from
66716	18403 ChEBI	L-arabitol	-	builds acid from
66716	18287 ChEBI	L-fucose	-	builds acid from
66716	62345 ChEBI	L-rhamnose	-	builds acid from
66716	17266 ChEBI	L-sorbose	-	builds acid from
66716	65328 ChEBI	L-xylose	-	builds acid from
66716	17716 ChEBI	lactose	-	builds acid from
66716	25115 ChEBI	malate	-	assimilation
66716	17306 ChEBI	maltose	-	assimilation
66716	17306 ChEBI	maltose	-	builds acid from
66716	6731 ChEBI	melezitose	-	builds acid from
66716	28053 ChEBI	melibiose	+	builds acid from
66716	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
66716	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
66716	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
66716	51850 ChEBI	methyl pyruvate	+	carbon source
66716	75146 ChEBI	monomethyl succinate	+	carbon source
66716	17268 ChEBI	myo-inositol	-	builds acid from
66716	59640 ChEBI	N-acetylglucosamine	-	assimilation
66716	59640 ChEBI	N-acetylglucosamine	-	builds acid from
66716	18401 ChEBI	phenylacetate	-	assimilation
66716		potassium 2-dehydro-D-gluconate	-	builds acid from
66716		potassium 5-dehydro-D-gluconate	-	builds acid from
66716	32032 ChEBI	potassium gluconate	-	assimilation
66716	32032 ChEBI	potassium gluconate	+	builds acid from
66716	16634 ChEBI	raffinose	-	builds acid from
66716	15963 ChEBI	ribitol	-	builds acid from
66716	17814 ChEBI	salicin	+	builds acid from
66716	53258 ChEBI	sodium citrate	-	assimilation
66716	28017 ChEBI	starch	+	builds acid from
66716	28017 ChEBI	starch	-	hydrolysis
66716	17992 ChEBI	sucrose	+	builds acid from
66716	27082 ChEBI	trehalose	-	builds acid from
66716	32528 ChEBI	turanose	-	builds acid from
66716	53424 ChEBI	tween 20	+	hydrolysis
66716	53423 ChEBI	tween 40	+	carbon source
66716	53423 ChEBI	tween 40	+	hydrolysis
66716	53426 ChEBI	tween 80	+	carbon source
66716	53426 ChEBI	tween 80	+	hydrolysis
66716	17151 ChEBI	xylitol	-	builds acid from

Enzymes

@ref	Value	Activity	Ec
66716	acid phosphatase	-	3.1.3.2
66716	alkaline phosphatase	+	3.1.3.1
66716	alpha-fucosidase	+	3.2.1.51
66716	alpha-galactosidase	-	3.2.1.22
66716	alpha-glucosidase	-	3.2.1.20
66716	alpha-mannosidase	-	3.2.1.24
66716	beta-galactosidase	+	3.2.1.23
66716	beta-glucosidase	-	3.2.1.21
66716	beta-glucuronidase	-	3.2.1.31
66716	catalase	-	1.11.1.6
66716	cytochrome oxidase	+	1.9.3.1
66716	esterase (C 4)	+
66716	esterase Lipase (C 8)	+
66716	gelatinase	+
66716	leucine arylamidase	+	3.4.11.1
66716	N-acetyl-beta-glucosaminidase	-	3.2.1.52
66716	naphthol-AS-BI-phosphohydrolase	+
66716	trypsin	-	3.4.21.4
66716	valine arylamidase	-

Fatty acid profile

Metadata FA analysis

@ref

66716

Fatty acid	Percentage
C18:1 w6c / C18:1 w7c	58.3
C12:0	7.22
C12:0 3OH	6.81
C18:0	6.57
C17:1 w6c	4.25
C16:0	4.03
C17:0	2.54
C17:0 10-methyl	1.94
C16:1 w5c	1.27
C20:1 w7c	1.24
C11:0	1.22
C10:0	1.05
C19:1 w6c / C19:0 cyclo	1.03

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture temperature	Isolation procedure
66716	the seawater at a depth of 1000 m in the Mariana Trench at station MT1	2015-11	1000 m in the Mariana Trench at station MT1 in the western Pacific Ocean, an average of 200 km to the east of the Mariana Islands, in the Western Pacific	Philippines	PHL	Asia	11.3839	142.5 11.3839/142.5	marine agar	28	The seawater samples were spread on marine agar 2216E plates and incubated atroom temperature (approximately 28°C) on board and 28°C in the laboratory.
67770	Seawater at a depth of 1000 m in the Mariana Trench
67771	From 1000m sea water		Marianas Trench of Pacific Ocean	International waters

Taxonmaps

69479

Global distribution of 16S sequence KY612316 (>99% sequence identity) for Abyssibacter profundi subclade from Microbeatlas

Aquatic Samples	620
Soil Samples	2
Animal Samples	26
Plant Samples	1
Total Samples	649

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM315113v1 assembly for Abyssibacter profundi OUC007	contig	GCA_003151135	2182787.3	2831460164	2182787	65.66

Genome browser: GCA_003151135

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66716	Abyssibacter profundi strain OUC007 16S ribosomal RNA gene, partial sequence	KY612316	1502		2182787

GC content

@ref	GC-content (mol%)	Method
66716	63.1	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Abyssibacter profundi OUC007
NCBI: GCA_003151135

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.80	no
125439	motility	BacteriaNetⓘ	yes	94.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	93.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Salifodinibacter halophilus gen. nov., sp. nov., a halophilic gammaproteobacterium in the family Salinisphaeraceae isolated from a salt mine in the Colombian Andes.	Parada-Pinilla MP, Diaz-Cardenas C, Lopez G, Diaz-Riano JI, Gonzalez LN, Restrepo S, Trujillo ME, Baena S	Int J Syst Evol Microbiol	10.1099/ijsem.0.004490	2020
Phylogeny	Abyssibacter profundi gen. nov., sp. nov., a marine bacterium isolated from seawater of the Mariana Trench.	Zhou S, Ren Q, Li Y, Liu J, Wang X, Wu Y, Zhang Y, Zhang XH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002999	2018

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 )
#66716	Shun Zhou, Qiaomeng Ren, Yuying Li, Jiwen Liu, Xiaolei Wang, Yanhong Wu, Yulin Zhang, Xiao-hua Zhang: Abyssibacter profundi gen. nov., sp. nov., a marine bacterium isolated from seawater of the Mariana Trench. IJSEM 68: 3423 - 3429 2018 ( DOI 10.1099/ijsem.0.002999 , PubMed 30204582 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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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Abyssibacter profundi (KCTC 52933, MCCC 1K03450, OUC007)

Name and taxonomic classification