Rubritalea profundi (NBRC 110691, KCTC 52460, SAORIC-165)

Name: Rubritalea profundi (NBRC 110691, KCTC 52460, SAORIC-165)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159705

Type strain

Strain Designation SAORIC-165

Culture col. no. NBRC 110691 KCTC 52460 SAORIC-165

NCBI tax ID(s) 1658618

Special Collections KCTC Literature strains

Rubritalea profundi SAORIC-165 is a facultative anaerobe, psychrophilic, Gram-negative prokaryote that forms circular colonies and was isolated from deep-seawater .

Gram-negative rod-shaped colony-forming facultative anaerobe psychrophilic genome sequence 16S sequence

Name and taxonomic classification

Culture Collection Numbers

NBRC 110691 KCTC 52460 SAORIC-165

@ref 20215

Last LPSN update 2025-12-16 10:08:19

Domain Pseudomonadati

Phylum Verrucomicrobiota

Class Verrucomicrobiia

Order Verrucomicrobiales

Family Rubritaleaceae

Genus Rubritalea

Species Rubritalea profundi

Full scientific name Rubritalea profundi Song et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
66553	negative	1.1-1.4 µm	0.9-1 µm	rod-shaped
125438	negative					94.995

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
66553	<1 mm	red	circular	10 days	marine R2A

Pigmentation

@ref	Production	Color	Name
66553		maximum spectral peaks are found at 494 nm and 523 nm	caroteniod pigments

Culture and growth conditions

Culture medium

@ref	Name	Growth
66553	marine R2A

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
66553	positive	optimum	10	psychrophilic
66553	positive	growth	4-15	psychrophilic

Culture pH

@ref	Ability	Type	PH	PH range
66553	positive	optimum	7
66553	positive	growth	6.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

66553

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125438		91.463

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66553	NaCl	positive	growth	2-4 %(w/v)

Observation

66553

ObservationDivides by binary fission.

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66553	63152 ChEBI	alpha-D-rhamnose	-	carbon source
66553	27613 ChEBI	amygdalin	-	builds acid from
66553	18305 ChEBI	arbutin	-	builds acid from
66553	17057 ChEBI	cellobiose	-	builds acid from
66553	17057 ChEBI	cellobiose	+	carbon source
66553	53258 ChEBI	citric acid	-	carbon source
66553	17108 ChEBI	D-arabinose	-	builds acid from
66553	18333 ChEBI	D-arabitol	-	builds acid from
66553	15824 ChEBI	D-fructose	-	builds acid from
66553	15824 ChEBI	D-fructose	-	carbon source
66553	28847 ChEBI	D-fucose	-	builds acid from
66553	12936 ChEBI	D-galactose	+	builds acid from
66553	12936 ChEBI	D-galactose	+	carbon source
66553	8391 ChEBI	D-gluconate	+	carbon source
66553	17634 ChEBI	D-glucose	+	builds acid from
66553	17634 ChEBI	D-glucose	+	carbon source
66553	15748 ChEBI	D-glucuronate	+	carbon source
66553	17378 ChEBI	D-glyceraldehyde	-	carbon source
66553	62318 ChEBI	D-lyxose	+	builds acid from
66553	16899 ChEBI	D-mannitol	-	builds acid from
66553	16899 ChEBI	D-mannitol	-	carbon source
66553	16024 ChEBI	D-mannose	-	builds acid from
66553	16024 ChEBI	D-mannose	+	carbon source
66553	16988 ChEBI	D-ribose	-	builds acid from
66553	16988 ChEBI	D-ribose	-	carbon source
66553	17924 ChEBI	D-sorbitol	-	builds acid from
66553	17924 ChEBI	D-sorbitol	-	carbon source
66553	16443 ChEBI	D-tagatose	+	builds acid from
66553	65327 ChEBI	D-xylose	+	builds acid from
66553	65327 ChEBI	D-xylose	+	carbon source
66553	17113 ChEBI	erythritol	-	builds acid from
66553	4853 ChEBI	esculin	+	hydrolysis
66553		esculin ferric citrate	+	builds acid from
66553	16236 ChEBI	ethanol	-	carbon source
66553	16813 ChEBI	galactitol	-	builds acid from
66553	28066 ChEBI	gentiobiose	-	builds acid from
66553	17234 ChEBI	glucose	-	fermentation
66553	17754 ChEBI	glycerol	-	builds acid from
66553	17754 ChEBI	glycerol	-	carbon source
66553	15428 ChEBI	glycine	-	carbon source
66553	28087 ChEBI	glycogen	-	builds acid from
66553	15443 ChEBI	inulin	-	builds acid from
66553	17240 ChEBI	itaconate	-	carbon source
66553	16977 ChEBI	L-alanine	-	carbon source
66553	30849 ChEBI	L-arabinose	-	builds acid from
66553	30849 ChEBI	L-arabinose	-	carbon source
66553	18403 ChEBI	L-arabitol	-	builds acid from
66553	18403 ChEBI	L-arabitol	-	carbon source
66553	16467 ChEBI	L-arginine	-	carbon source
66553	18287 ChEBI	L-fucose	-	builds acid from
66553	29985 ChEBI	L-glutamate	-	carbon source
66553	15971 ChEBI	L-histidine	-	carbon source
66553	15603 ChEBI	L-leucine	-	carbon source
66553	18019 ChEBI	L-lysine	-	carbon source
66553	15729 ChEBI	L-ornithine	-	carbon source
66553	62345 ChEBI	L-rhamnose	+	builds acid from
66553	17115 ChEBI	L-serine	-	carbon source
66553	17266 ChEBI	L-sorbose	-	builds acid from
66553	65328 ChEBI	L-xylose	-	builds acid from
66553	17716 ChEBI	lactose	-	builds acid from
66553	17716 ChEBI	lactose	+	carbon source
66553	15792 ChEBI	malonate	-	carbon source
66553	17306 ChEBI	maltose	-	builds acid from
66553	17306 ChEBI	maltose	-	carbon source
66553	6731 ChEBI	melezitose	-	builds acid from
66553	6731 ChEBI	melezitose	-	carbon source
66553	28053 ChEBI	melibiose	-	builds acid from
66553	28053 ChEBI	melibiose	-	carbon source
66553	17790 ChEBI	methanol	-	carbon source
66553	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
66553	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
66553	74863 ChEBI	methyl beta-D-xylopyranoside	+	builds acid from
66553	16830 ChEBI	methylamine	-	carbon source
66553	17268 ChEBI	myo-inositol	-	builds acid from
66553	17268 ChEBI	myo-inositol	-	carbon source
66553	59640 ChEBI	N-acetylglucosamine	-	builds acid from
66553	59640 ChEBI	N-acetylglucosamine	+	carbon source
66553	17632 ChEBI	nitrate	-	reduction
66553		potassium 2-dehydro-D-gluconate	+	builds acid from
66553		potassium 5-dehydro-D-gluconate	+	builds acid from
66553	32032 ChEBI	potassium gluconate	-	builds acid from
66553	26271 ChEBI	proline	-	carbon source
66553	17272 ChEBI	propionate	-	carbon source
66553	15361 ChEBI	pyruvate	-	carbon source
66553	16634 ChEBI	raffinose	-	builds acid from
66553	16634 ChEBI	raffinose	-	carbon source
66553	15963 ChEBI	ribitol	-	builds acid from
66553	15963 ChEBI	ribitol	-	carbon source
66553	17814 ChEBI	salicin	-	builds acid from
66553	26710 ChEBI	sodium chloride	+	required for growth
66553	28017 ChEBI	starch	-	builds acid from
66553	30031 ChEBI	succinate	-	carbon source
66553	17992 ChEBI	sucrose	-	builds acid from
66553	17992 ChEBI	sucrose	-	carbon source
66553	27082 ChEBI	trehalose	-	builds acid from
66553	27082 ChEBI	trehalose	-	carbon source
66553	32528 ChEBI	turanose	+	builds acid from
66553	17151 ChEBI	xylitol	-	builds acid from
66553	17151 ChEBI	xylitol	-	carbon source

Antibiotic resistance

@ref	ChEBI	Metabolite	Resistance conc.	Sensitivity conc.
66553	28971	ampicillin	10 µg (disc)
66553	17698	chloramphenicol		30 µg (disc)
66553	48923	erythromycin		15 µg (disc)
66553	17833	gentamicin	10 µg (disc)
66553	6104	kanamycin	30 µg (disc)
66553	100147	nalidixic acid	30 µg (disc)
66553	28077	rifampicin		50 µg (disc)
66553	27902	tetracycline		30 µg (disc)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
66553	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
66553	acid phosphatase	+	3.1.3.2
66553	alkaline phosphatase	+	3.1.3.1
66553	alpha-chymotrypsin	+	3.4.21.1
66553	alpha-fucosidase	-	3.2.1.51
66553	alpha-galactosidase	-	3.2.1.22
66553	alpha-glucosidase	-	3.2.1.20
66553	alpha-mannosidase	-	3.2.1.24
66553	arginine dihydrolase	-	3.5.3.6
66553	beta-galactosidase	-	3.2.1.23
66553	beta-glucosidase	-	3.2.1.21
66553	beta-glucuronidase	-	3.2.1.31
66553	catalase	+	1.11.1.6
66553	cystine arylamidase	-	3.4.11.3
66553	cytochrome oxidase	-	1.9.3.1
66553	esterase (C 4)	-
66553	esterase Lipase (C 8)	-
66553	gelatinase	-
66553	leucine arylamidase	-	3.4.11.1
66553	N-acetyl-beta-glucosaminidase	-	3.2.1.52
66553	naphthol-AS-BI-phosphohydrolase	+
66553	trypsin	-	3.4.21.4
66553	urease	-	3.5.1.5
66553	valine arylamidase	-

Fatty acid profile

Metadata FA analysis

@ref

66553

Fatty acid	Percentage
C16:1 w7c and/or C16:1 w6c	30.2
C14:0 iso	23
C15:0 anteiso	19
C16:0	13.1
C14:0	10.9
C18:1 w7c and/or C18:1 w6c	3.9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Sampling date	Country	Latitude	Longitude	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
66553	deep-seawater (depth: 2000m)	2011-03	Pacific Ocean	47	160 47/160	marine R2A agar	aged seawater was added	30 days	10	The deep-seawater sample was immediately transferred into a cleanroom of the RV. A portion of 100 µl of the seawater sample was inoculated onto 1/10 strength marine Reasoner's 2A agar (R2A; BD Difco), into which aged seawater was added. The agar plates were incubated at 10°C for 30 days.

Taxonmaps

69479

Global distribution of 16S sequence KR108285 (>99% sequence identity) for Rubritalea profundi subclade from Microbeatlas

Aquatic Samples	401
Soil Samples	14
Animal Samples	8
Plant Samples
Total Samples	423

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	ASM295444v1 assembly for Rubritalea profundi SAORIC-165	scaffold	GCA_002954445	1658618.8	1658618	47.67

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66553	Rubritalea profundi strain SAORIC-165 16S ribosomal RNA gene, partial sequence	KR108285	1456		1658618

GC content

@ref	GC-content (mol%)	Method
66553	50.7	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rubritalea profundi SAORIC-165
NCBI: GCA_002954445.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.00	no
125438	anaerobic	anaerobicⓘ	no	88.75	yes
125438	aerobic	aerobicⓘ	yes	64.51	yes
125438	spore-forming	spore-formingⓘ	no	91.46	no
125438	thermophilic	thermophileⓘ	no	96.78	yes
125438	flagellated	motile2+ⓘ	no	78.06	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Genome analysis of Rubritalea profundi SAORIC-165(T), the first deep-sea verrucomicrobial isolate, from the northwestern Pacific Ocean.	Song J, Kang I, Joung Y, Yoshizawa S, Kaneko R, Oshima K, Hattori M, Hamasaki K, Kogure K, Kim S, Lee K, Cho JC	J Microbiol	10.1007/s12275-019-8712-8	2019
Phylogeny	Rubritalea profundi sp. nov., isolated from deep-seawater and emended description of the genus Rubritalea in the phylum Verrucomicrobia.	Song J, Lim Y, Joung Y, Cho JC, Kogure K	Int J Syst Evol Microbiol	10.1099/ijsem.0.002686	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 )
#66553	Jaeho Song, Yeonjung Lim, Yochan Joung, Jang-Cheon Cho, Kazuhiro Kogure: Rubritalea profundi sp. nov., isolated from deep-seawater and emended description of the genus Rubritalea in the phylum Verrucomicrobia. IJSEM 68: 1384 - 1389 2018 ( DOI 10.1099/ijsem.0.002686 , PubMed 29509135 )
#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) .
#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 )

Rate our new design

Content

About us

Rubritalea profundi (NBRC 110691, KCTC 52460, SAORIC-165)

Name and taxonomic classification

Culture Collection Numbers

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

Fatty acid profile?

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_002954445

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media

Fatty acid profile