Name: Rubrivirga profundi SAORIC-476
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140498

Type strain:

Species: Rubrivirga profundi

Strain Designation: SAORIC-476

Culture col. no.: NBRC 110607, KACC 18401

NCBI tax ID(s): 1658620 (species)

Section

Rubrivirga profundi SAORIC-476 is a facultative anaerobe, thermophilic, Gram-negative bacterium that forms circular colonies and was isolated from deep-sea water sample from 3000m depth.

colony-forming
Gram-negative
rod-shaped
facultative anaerobe
thermophilic
16S sequence
Bacteria

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Rhodothermota*
	Class	*Rhodothermia*
	Order	*Rhodothermales*
	Family	*Rubricoccaceae*
	Genus	*Rubrivirga*
	Species	**Rubrivirga profundi**
	Full Scientific Name (LPSN)	Rubrivirga profundi Song et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43116]	Gram stain	negative

[Ref.: #43116]	Cell length	1.8-3.0 µm

[Ref.: #43116]	Cell width	0.6-0.8 µm

[Ref.: #43116]	Cell shape	rod-shaped

[Ref.: #43116]	Motility	no

[Ref.: #43116]	Colony size	0.5-1.0 mm
[Ref.: #43116]	Colony shape	circular
[Ref.: #43116]	Incubation period	5 days
[Ref.: #43116]	Cultivation medium used	marine agar (MA)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43116]

Culture medium

marine agar (MA)

[Ref.: #43116]

Culture medium growth

[Ref.: #43116]

Culture medium

artificial seawater medium (ASW)

[Ref.: #43116]

Culture medium growth

[Ref.: #43116]

Culture medium composition

expand / minimize

	Kind of temperature		Temperature
[Ref.: #43116]	no	growth	45 °C
[Ref.: #43116]		optimum	25 °C
[Ref.: #43116]		growth	4-42 °C

[Ref.: #43116]	Temperature range	thermophilic
[Ref.: #43116]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43116]			optimum	7.5
[Ref.: #43116]			growth	6.0-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43116]

Oxygen tolerance

facultative anaerobe

	Salt	Tested relation		Salt conc.
[Ref.: #43116]	NaCl		maximum	5	%(w/v)
[Ref.: #43116]	NaCl		optimum	3	%(w/v)
[Ref.: #43116]	NaCl	no	growth	0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43116]	2-dehydro-D-gluconate ChEBI	+	builds acid from
[Ref.: #43116]	5-dehydro-D-gluconate ChEBI	+	builds acid from
[Ref.: #43116]	alpha-L-rhamnose ChEBI	-	carbon source
[Ref.: #43116]	alpha-lactose ChEBI	-	carbon source
[Ref.: #43116]	arbutin ChEBI	-	builds acid from
[Ref.: #43116]	cellobiose ChEBI	+	carbon source
[Ref.: #43116]	cellobiose ChEBI	-	builds acid from
[Ref.: #43116]	citrate ChEBI	-	carbon source
[Ref.: #43116]	D-arabinose ChEBI	-	builds acid from
[Ref.: #43116]	D-arabitol ChEBI	-	builds acid from
[Ref.: #43116]	D-fructose ChEBI	-	carbon source
[Ref.: #43116]	D-fructose ChEBI	-	builds acid from
[Ref.: #43116]	D-galactose ChEBI	-	carbon source
[Ref.: #43116]	D-galactose ChEBI	-	builds acid from
[Ref.: #43116]	D-gluconate ChEBI	+	carbon source
[Ref.: #43116]	D-glucose ChEBI	-	carbon source
[Ref.: #43116]	D-glucose ChEBI	-	builds acid from
[Ref.: #43116]	D-glucuronate ChEBI	+	carbon source
[Ref.: #43116]	D-glyceraldehyde ChEBI	-	carbon source
[Ref.: #43116]	D-lyxose ChEBI	-	builds acid from
[Ref.: #43116]	D-mannitol ChEBI	-	carbon source
[Ref.: #43116]	D-mannitol ChEBI	-	builds acid from
[Ref.: #43116]	D-mannose ChEBI	-	carbon source
[Ref.: #43116]	D-mannose ChEBI	-	builds acid from
[Ref.: #43116]	D-ribose ChEBI	-	carbon source
[Ref.: #43116]	D-sorbitol ChEBI	-	carbon source
[Ref.: #43116]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #43116]	D-tagatose ChEBI	-	builds acid from
[Ref.: #43116]	D-trehalose ChEBI	-	builds acid from
[Ref.: #43116]	D-xylose ChEBI	-	carbon source
[Ref.: #43116]	D-xylose ChEBI	-	builds acid from
[Ref.: #43116]	erythritol ChEBI	-	builds acid from
[Ref.: #43116]	esculin ChEBI	+	hydrolysis
[Ref.: #43116]	esculin ChEBI	-	builds acid from
[Ref.: #43116]	ethanol ChEBI	-	carbon source
[Ref.: #43116]	galactitol ChEBI	-	builds acid from
[Ref.: #43116]	gentiobiose ChEBI	-	builds acid from
[Ref.: #43116]	gluconate ChEBI	-	builds acid from
[Ref.: #43116]	glucose ChEBI	-	fermentation
[Ref.: #43116]	glycerol ChEBI	-	carbon source
[Ref.: #43116]	glycerol ChEBI	-	builds acid from
[Ref.: #43116]	glycine ChEBI	-	carbon source
[Ref.: #43116]	glycogen ChEBI	-	builds acid from
[Ref.: #43116]	inulin ChEBI	-	builds acid from
[Ref.: #43116]	itaconate ChEBI	-	carbon source
[Ref.: #43116]	L-alanine ChEBI	-	carbon source
[Ref.: #43116]	L-arabinose ChEBI	-	carbon source
[Ref.: #43116]	L-arabitol ChEBI	-	carbon source
[Ref.: #43116]	L-arabitol ChEBI	-	builds acid from
[Ref.: #43116]	L-arginine ChEBI	-	carbon source
[Ref.: #43116]	L-fucose ChEBI	-	builds acid from
[Ref.: #43116]	L-glutamate ChEBI	-	carbon source
[Ref.: #43116]	L-histidine ChEBI	-	carbon source
[Ref.: #43116]	L-leucine ChEBI	-	carbon source
[Ref.: #43116]	L-lysine ChEBI	-	carbon source
[Ref.: #43116]	L-ornithine ChEBI	-	carbon source
[Ref.: #43116]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #43116]	L-serine ChEBI	-	carbon source
[Ref.: #43116]	L-sorbose ChEBI	-	builds acid from
[Ref.: #43116]	lactose ChEBI	-	builds acid from
[Ref.: #43116]	malonate ChEBI	-	carbon source
[Ref.: #43116]	maltose ChEBI	+	carbon source
[Ref.: #43116]	maltose ChEBI	-	builds acid from
[Ref.: #43116]	melezitose ChEBI	-	carbon source
[Ref.: #43116]	melezitose ChEBI	-	builds acid from
[Ref.: #43116]	melibiose ChEBI	+	builds acid from
[Ref.: #43116]	melibiose ChEBI	-	carbon source
[Ref.: #43116]	methanol ChEBI	-	carbon source
[Ref.: #43116]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #43116]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #43116]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #43116]	methylamine ChEBI	-	carbon source
[Ref.: #43116]	myo-inositol ChEBI	-	carbon source
[Ref.: #43116]	myo-inositol ChEBI	-	builds acid from
[Ref.: #43116]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #43116]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #43116]	nitrate ChEBI	-	reduction
[Ref.: #43116]	proline ChEBI	-	carbon source
[Ref.: #43116]	propionate ChEBI	-	carbon source
[Ref.: #43116]	pyruvate ChEBI	-	carbon source
[Ref.: #43116]	raffinose ChEBI	+	carbon source
[Ref.: #43116]	raffinose ChEBI	-	builds acid from
[Ref.: #43116]	ribitol ChEBI	-	carbon source
[Ref.: #43116]	ribitol ChEBI	-	builds acid from
[Ref.: #43116]	ribose ChEBI	+	builds acid from
[Ref.: #43116]	salicin ChEBI	-	builds acid from
[Ref.: #43116]	starch ChEBI	-	builds acid from
[Ref.: #43116]	succinate ChEBI	-	carbon source
[Ref.: #43116]	sucrose ChEBI	+	carbon source
[Ref.: #43116]	sucrose ChEBI	-	builds acid from
[Ref.: #43116]	trehalose ChEBI	+	carbon source
[Ref.: #43116]	turanose ChEBI	-	builds acid from
[Ref.: #43116]	xylitol ChEBI	-	carbon source
[Ref.: #43116]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43116]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #43116]	penicillin g ChEBI				yes	10	µg (disc)
[Ref.: #43116]	rifampicin ChEBI	yes	50	µg (disc)
[Ref.: #43116]	streptomycin ChEBI				yes	10	µg (disc)
[Ref.: #43116]	tetracycline ChEBI	yes	30	µg (disc)
[Ref.: #43116]	vancomycin ChEBI	yes	30	µg (disc)

	Metabolite production	Metabolite	Production
[Ref.: #43116]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43116]	acid phosphatase	-	3.1.3.2
[Ref.: #43116]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43116]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43116]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43116]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43116]	alpha-glucosidase	-	3.2.1.20
[Ref.: #43116]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43116]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43116]	beta-galactosidase	+/-	3.2.1.23
[Ref.: #43116]	beta-glucosidase	-	3.2.1.21
[Ref.: #43116]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43116]	catalase	+	1.11.1.6
[Ref.: #43116]	cystine arylamidase	-	3.4.11.3
[Ref.: #43116]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43116]	esterase (C 4)	+
[Ref.: #43116]	esterase Lipase (C 8)	-
[Ref.: #43116]	gelatinase	+
[Ref.: #43116]	leucine arylamidase	-	3.4.11.1
[Ref.: #43116]	lipase (C 14)	-
[Ref.: #43116]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43116]	naphthol-AS-BI-phosphohydrolase	-
[Ref.: #43116]	trypsin	-	3.4.21.4
[Ref.: #43116]	urease	-	3.5.1.5
[Ref.: #43116]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43116]

Fatty acid	Percentage
C17:1 iso ω9c / C16:0 10-methyl	23.8
C17:0 iso	15.1
C17:1ω8c	12.7
C15:0 iso	12
C16:1ω7c / C16:1ω6c	8.7
C17:1ω6c	7.2
C16:0	5.6
C17:0	4.7
C16:1ω9c	4.4
C15:1ω6c	3.8
C16:0 iso	1.9

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #43116]	Sample type/isolated from	deep-sea water sample from 3000m depth
[Ref.: #43116]	Geographic location (country and/or sea, region)	western North Pacific Ocean
[Ref.: #43116]	Geographic location	32.0000°/145.0000°
[Ref.: #43116]	Enrichment culture	marine agar 2216 (MA; BD Difco)
[Ref.: #43116]	Enrichment culture composition	diluted 1:5 (v/v) with aged seawater
[Ref.: #43116]	Enrichment culture duration	30 days
[Ref.: #43116]	Enrichment culture temperature	10 ̊C
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Core sample

What are isolation sources categories?

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #43116]	Rubrivirga profundi 16S ribosomal RNA gene, partial sequence	KR108283	1462	GenBank	1658620 tax ID

[Ref.: #43116]

GC-content

66.2 mol%

Thermal denaturation, fluorometry

Availability in culture collections External links

[Ref.: #43116]

Culture collection no.

NBRC 110607, KACC 18401

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rubrivirga profundi sp. nov., isolated from deep-sea water, and emended description of the genus Rubrivirga.	Song J, Joung Y, Park S, Cho JC, Kogure K	Int J Syst Evol Microbiol	10.1099/ijsem.0.001182	2016	*

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 )

#43116

Jaeho Song, Yochan Joung, Sanghwa Park, Jang-Cheon Cho, Kazuhiro Kogure: Rubrivirga profundi sp. nov., isolated from deep-sea water, and emended description of the genus Rubrivirga. IJSEM 66: 3253 - 3257 2016 ( DOI 10.1099/ijsem.0.001182 , PubMed 27220700 )

* These data were automatically processed and therefore are not curated

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