Name: Rubritalea profundi SAORIC-165
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 159705

Type strain:

Species: Rubritalea profundi

Strain Designation: SAORIC-165

Culture col. no.: NBRC 110691, KCTC 52460

NCBI tax ID(s): 1658618 (species)

Section

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

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

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Verrucomicrobiota*
	Class	*Verrucomicrobiia*
	Order	*Verrucomicrobiales*
	Family	*Rubritaleaceae*
	Genus	*Rubritalea*
	Species	**Rubritalea profundi**
	Full Scientific Name (LPSN)	Rubritalea profundi Song et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66553]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.807

[Ref.: #66553]	Cell length	1.1-1.4 µm

[Ref.: #66553]	Cell width	0.9-1 µm

[Ref.: #66553]	Cell shape	rod-shaped

[Ref.: #66553]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %93.881

[Ref.: #66553]	Colony size	<1 mm
[Ref.: #66553]	Colony color	red
[Ref.: #66553]	Colony shape	circular
[Ref.: #66553]	Incubation period	10 days
[Ref.: #66553]	Cultivation medium used	marine R2A

[Ref.: #66553]	Pigment production	yes
[Ref.: #66553]	Pigmentation color	maximum spectral peaks are found at 494 nm and 523 nm
[Ref.: #66553]	Pigment name	caroteniod pigments

Information on culture and growth conditions Culture and growth conditions

[Ref.: #66553]

Culture medium

marine R2A

[Ref.: #66553]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #66553]			optimum	10 °C
[Ref.: #66553]			growth	4-15 °C

[Ref.: #66553]

Temperature range

psychrophilic

	pH	Kind of pH		pH
[Ref.: #66553]			optimum	7
[Ref.: #66553]			growth	6.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66553]

Oxygen tolerance

facultative anaerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.975
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66553]		NaCl		growth	2-4	%(w/v)

[Ref.: #66553]

Observation

Divides by binary fission.

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66553]	alpha-D-rhamnose ChEBI	-	carbon source
[Ref.: #66553]	amygdalin ChEBI	-	builds acid from
[Ref.: #66553]	arbutin ChEBI	-	builds acid from
[Ref.: #66553]	cellobiose ChEBI	-	builds acid from
[Ref.: #66553]	cellobiose ChEBI	+	carbon source
[Ref.: #66553]	citric acid ChEBI	-	carbon source
[Ref.: #66553]	D-arabinose ChEBI	-	builds acid from
[Ref.: #66553]	D-arabitol ChEBI	-	builds acid from
[Ref.: #66553]	D-fructose ChEBI	-	builds acid from
[Ref.: #66553]	D-fructose ChEBI	-	carbon source
[Ref.: #66553]	D-fucose ChEBI	-	builds acid from
[Ref.: #66553]	D-galactose ChEBI	+	builds acid from
[Ref.: #66553]	D-galactose ChEBI	+	carbon source
[Ref.: #66553]	D-gluconate ChEBI	+	carbon source
[Ref.: #66553]	D-glucose ChEBI	+	builds acid from
[Ref.: #66553]	D-glucose ChEBI	+	carbon source
[Ref.: #66553]	D-glucuronate ChEBI	+	carbon source
[Ref.: #66553]	D-glyceraldehyde ChEBI	-	carbon source
[Ref.: #66553]	D-lyxose ChEBI	+	builds acid from
[Ref.: #66553]	D-mannitol ChEBI	-	builds acid from
[Ref.: #66553]	D-mannitol ChEBI	-	carbon source
[Ref.: #66553]	D-mannose ChEBI	-	builds acid from
[Ref.: #66553]	D-mannose ChEBI	+	carbon source
[Ref.: #66553]	D-ribose ChEBI	-	builds acid from
[Ref.: #66553]	D-ribose ChEBI	-	carbon source
[Ref.: #66553]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #66553]	D-sorbitol ChEBI	-	carbon source
[Ref.: #66553]	D-tagatose ChEBI	+	builds acid from
[Ref.: #66553]	D-xylose ChEBI	+	builds acid from
[Ref.: #66553]	D-xylose ChEBI	+	carbon source
[Ref.: #66553]	erythritol ChEBI	-	builds acid from
[Ref.: #66553]	esculin ChEBI	+	hydrolysis
[Ref.: #66553]	esculin ferric citrate	+	builds acid from
[Ref.: #66553]	ethanol ChEBI	-	carbon source
[Ref.: #66553]	galactitol ChEBI	-	builds acid from
[Ref.: #66553]	gentiobiose ChEBI	-	builds acid from
[Ref.: #66553]	glucose ChEBI	-	fermentation
[Ref.: #66553]	glycerol ChEBI	-	builds acid from
[Ref.: #66553]	glycerol ChEBI	-	carbon source
[Ref.: #66553]	glycine ChEBI	-	carbon source
[Ref.: #66553]	glycogen ChEBI	-	builds acid from
[Ref.: #66553]	inulin ChEBI	-	builds acid from
[Ref.: #66553]	itaconate ChEBI	-	carbon source
[Ref.: #66553]	L-alanine ChEBI	-	carbon source
[Ref.: #66553]	L-arabinose ChEBI	-	builds acid from
[Ref.: #66553]	L-arabinose ChEBI	-	carbon source
[Ref.: #66553]	L-arabitol ChEBI	-	builds acid from
[Ref.: #66553]	L-arabitol ChEBI	-	carbon source
[Ref.: #66553]	L-arginine ChEBI	-	carbon source
[Ref.: #66553]	L-fucose ChEBI	-	builds acid from
[Ref.: #66553]	L-glutamate ChEBI	-	carbon source
[Ref.: #66553]	L-histidine ChEBI	-	carbon source
[Ref.: #66553]	L-leucine ChEBI	-	carbon source
[Ref.: #66553]	L-lysine ChEBI	-	carbon source
[Ref.: #66553]	L-ornithine ChEBI	-	carbon source
[Ref.: #66553]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #66553]	L-serine ChEBI	-	carbon source
[Ref.: #66553]	L-sorbose ChEBI	-	builds acid from
[Ref.: #66553]	L-xylose ChEBI	-	builds acid from
[Ref.: #66553]	lactose ChEBI	-	builds acid from
[Ref.: #66553]	lactose ChEBI	+	carbon source
[Ref.: #66553]	malonate ChEBI	-	carbon source
[Ref.: #66553]	maltose ChEBI	-	builds acid from
[Ref.: #66553]	maltose ChEBI	-	carbon source
[Ref.: #66553]	melezitose ChEBI	-	builds acid from
[Ref.: #66553]	melezitose ChEBI	-	carbon source
[Ref.: #66553]	melibiose ChEBI	-	builds acid from
[Ref.: #66553]	melibiose ChEBI	-	carbon source
[Ref.: #66553]	methanol ChEBI	-	carbon source
[Ref.: #66553]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #66553]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #66553]	methyl beta-D-xylopyranoside ChEBI	+	builds acid from
[Ref.: #66553]	methylamine ChEBI	-	carbon source
[Ref.: #66553]	myo-inositol ChEBI	-	builds acid from
[Ref.: #66553]	myo-inositol ChEBI	-	carbon source
[Ref.: #66553]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #66553]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #66553]	nitrate ChEBI	-	reduction
[Ref.: #66553]	potassium 2-dehydro-D-gluconate	+	builds acid from
[Ref.: #66553]	potassium 5-dehydro-D-gluconate	+	builds acid from
[Ref.: #66553]	potassium gluconate ChEBI	-	builds acid from
[Ref.: #66553]	proline ChEBI	-	carbon source
[Ref.: #66553]	propionate ChEBI	-	carbon source
[Ref.: #66553]	pyruvate ChEBI	-	carbon source
[Ref.: #66553]	raffinose ChEBI	-	builds acid from
[Ref.: #66553]	raffinose ChEBI	-	carbon source
[Ref.: #66553]	ribitol ChEBI	-	builds acid from
[Ref.: #66553]	ribitol ChEBI	-	carbon source
[Ref.: #66553]	salicin ChEBI	-	builds acid from
[Ref.: #66553]	sodium chloride ChEBI	+	required for growth
[Ref.: #66553]	starch ChEBI	-	builds acid from
[Ref.: #66553]	succinate ChEBI	-	carbon source
[Ref.: #66553]	sucrose ChEBI	-	builds acid from
[Ref.: #66553]	sucrose ChEBI	-	carbon source
[Ref.: #66553]	trehalose ChEBI	-	builds acid from
[Ref.: #66553]	trehalose ChEBI	-	carbon source
[Ref.: #66553]	turanose ChEBI	+	builds acid from
[Ref.: #66553]	xylitol ChEBI	-	builds acid from
[Ref.: #66553]	xylitol ChEBI	-	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #66553]	ampicillin ChEBI				yes	10	µg (disc)
[Ref.: #66553]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #66553]	erythromycin ChEBI	yes	15	µg (disc)
[Ref.: #66553]	gentamicin ChEBI				yes	10	µg (disc)
[Ref.: #66553]	kanamycin ChEBI				yes	30	µg (disc)
[Ref.: #66553]	nalidixic acid ChEBI				yes	30	µg (disc)
[Ref.: #66553]	rifampicin ChEBI	yes	50	µg (disc)
[Ref.: #66553]	tetracycline ChEBI	yes	30	µg (disc)

	Metabolite production	Metabolite	Production
[Ref.: #66553]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #66553]	acid phosphatase	+	3.1.3.2
[Ref.: #66553]	alkaline phosphatase	+	3.1.3.1
[Ref.: #66553]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #66553]	alpha-fucosidase	-	3.2.1.51
[Ref.: #66553]	alpha-galactosidase	-	3.2.1.22
[Ref.: #66553]	alpha-glucosidase	-	3.2.1.20
[Ref.: #66553]	alpha-mannosidase	-	3.2.1.24
[Ref.: #66553]	arginine dihydrolase	-	3.5.3.6
[Ref.: #66553]	beta-galactosidase	-	3.2.1.23
[Ref.: #66553]	beta-glucosidase	-	3.2.1.21
[Ref.: #66553]	beta-glucuronidase	-	3.2.1.31
[Ref.: #66553]	catalase	+	1.11.1.6
[Ref.: #66553]	cystine arylamidase	-	3.4.11.3
[Ref.: #66553]	cytochrome oxidase	-	1.9.3.1
[Ref.: #66553]	esterase (C 4)	-
[Ref.: #66553]	esterase Lipase (C 8)	-
[Ref.: #66553]	gelatinase	-
[Ref.: #66553]	leucine arylamidase	-	3.4.11.1
[Ref.: #66553]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #66553]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #66553]	trypsin	-	3.4.21.4
[Ref.: #66553]	urease	-	3.5.1.5
[Ref.: #66553]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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

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

[Ref.: #66553]	Sample type/isolated from	deep-seawater (depth: 2000m)
[Ref.: #66553]	Sampling date	2011-03
[Ref.: #66553]	Country	Pacific Ocean
[Ref.: #66553]	Geographic location	47.0000°/160.0000°
[Ref.: #66553]	Enrichment culture	marine R2A agar
[Ref.: #66553]	Enrichment culture composition	aged seawater was added
[Ref.: #66553]	Enrichment culture duration	30 days
[Ref.: #66553]	Enrichment culture temperature	10 ̊C
[Ref.: #66553]	Isolation/enrichment procedure	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.
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

[Ref.: #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

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.: #66553]	Rubritalea profundi strain SAORIC-165 16S ribosomal RNA gene, partial sequence	KR108285	1456	ENA	1658618 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rubritalea profundi SAORIC-165	GCA_002954445	scaffold	GenBank	1658618 tax ID	*

[Ref.: #66553]

GC-content

50.7 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rubritalea profundi SAORIC-165 NCBI: GCA_002954445.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rubritalea profundi SAORIC-165 NCBI: GCA_002954445.1
[Ref.: #69480]	flagellated	no	95.425	no
[Ref.: #69480]	gram-positive	no	97.467	yes
[Ref.: #69480]	anaerobic	no	98.609	yes
[Ref.: #69480]	aerobic	yes	79.33	yes
[Ref.: #69480]	halophile	yes	62.675	no
[Ref.: #69480]	spore-forming	no	97.916	no
[Ref.: #69480]	glucose-util	yes	81.591	no
[Ref.: #69480]	thermophile	no	99.044	yes
[Ref.: #69480]	motile	no	91.082	yes
[Ref.: #69480]	glucose-ferment	no	78.301	no

Availability in culture collections External links

[Ref.: #66553]

Culture collection no.

NBRC 110691, KCTC 52460

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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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