Name: Rubritalea squalenifaciens HOact 23
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17851

Type strain:

Species: Rubritalea squalenifaciens

Strain Designation: HOact 23

Culture col. no.: DSM 18772, MBIC 08254, NBRC 103619

Strain history: <- H. Kasai, Marine Biotechnol. Inst., Kamaishi, Japan; HOact 23

NCBI tax ID(s): 1123071 (strain), 407226 (species)

SI-ID 398555

DSM 18772

Section

Rubritalea squalenifaciens HOact 23 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from marine sponge Halichondria okadai.

Gram-negative
rod-shaped
aerobe
mesophilic
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 squalenifaciens**
	Full Scientific Name (LPSN)	Rubritalea squalenifaciens Kasai et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32126]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.857

[Ref.: #32126]	Cell shape	rod-shaped

[Ref.: #32126]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %94.512

[Ref.: #32126]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7689]

Culture medium

RUBITELEA MEDIUM (DSMZ Medium 1177)

[Ref.: #7689]

Culture medium growth

[Ref.: #7689]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7689]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7689]	growth	28 °C
[Ref.: #32126]	growth	15-37 °C
[Ref.: #32126]	optimum	26 °C

[Ref.: #7689]	Temperature range	mesophilic
[Ref.: #32126]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32126]			optimum	8
[Ref.: #32126]			growth	7.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32126]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.951

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32126]		NaCl		growth	01-04	%
[Ref.: #32126]		NaCl		optimum	2.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32126]	galactose ChEBI	+	carbon source
[Ref.: #32126]	glucose ChEBI	+	carbon source
[Ref.: #32126]	lactose ChEBI	+	carbon source
[Ref.: #32126]	melibiose ChEBI	+	carbon source
[Ref.: #32126]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #32126]	nitrate ChEBI	+	reduction
[Ref.: #32126]	raffinose ChEBI	+	carbon source
[Ref.: #32126]	sucrose ChEBI	+	carbon source
[Ref.: #32126]	xylose ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #32126]	acid phosphatase	+	3.1.3.2
[Ref.: #32126]	alkaline phosphatase	+	3.1.3.1
[Ref.: #32126]	catalase	+	1.11.1.6
[Ref.: #32126]	cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	purine metabolism	71.28	67 of 94
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	polyamine pathway	65.22	15 of 23
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	oxidative phosphorylation	48.35	44 of 91
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	ppGpp biosynthesis	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #7689]	Sample type/isolated from	marine sponge Halichondria okadai
[Ref.: #7689]	Host species	Halichondria okadai
[Ref.: #7689]	Geographic location (country and/or sea, region)	Kanagawa, Miura peninsula
[Ref.: #7689]	Country	Japan
[Ref.: #7689]	Country ISO 3 Code	JPN
[Ref.: #7689]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Host	#Invertebrates (Other)	#Porifera (Sponges)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB277853 (>99% sequence identity) for Rubritalea from Microbeatlas

Aquatic Samples	1647
Soil Samples	175
Animal Samples	757
Plant Samples	10
Total Samples	2589

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7689]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #7689]	Rubritalea squalenifaciens gene for 16S rRNA, partial sequence	AB277853	1424	ENA	407226 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rubritalea squalenifaciens DSM 18772	GCA_900141815	scaffold	GenBank	1123071 tax ID	*
[Ref.: #66792]	Rubritalea squalenifaciens DSM 18772	1123071.3	wgs	PATRIC	1123071 tax ID	*
[Ref.: #66792]	Rubritalea squalenifaciens DSM 18772	2582581871	draft	JGI IMG/M	1123071 tax ID	*

[Ref.: #7689]

GC-content

52.6 mol%

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 squalenifaciens DSM 18772 DSM 18772 NCBI: GCA_900141815.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rubritalea squalenifaciens DSM 18772 DSM 18772 NCBI: GCA_900141815.1
[Ref.: #69480]	flagellated	no	96.862	yes
[Ref.: #69480]	gram-positive	no	98.112	yes
[Ref.: #69480]	anaerobic	no	98.543	yes
[Ref.: #69480]	aerobic	yes	90.144	yes
[Ref.: #69480]	halophile	no	55.544	no
[Ref.: #69480]	spore-forming	no	96.997	no
[Ref.: #69480]	thermophile	no	97.55	yes
[Ref.: #69480]	glucose-util	yes	87.791	yes
[Ref.: #69480]	motile	no	90.835	yes
[Ref.: #69480]	glucose-ferment	no	84.454	no

Availability in culture collections External links

[Ref.: #7689]

Culture collection no.

DSM 18772, MBIC 08254, NBRC 103619

[Ref.: #86842]

SI-ID 398555

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rubritalea squalenifaciens sp. nov., a squalene-producing marine bacterium belonging to subdivision 1 of the phylum 'Verrucomicrobia'.	Kasai H, Katsuta A, Sekiguchi H, Matsuda S, Adachi K, Shindo K, Yoon J, Yokota A, Shizuri Y	Int J Syst Evol Microbiol	10.1099/ijs.0.65010-0	2007	*

References

#7689

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18772

#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 )

#32126

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28370 (see below)

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 )

#86842

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID398555.1 )

#28370

IJSEM 1630 2007 ( DOI 10.1099/ijs.0.65010-0 , PubMed 17625207 )

* These data were automatically processed and therefore are not curated

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Rubritalea squalenifaciens DSM 18772 DSM 18772

Rubritalea squalenifaciens DSM 18772 DSM 18772

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