Name: Rhodovarius lipocyclicus DSM 15909
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 131146

Type strain:

Species: Rhodovarius lipocyclicus

Culture col. no.: DSM 15909, CCUG 44693, CIP 108310

Strain history: CIP <- 2004, CCUG <- Anonymous

NCBI tax ID(s): 268410 (species)

SI-ID 110112

CCUG 44693, CIP 108310, DSM 15909

Special Collections

Section

Rhodovarius lipocyclicus DSM 15909 is an aerobe, Gram-negative bacterium that was isolated from Industrial hygiene control, Rodac medium.

Gram-negative
aerobe
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodospirillales*
	Family	*Acetobacteraceae*
	Genus	*Rhodovarius*
	Species	**Rhodovarius lipocyclicus**
	Full Scientific Name (LPSN)	Rhodovarius lipocyclicus Kämpfer et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #120618]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %97.833

[Ref.: #120618]	Cell shape	oval-shaped

[Ref.: #120618]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22438]

Culture medium

SABOURAND GLUCOSE MEDIUM (DSMZ Medium 1429)

[Ref.: #22438]

Culture medium growth

[Ref.: #22438]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22438]

Culture medium composition

expand / minimize

[Ref.: #34318]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #34318]

Culture medium growth

[Ref.: #34318]

Culture medium composition

expand / minimize

[Ref.: #120618]

Culture medium

CIP Medium 72

[Ref.: #120618]

Culture medium growth

[Ref.: #120618]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #22438]	growth	28 °C
[Ref.: #34318]	growth	30 °C
[Ref.: #56438]	growth	30 °C
[Ref.: #120618]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #56438]	Oxygen tolerance	aerobe
[Ref.: #120618]	Oxygen tolerance	obligate aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %98

	Salt	Tested relation		Salt conc.
[Ref.: #120618]	NaCl		growth	0	%
[Ref.: #120618]	NaCl	no	growth	2	%
[Ref.: #120618]	NaCl	no	growth	4	%
[Ref.: #120618]	NaCl	no	growth	6	%
[Ref.: #120618]	NaCl	no	growth	8	%
[Ref.: #120618]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #120618]	nitrate ChEBI	-	reduction
[Ref.: #120618]	nitrate ChEBI	-	respiration
[Ref.: #120618]	nitrite ChEBI	-	reduction

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #120618]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #120618]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #120618]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #120618]	amylase	-
[Ref.: #120618]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #120618]	caseinase	-	3.4.21.50
[Ref.: #120618]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #120618]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #120618]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #120618]	gelatinase	-
[Ref.: #120618]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #120618]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #120618]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120618]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120618]	oxidase	-
[Ref.: #120618]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #120618]	tryptophan deaminase	-
[Ref.: #120618]	tween esterase	-
[Ref.: #120618]	urease	+	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #120618]	11075	-	+	+	-	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #22438]	Sample type/isolated from	Industrial hygiene control, Rodac medium
[Ref.: #22438]	Country	Sweden
[Ref.: #22438]	Country ISO 3 Code	SWE
[Ref.: #22438]	Continent	Europe

[Ref.: #56438]	Sample type/isolated from	Industrial hygiene control,Rodac medium
[Ref.: #56438]	Sampling date	2000-11-01
[Ref.: #56438]	Country	Sweden
[Ref.: #56438]	Country ISO 3 Code	SWE
[Ref.: #56438]	Continent	Europe

[Ref.: #120618]	Sample type/isolated from	Environment, Industrial hygiene control, Rodac medium
[Ref.: #120618]	Country	Sweden
[Ref.: #120618]	Country ISO 3 Code	SWE
[Ref.: #120618]	Continent	Europe
[Ref.: #120618]	Isolation date	2000
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	-
#Engineered	#Laboratory	#Defined media

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ633644 (>99% sequence identity) for Rhodovarius lipocyclicus subclade from Microbeatlas

Aquatic Samples	2166
Soil Samples	455
Animal Samples	1354
Plant Samples	216
Total Samples	4191

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

[Ref.: #22438]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120618]	Biosafety level	1	Risk group (French classification)

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.: #22438]	Rhodovarius lipocyclicus partial 16S rRNA gene, type strain CCUG 44693T	AJ633644	1458	GenBank ENA	268410 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodovarius lipocyclicus CCUG 44693	GCA_009900765	contig	GenBank ENA	268410 tax ID	*
[Ref.: #66792]	Rhodovarius lipocyclicus strain CCUG 44693	268410.3	wgs	PATRIC	268410 tax ID	*

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rhodovarius lipocyclicus strain CCUG 44693 PATRIC: 268410.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	98	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodovarius lipocyclicus strain CCUG 44693 PATRIC: 268410.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.833	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	92.811	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	86.81	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	82.804	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94.972	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	69.767	no

Availability in culture collections External links

[Ref.: #22438]

Culture collection no.

DSM 15909, CCUG 44693, CIP 108310

[Ref.: #89599]

SI-ID 110112

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodovarius lipocyclicus gen. nov. sp. nov., a new genus of the alpha-1 subclass of the Proteobacteria.	Kampfer P, Busse HJ, Rossello-Mora R, Kjellin E, Falsen E	Syst Appl Microbiol	10.1078/0723202041748235	2004	*
Phylogeny	Rhodovarius crocodyli sp. nov., isolated from a crocodile pond.	Chen WM, Xie YR, Sheu DS, Tsai JM, Sheu SY	Int J Syst Evol Microbiol	10.1099/ijsem.0.004396	2020	*

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 )

#22438

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15909

#34318 ; Curators of the CIP;
#56438 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 44693

#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) .

#68382

Automatically annotated from API zym .

#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 )

#89599

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-ID110112.1 )

#120618 Collection of Institut Pasteur ; Curators of the CIP; CIP 108310
* These data were automatically processed and therefore are not curated

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Rhodovarius lipocyclicus strain CCUG 44693

Rhodovarius lipocyclicus strain CCUG 44693

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