Name: Rubrivivax gelatinosus DSM 1709
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17933

Type strain:

Species: Rubrivivax gelatinosus

Culture col. no.: DSM 1709, ATCC 17011, NCIB 8290, JCM 21318, ATCC 11169, CCTM 1912, CCUG 15841, CCUG 21977, CCUG 21990, CIP 107072, IAM 14808, IFO 16663, LMG 4311, LMG 4438, NBRC 16663, NCIMB 8290

Strain history: CIP <- 2001, CCUG <- K. Kersters <- 1973, NCIB, Rhodopseudomonas gelatinosa <- 1951, C. van Niel

NCBI tax ID(s): 28068 (species)

SI-ID 4936

LMG 4311, ATCC 11169, ATCC 17011, DSM 1709, LMG 4438, NCIB 8290, CCUG 15841, CCUG 21977, CCUG 21990, NCIMB 8290, KCTC 1373, CIP 107072, IFO 16663, IAM 14808, NBRC 16663, BCRC 16415, CCRC 16415, JCM 21318

Special Collections

Other strains from Rubrivivax gelatinosus

Section

Rubrivivax gelatinosus DSM 1709 is an anaerobe, Gram-negative bacterium that was isolated from Acetate enrichment .

Gram-negative
anaerobe
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	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Rubrivivax*
	Species	**Rubrivivax gelatinosus**
	Full Scientific Name (LPSN)	Rubrivivax gelatinosus (Molisch 1907) Willems et al. 1991

	Synonym	Rhodocyclus gelatinosus
	Synonym	Rhodopseudomonas gelatinosa
	Synonym	"Rhodocystis* gelatinosa"*

Information on morphological and physiological properties Morphology

[Ref.: #119561]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %97.5

[Ref.: #119561]	Cell shape	rod-shaped

[Ref.: #119561]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #866]

Culture medium

RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)

[Ref.: #866]

Culture medium growth

[Ref.: #866]

Culture medium link

Medium recipe at MediaDive

[Ref.: #866]

Culture medium composition

expand / minimize

[Ref.: #40648]

Culture medium

MEDIUM 328- for nutrient agar

[Ref.: #40648]

Culture medium growth

[Ref.: #40648]

Culture medium composition

expand / minimize

[Ref.: #119561]

Culture medium

CIP Medium 403

[Ref.: #119561]

Culture medium growth

[Ref.: #119561]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #119561]

Culture medium

CIP Medium 328

[Ref.: #119561]

Culture medium growth

[Ref.: #119561]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #866]	growth	25 °C
[Ref.: #40648]	growth	25 °C
[Ref.: #67770]	growth	27 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #866]

Oxygen tolerance

anaerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %90.983
[Ref.: #69481]	Ability of spore formation	no Confidence in %99

[Ref.: #866]

Name of produced compound

carotenoids

	Salt	Tested relation		Salt conc.
[Ref.: #119561]	NaCl		growth	0	%
[Ref.: #119561]	NaCl	no	growth	2	%
[Ref.: #119561]	NaCl	no	growth	4	%
[Ref.: #119561]	NaCl	no	growth	6	%
[Ref.: #119561]	NaCl	no	growth	8	%
[Ref.: #119561]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #119561]	citrate ChEBI	-	carbon source
[Ref.: #119561]	esculin ChEBI	-	hydrolysis
[Ref.: #119561]	glucose ChEBI	-	fermentation
[Ref.: #119561]	lactose ChEBI	-	fermentation
[Ref.: #119561]	nitrate ChEBI	-	reduction
[Ref.: #119561]	nitrate ChEBI	+	respiration
[Ref.: #119561]	nitrite ChEBI	+	reduction
[Ref.: #119561]	sodium thiosulfate ChEBI	-	builds gas from

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #119561]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	yes	no

	Metabolite production	Metabolite	Production
[Ref.: #119561]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #119561]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[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.: #119561]	amylase	+
[Ref.: #119561]	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.: #119561]	caseinase	-	3.4.21.50
[Ref.: #119561]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #119561]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #119561]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #119561]	gelatinase	+
[Ref.: #119561]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #119561]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #119561]	oxidase	-
[Ref.: #119561]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #119561]	tryptophan deaminase	-
[Ref.: #119561]	tween esterase	+
[Ref.: #119561]	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.: #119561]	10040	-	+	+	+	-	+	+	-	-	-	-	+	-	-	-	-	-	-	-	-

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

[Ref.: #67770]	Sample type/isolated from	Acetate enrichment (pH 6.6)

[Ref.: #119561]	Sample type/isolated from	Acetate enrichment
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence D16213 (>99% sequence identity) for Rubrivivax from Microbeatlas

Aquatic Samples	2410
Soil Samples	714
Animal Samples	348
Plant Samples	429
Total Samples	3901

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

[Ref.: #866]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #119561]	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.: #866]	Rubrivivax gelatinosus gene for 16S ribosomal RNA, partial sequence, strain: ATCC 17011	D16213	1451	GenBank ENA	28068 tax ID
[Ref.: #20218]	Rhodocyclus gelatinosus 16S ribosomal RNA	M60682	1532	GenBank ENA	28068 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Rubrivivax gelatinosus DSM 1709	GCA_004340905	scaffold	GenBank ENA	28068 tax ID
[Ref.: #66792]	Rubrivivax gelatinosus DSM 1709	GCA_016583525	contig	GenBank ENA	28068 tax ID	*
[Ref.: #66792]	Rubrivivax gelatinosus strain DSM 1709	28068.10	wgs	PATRIC	28068 tax ID	*
[Ref.: #66792]	Rubrivivax gelatinosus strain DSM 1709	28068.13	wgs	PATRIC	28068 tax ID	*
[Ref.: #66792]	Rubrivivax gelatinosus DSM 1709	2795385456	draft	JGI IMG/M	28068 tax ID	*

[Ref.: #67770]

GC-content

71.9 mol%

thermal denaturation, midpoint method (Tm)

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: Rubrivivax gelatinosus DSM 1709 NCBI: GCA_004340905.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	99	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rubrivivax gelatinosus strain DSM 1709 PATRIC: 28068.10
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.5	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	60.622	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	90.983	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	52.563	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93.714	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	83.869	no

Availability in culture collections External links

[Ref.: #866]

Culture collection no.

DSM 1709, ATCC 17011, NCIB 8290, JCM 21318, ATCC 11169, CCTM 1912, CCUG 15841, CCUG 21977, CCUG 21990, CIP 107072, IAM 14808, IFO 16663, LMG 4311, LMG 4438, NBRC 16663, NCIMB 8290

[Ref.: #86922]

SI-ID 4936

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rubrivivax albus sp. nov., isolated from a freshwater pond.	Sheu SY, Li ZH, Young CC, Chen WM	Int J Syst Evol Microbiol	10.1099/ijsem.0.003829	2020	*

References

#866	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1709

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#40648 ; Curators of the CIP;

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

#86922

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-ID4936.1 )

#119561 Collection of Institut Pasteur ; Curators of the CIP; CIP 107072
* These data were automatically processed and therefore are not curated

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Rubrivivax gelatinosus DSM 1709

Rubrivivax gelatinosus strain DSM 1709

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