Rubrivivax gelatinosus (DSM 1709, ATCC 17011, NCIB 8290)

Name: Rubrivivax gelatinosus (DSM 1709, ATCC 17011, NCIB 8290)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17933

Type strain

Culture col. no. DSM 1709 ATCC 17011 NCIB 8290 NCIMB 8290 NBRC 16663 11 more

NCBI tax ID(s) 28068

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- NCIB <- C.B. van Niel JCM <-- IAM 14808 <-- DSM 1709 <-- NCIB 8290 <-- C. B. Van Niel. CIP <- 2001, CCUG <- K. Kersters <- 1973, NCIB, Rhodopseudomonas gelatinosa <- 1951, C. van Niel

Links

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

Gram-negative motile rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

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

@ref 20215

Last LPSN update 2026-05-29 08:29:08

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Sphaerotilaceae

Genus Rubrivivax

Species Rubrivivax gelatinosus

Full scientific name Rubrivivax gelatinosus (Molisch 1907) Willems et al. 1991

Synonyms (3)

Rhodopseudomonas gelatinosa
Rhodocyclus gelatinosus
"Rhodocystis gelatinosa"

BacDive ID	Other strains from **Rubrivivax gelatinosus** (3)	Type strain
17934	R. gelatinosus 2150, DSM 149, Pfennig 2150
17935	R. gelatinosus Dr 2, DSM 151, CCUG 15842
17936	R. gelatinosus O.U. 007, DSM 6859

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125439	negative		94.97
125438	negative		97.5
119561	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
866	RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)	Medium recipe at MediaDive	Name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27) Composition: Disodium succinate 1.0 g/l KH2PO4 0.5 g/l Ammonium acetate 0.5 g/l NaCl 0.4 g/l NH4Cl 0.4 g/l MgSO4 x 7 H2O 0.4 g/l Yeast extract 0.3 g/l L-Cysteine HCl 0.3 g/l CaCl2 x 2 H2O 0.05 g/l Fe(III) citrate 0.005 g/l Resazurin 0.005 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Vitamin B12 Distilled water
40648	MEDIUM 328- for nutrient agar		Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
119561	CIP Medium 403	Medium recipe at CIP
119561	CIP Medium 328	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
866	positive	growth	28
40648	positive	growth	25
67770	positive	growth	27

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
866	anaerobe
125439	obligate aerobe	99.632

Spore formation

@ref	Spore formation	Confidence
125439		99.421
125438		90.983

Compound production

866

Compoundcarotenoids

Halophily

@ref	Salt	Growth	Tested relation	Concentration
119561	NaCl	positive	growth	0 %
119561	NaCl		growth	2 %
119561	NaCl		growth	4 %
119561	NaCl		growth	6 %
119561	NaCl		growth	8 %
119561	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
119561	16947 ChEBI	citrate	-	carbon source
119561	4853 ChEBI	esculin	-	hydrolysis
119561	17234 ChEBI	glucose	-	fermentation
119561	17716 ChEBI	lactose	-	fermentation
119561	17632 ChEBI	nitrate	-	reduction
119561	17632 ChEBI	nitrate	+	respiration
119561	16301 ChEBI	nitrite	+	reduction
119561	132112 ChEBI	sodium thiosulfate	-	builds gas from

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
119561	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119561	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
119561	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
119561	amylase	+
68382	beta-galactosidase	-	3.2.1.23	from API zym
119561	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
119561	caseinase	-	3.4.21.50
119561	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
119561	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
119561	gamma-glutamyltransferase	+	2.3.2.2
119561	gelatinase	+
119561	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
119561	lipase	-
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119561	oxidase	-
119561	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
119561	tryptophan deaminase	-
119561	tween esterase	+
119561	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
119561	-	+	+	+	-	+	+	-	-	-	-	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type
67770	Acetate enrichment (pH 6.6)
119561	Acetate enrichment

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
866	1	Risk group (German classification) According to TRBA 466
119561	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM434090v1 assembly for Rubrivivax gelatinosus DSM 1709	scaffold	GCA_004340905	28068.10	2795385456	28068	69.09
66792	ASM1658352v1 assembly for Rubrivivax gelatinosus DSM 1709	contig	GCA_016583525	28068.13	8001957713	28068	48.61

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Rhodocyclus gelatinosus 16S ribosomal RNA	M60682	1532		28068
866	Rubrivivax gelatinosus gene for 16S ribosomal RNA, partial sequence, strain: ATCC 17011	D16213	1451		28068

GC content

@ref	GC-content (mol%)	Method
67770	71.9	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM434090v1 assembly for Rubrivivax gelatinosus DSM 1709
NCBI: GCA_004340905

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	94.97	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.63	no
125439	motility	BacteriaNetⓘ	yes	80.93	no
125439	spore_formation	BacteriaNetⓘ	no	99.42	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rubrivivax gelatinosus strain DSM 1709
PATRIC: 28068.10

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.50	no
125438	anaerobic	anaerobicⓘ	no	60.62	yes
125438	spore-forming	spore-formingⓘ	no	90.98	no
125438	aerobic	aerobicⓘ	no	52.56	yes
125438	thermophilic	thermophileⓘ	no	93.71	yes
125438	flagellated	motile2+ⓘ	yes	83.87	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Osmotic Adaptation and Compatible Solute Biosynthesis of Phototrophic Bacteria as Revealed from Genome Analyses.	Imhoff JF, Rahn T, Kunzel S, Keller A, Neulinger SC.	Microorganisms	10.3390/microorganisms9010046	2020
Metabolism	Enumeration and detection of anaerobic ferrous iron-oxidizing, nitrate-reducing bacteria from diverse European sediments.	Straub KL, Buchholz-Cleven BE.	Appl Environ Microbiol	10.1128/aem.64.12.4846-4856.1998	1998
Genetics	Draft genome sequence of Rubrivivax gelatinosus CBS.	Hu P, Lang J, Wawrousek K, Yu J, Maness PC, Chen J.	J Bacteriol	10.1128/jb.00515-12	2012
Phylogeny	Microbial community analysis in the roots of aquatic plants and isolation of novel microbes including an organism of the candidate phylum OP10.	Tanaka Y, Tamaki H, Matsuzawa H, Nigaya M, Mori K, Kamagata Y.	Microbes Environ	10.1264/jsme2.me11288	2012
	Isolation and molecular characterization of pMG160, a mobilizable cryptic plasmid from Rhodobacter blasticus.	Inui M, Nakata K, Roh JH, Vertes AA, Yukawa H.	Appl Environ Microbiol	10.1128/aem.69.2.725-733.2003	2003
	Characterization of naturally occurring atrazine-resistant isolates of the purple non-sulfur bacteria.	Brown AE, Luttrell R, Highfill CT, Rushing AE.	Appl Environ Microbiol	10.1128/aem.56.2.507-513.1990	1990
Metabolism	Development and application of 16S rRNA-targeted probes for detection of iron- and manganese-oxidizing sheathed bacteria in environmental samples.	Siering PL, Ghiorse WC.	Appl Environ Microbiol	10.1128/aem.63.2.644-651.1997	1997
Metabolism	Methane utilization by a strain of Rhodopseudomonas gelatinosa.	Wertlieb D, Vishniac W.	J Bacteriol	10.1128/jb.93.5.1722-1724.1967	1967
	Promotion of Nitrogen Fixation of Diverse Heterotrophs by Solid-Phase Humin.	Dey S, Kasai T, Katayama A.	Front Microbiol	10.3389/fmicb.2022.853411	2022
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 .
#119561	Collection of Institut Pasteur ; Curators of the CIP; CIP 107072
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Rubrivivax gelatinosus (DSM 1709, ATCC 17011, NCIB 8290)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004340905

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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