Sphingorhabdus rigui (DSM 29050, 01SU5-P, JCM 17509)

Name: Sphingorhabdus rigui (DSM 29050, 01SU5-P, JCM 17509)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24567

Type strain

Strain Designation 01SU5-P

Culture col. no. DSM 29050 01SU5-P JCM 17509 KCTC 23326

NCBI tax ID(s) 1282858

Special Collections DSMZ JCM KCTC

Links

Sphingorhabdus rigui 01SU5-P is a mesophilic prokaryote that was isolated from surface freshwater of wetland.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 407155

JCM 17509,KCTC 23326,DSM 29050

@ref 20215

Last LPSN update 2025-12-16 09:52:52

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingorhabdus

Species Sphingorhabdus rigui

Full scientific name Sphingorhabdus rigui (Baik et al. 2013) Park et al. 2014

Synonyms (1)

Sphingopyxis rigui

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.7
125438	negative	97.969

Colony morphology

20822

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20822	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
20822	positive	growth	25	mesophilic
67770	positive	growth	25	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	99.4

Spore formation

@ref	Spore formation	Confidence
125439		98.8
125438		92.566

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	+	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
20822	-	-	-	-	-	+	-	+	+	-	+	-	-	-	-	-	+	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Surface water
#Environmental	#Terrestrial	#Wetland (Swamp)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
20822	surface freshwater of wetland	Woopo Wetland	Republic of Korea	KOR	Asia	35.55	128.417 35.55/128.417
67770	Freshwater of Woopo wetland (35° 33' N 128° 25' E) in Gyeongnam Province		Republic of Korea	KOR	Asia	35.55	128.417 35.55/128.417

Taxonmaps

69479

Global distribution of 16S sequence HQ436492 (>99% sequence identity) for Sphingorhabdus from Microbeatlas

Aquatic Samples	11197
Soil Samples	892
Animal Samples	834
Plant Samples	144
Total Samples	13067

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20822	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1419659v1 assembly for Sphingorhabdus rigui DSM 29050	scaffold	GCA_014196595	1282858.3	2829934109	1282858	75.84
124043	ASM3953783v1 assembly for Sphingorhabdus rigui JCM 17509	contig	GCA_039537835			1282858	73.13

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20822	Sphingopyxis rigui strain 01SU5-P 16S ribosomal RNA gene, partial sequence	HQ436492	1435		1282858

GC content

@ref	GC-content (mol%)	Method
67770	57.3	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingorhabdus rigui DSM 29050
NCBI: GCA_014196595

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.80	no
125439	motility	BacteriaNetⓘ	yes	72.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	99.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingorhabdus rigui DSM 29050
NCBI: GCA_014196595.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.97	no
125438	anaerobic	anaerobicⓘ	no	96.44	no
125438	aerobic	aerobicⓘ	yes	86.74	no
125438	spore-forming	spore-formingⓘ	no	92.57	no
125438	thermophilic	thermophileⓘ	no	94.03	no
125438	flagellated	motile2+ⓘ	no	68.73	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingopyxis rigui sp. nov. and Sphingopyxis wooponensis sp. nov., isolated from wetland freshwater, and emended description of the genus Sphingopyxis.	Baik KS, Choe HN, Park SC, Hwang YM, Kim EM, Park C, Seong CN	Int J Syst Evol Microbiol	10.1099/ijs.0.044057-0	2012
Phylogeny	Sphingorhabdus pulchriflava sp. nov., isolated from a river.	Jung GY, Nam IH, Han YS, Ahn JS, Rhee SK, Kim SJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003503	2019

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 )
#20822	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29050
#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;
#68369	Automatically annotated from API 20NE .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Sphingorhabdus rigui (DSM 29050, 01SU5-P, JCM 17509)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014196595

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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