Sphingorhabdus lutea (KACC 18891, JCM 31568, LPB0140)

Name: Sphingorhabdus lutea (KACC 18891, JCM 31568, LPB0140)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 164092

Type strain

Strain Designation LPB0140

Culture col. no. KACC 18891 JCM 31568 LPB0140

NCBI tax ID(s) 1913578

Special Collections JCM Literature strains

History JCM <-- H. Yi; Korea Univ., South Korea; LPB0140.

Links

Sphingorhabdus lutea LPB0140 is an obligate aerobe, Gram-negative, rod-shaped bacterium that was isolated from Sea water sample extracted from Orukdo Island.

Gram-negative rod-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 286424

JCM 31568

@ref 20215

Last LPSN update 2026-05-29 08:45:19

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingorhabdus

Species Sphingorhabdus lutea

Full scientific name Sphingorhabdus lutea Baek et al. 2019

Synonyms (1)

Alterisphingorhabdus lutea

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
68221	negative	0.66-1.33 µm	0.25-0.4 µm	rod-shaped
125438	negative					98

Colony morphology

@ref	Colony color	Medium used
68221	golden-yellow	Marine agar (MA)

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
67770	positive	growth	25
68221	positive	growth	4-40
68221	positive	optimum	35

Culture pH

@ref	Ability	Type	PH	PH range
68221	positive	optimum	6
68221	positive	growth	5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

68221

Oxygen toleranceobligate aerobe

Spore formation

@ref	Spore formation	Confidence
125438		93.395

Halophily

@ref	Salt	Growth	Tested relation	Concentration
68221	NaCl	positive	growth	0-3 %(w/v)
68221	NaCl	positive	optimum	1 %(w/v)

Observation

@ref	Observation
67770	quinones: Q-10
68221	outer sheath-like structure

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68221	16193 ChEBI	3-hydroxybenzoate	-	assimilation
68221	37054 ChEBI	3-hydroxybutyrate	+	carbon source
68221	17879 ChEBI	4-hydroxybenzoate	-	assimilation
68221	16708 ChEBI	adenine	-	hydrolysis
68221	17128 ChEBI	adipate	-	assimilation
68221	58187 ChEBI	alginate	-	hydrolysis
68221	85146 ChEBI	carboxymethylcellulose	-	hydrolysis
68221	17029 ChEBI	chitin	-	hydrolysis
68221	16899 ChEBI	D-mannitol	-	assimilation
68221	16024 ChEBI	D-mannose	-	assimilation
68221	16988 ChEBI	D-ribose	-	assimilation
68221	17924 ChEBI	D-sorbitol	-	assimilation
68221	27689 ChEBI	decanoate	-	assimilation
68221	16991 ChEBI	dna	-	hydrolysis
68221	4853 ChEBI	esculin	-	hydrolysis
68221	5291 ChEBI	gelatin	-	hydrolysis
68221	17234 ChEBI	glucose	-	builds acid from
68221	17234 ChEBI	glucose	+	carbon source
68221	28087 ChEBI	glycogen	+	carbon source
68221	17368 ChEBI	hypoxanthine	-	hydrolysis
68221	17240 ChEBI	itaconate	-	assimilation
68221	16977 ChEBI	L-alanine	-	assimilation
68221	30849 ChEBI	L-arabinose	-	assimilation
68221	18287 ChEBI	L-fucose	-	assimilation
68221	15971 ChEBI	L-histidine	-	assimilation
68221	17203 ChEBI	L-proline	-	assimilation
68221	62345 ChEBI	L-rhamnose	-	assimilation
68221	17115 ChEBI	L-serine	-	assimilation
68221	17895 ChEBI	L-tyrosine	+	hydrolysis
68221	24996 ChEBI	lactate	-	assimilation
68221	25115 ChEBI	malate	-	assimilation
68221	17306 ChEBI	maltose	+	carbon source
68221	28053 ChEBI	melibiose	-	assimilation
68221	17268 ChEBI	myo-inositol	-	assimilation
68221	59640 ChEBI	N-acetylglucosamine	-	assimilation
68221	17632 ChEBI	nitrate	-	reduction
68221	18401 ChEBI	phenylacetate	-	assimilation
68221		potassium 2-dehydro-D-gluconate	-	assimilation
68221		potassium 5-dehydro-D-gluconate	-	assimilation
68221	17272 ChEBI	propionate	-	assimilation
68221	17814 ChEBI	salicin	-	assimilation
68221	32954 ChEBI	sodium acetate	-	assimilation
68221	53258 ChEBI	sodium citrate	-	assimilation
68221	62983 ChEBI	sodium malonate	-	assimilation
68221	28017 ChEBI	starch	-	hydrolysis
68221	76282 ChEBI	suberate	-	assimilation
68221	17992 ChEBI	sucrose	-	assimilation
68221	53424 ChEBI	tween 20	+	hydrolysis
68221	53423 ChEBI	tween 40	+	hydrolysis
68221	53425 ChEBI	tween 60	+	hydrolysis
68221	53426 ChEBI	tween 80	+	hydrolysis
68221	31011 ChEBI	valerate	-	assimilation
68221	15318 ChEBI	xanthine	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68221	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68221	acid phosphatase	+/-	3.1.3.2
68221	alkaline phosphatase	+	3.1.3.1
68221	alpha-chymotrypsin	-	3.4.21.1
68221	alpha-fucosidase	-	3.2.1.51
68221	alpha-galactosidase	-	3.2.1.22
68221	alpha-glucosidase	-	3.2.1.20
68221	alpha-mannosidase	-	3.2.1.24
68221	arginine dihydrolase	-	3.5.3.6
68221	beta-galactosidase	-	3.2.1.23
68221	beta-glucosidase	-	3.2.1.21
68221	beta-glucuronidase	-	3.2.1.31
68221	catalase	+	1.11.1.6
68221	cystine arylamidase	-	3.4.11.3
68221	cytochrome oxidase	+	1.9.3.1
68221	esterase (C 4)	-
68221	esterase Lipase (C 8)	-
68221	leucine arylamidase	+	3.4.11.1
68221	lipase (C 14)	-
68221	N-acetyl-beta-glucosaminidase	-	3.2.1.52
68221	naphthol-AS-BI-phosphohydrolase	-
68221	trypsin	-	3.4.21.4
68221	urease	-	3.5.1.5
68221	valine arylamidase	-

Fatty acid profile

Metadata FA analysis

@ref

68221

Fatty acid	Percentage
C18:1 w7c/C18:1 w6c	31.8
C16:1 w7c/C16:1 w6c	30.9
C14:0 2OH	12.2
C17:1 w6c	7.6
C16:0	5.9
C18:1 w7c 11-methyl	4.6
C15:0 2OH	1.9
C16:1 w5c	1.8
C17:1 w8c	1.4

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture temperature
67770	Sea water sample extracted from Orukdo Island			Republic of Korea	KOR	Asia
68221	sea water sample	2015-08-01	Orukdo Island	Republic of Korea	KOR	Asia	35.0936	129.127 35.0936/129.127	marine agar 2216	25

Taxonmaps

69479

Global distribution of 16S sequence KX066860 (>99% sequence identity) for Sphingorhabdus from Microbeatlas

Aquatic Samples	2158
Soil Samples	487
Animal Samples	145
Plant Samples	115
Total Samples	2905

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
67770	ASM188902v1 assembly for Sphingorhabdus lutea LPB0140	complete	GCA_001889025	2718217855	1913578	98.19

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
68221	Sphingorhabdus lutea strain LPB0140 16S ribosomal RNA gene, partial sequence	KX066860	1421		1850251

GC content

@ref	GC-content (mol%)	Method
67770	46.1	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM188902v1 assembly for Sphingorhabdus lutea LPB0140
NCBI: GCA_001889025

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	62.82	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	85.05	no
125439	motility	BacteriaNetⓘ	no	66.97	no
125439	spore_formation	BacteriaNetⓘ	no	73.32	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingorhabdus lutea LPB0140
NCBI: GCA_001889025.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	yes
125438	anaerobic	anaerobicⓘ	no	96.12	no
125438	aerobic	aerobicⓘ	yes	85.30	yes
125438	spore-forming	spore-formingⓘ	no	93.40	no
125438	thermophilic	thermophileⓘ	no	94.77	no
125438	flagellated	motile2+ⓘ	no	63.97	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingorhabdus lutea sp. nov., isolated from sea water.	Baek MG, Shin SK, Yi H	Int J Syst Evol Microbiol	10.1099/ijsem.0.003662	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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68221	Min-gyung Baek, Su-Kyoung Shin and Hana Yi: Sphingorhabdus lutea sp. nov., isolated from sea water. IJSEM 69: 3593 - 3598 2019 ( DOI 10.1099/ijsem.0.003662 )
#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 .
#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 lutea (KACC 18891, JCM 31568, LPB0140)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_001889025

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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