Sphingobium limneticum (KACC 19283, JCM 32054, Pch-B)

Name: Sphingobium limneticum (KACC 19283, JCM 32054, Pch-B)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 141162

Type strain

Strain Designation Pch-B

Culture col. no. KACC 19283 JCM 32054 Pch-B

NCBI tax ID(s) 1007511

Special Collections JCM Literature strains

History C. O. Jeon; Chung-Ang Univ., South Korea; Pch-B.

Links

Sphingobium limneticum Pch-B is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from from a freshwater green alga Paulinella chromatophora.

Gram-negative motile rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 28207

JCM 32054

@ref 20215

Last LPSN update 2026-02-09 11:33:50

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingobium

Species Sphingobium limneticum

Full scientific name Sphingobium limneticum Chen et al. 2013

Synonyms (2)

Sphingobium algicola
Sphingobium paulinellae

BacDive ID	Other strains from **Sphingobium limneticum** (1)	Type strain
23272	S. limneticum 301, DSM 25076, LMG 26659 (type strain)

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
44083	negative	1.0-1.2 µm	0.8-0.9 µm	rod-shaped
125438	negative				98.397
125439	negative				97.3

Colony morphology

@ref	Colony color	Colony shape	Medium used
44083	yellow	circular	R2A agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
44083	Reasoner's 2A agar (R2A)

Culture temp

@ref	Growth	Type	Temperature (°C)
44083	positive	growth	5-30
44083	positive	optimum	25-30
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
44083	positive	optimum	6.0-7.0
44083	positive	growth	4.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
44083	aerobe
125438	aerobe	90.541
125439	obligate aerobe	97.9

Spore formation

@ref	Spore formation	Confidence
125439		95.3

Halophily

@ref	Salt	Growth	Tested relation	Concentration
44083	NaCl	positive	growth	0-3.0 %(w/v)
44083	NaCl	positive	optimum	0-1.0 %(w/v)

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
44083	17128 ChEBI	adipate	-	assimilation
44083		casein	-	hydrolysis
44083	17634 ChEBI	D-glucose	+	assimilation
44083	16899 ChEBI	D-mannitol	+	assimilation
44083	16024 ChEBI	D-mannose	-	assimilation
44083	27689 ChEBI	decanoate	-	assimilation
44083	4853 ChEBI	esculin	+	hydrolysis
44083	5291 ChEBI	gelatin	-	hydrolysis
44083	30849 ChEBI	L-arabinose	+	assimilation
44083	25115 ChEBI	malate	+	assimilation
44083	17306 ChEBI	maltose	+	assimilation
44083	506227 ChEBI	N-acetylglucosamine	+	assimilation
44083	17632 ChEBI	nitrate	-	reduction
44083	18401 ChEBI	phenylacetate	-	assimilation
44083	32032 ChEBI	potassium gluconate	+	assimilation
44083	53258 ChEBI	sodium citrate	+	assimilation
44083	28017 ChEBI	starch	-	hydrolysis
44083	53424 ChEBI	tween 20	-	hydrolysis
44083	53426 ChEBI	tween 80	-	hydrolysis
44083	18186 ChEBI	tyrosine	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
44083	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
44083	acid phosphatase	+	3.1.3.2
44083	alkaline phosphatase	+	3.1.3.1
44083	alpha-chymotrypsin	+	3.4.21.1
44083	alpha-fucosidase	-	3.2.1.51
44083	alpha-galactosidase	+	3.2.1.22
44083	alpha-glucosidase	+	3.2.1.20
44083	alpha-mannosidase	-	3.2.1.24
44083	arginine dihydrolase	-	3.5.3.6
44083	beta-galactosidase	+	3.2.1.23
44083	beta-glucosidase	+	3.2.1.21
44083	beta-glucuronidase	+	3.2.1.31
44083	catalase	+	1.11.1.6
44083	cystine arylamidase	+	3.4.11.3
44083	cytochrome oxidase	+	1.9.3.1
44083	esterase (C 4)	+
44083	esterase Lipase (C 8)	+
44083	leucine arylamidase	+	3.4.11.1
44083	lipase (C 14)	+
44083	N-acetyl-beta-glucosaminidase	-	3.2.1.52
44083	naphthol-AS-BI-phosphohydrolase	+
44083	trypsin	+	3.4.21.4
44083	urease	-	3.5.1.5
44083	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

44083

Fatty acid	Percentage
C18:1ω7c / C18:1ω6c	43.4
C16:1ω7c / C16:1ω6c	20.7
C16:0	16.8
C14:0 2OH	6.9
11-methyl C18:1ω7c	3.7
C16:1ω5c	2.7
C17:1ω6c	1.6
C15:0 2OH	0.6
C8:0 3OH	0.6
C18:0	0.5
C14:0	0.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Algae	#Green algae

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Isolation procedure	Host species
44083	from a freshwater green alga Paulinella chromatophora	Mangae lake, Chungcheongnam-do	Republic of Korea	KOR	Asia	36.5611	126.763 36.5611/126.763	P. chromatophora was cultivated in DY-V medium at 25°C for 4 weeks under daily alternative light and dark conditions. Cells were homogenized and serially diluted. Aliquots were spread on R2A agar and incubated at 25°C for 3 days.
67770	Green alga Paulinella chromatophora	Chungcheongnam-do	Republic of Korea	KOR	Asia				Paulinella chromatophora

Taxonmaps

69479

Global distribution of 16S sequence KY864399 (>99% sequence identity) for Sphingobium from Microbeatlas

Aquatic Samples	525
Soil Samples	122
Animal Samples	850
Plant Samples	121
Total Samples	1618

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM871016v1 assembly for Sphingobium limneticum KACC 19283	contig	GCA_008710165	2048545.3	8003411301	1007511	60.33

16S sequences

@ref	Description	Accession	Database
44083	Sphingobium limneticum strain Pch-B 16S ribosomal RNA gene, partial sequence	KY864399

GC content

@ref	GC-content (mol%)	Method
44083	61.4	Thermal denaturation, fluorometry
67770	61.4	thermal denaturation, midpoint method (Tm)
67770	63.35	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingobium limneticum KACC 19283
NCBI: GCA_008710165

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.30	no
125439	motility	BacteriaNetⓘ	yes	66.00	no
125439	gram_stain	BacteriaNetⓘ	negative	97.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingobium paulinellae strain KACC 19283
PATRIC: 2048545.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.40	no
125438	anaerobic	anaerobicⓘ	no	96.52	yes
125438	spore-forming	spore-formingⓘ	no	89.69	no
125438	aerobic	aerobicⓘ	yes	90.54	yes
125438	thermophilic	thermophileⓘ	no	96.41	yes
125438	flagellated	motile2+ⓘ	yes	70.79	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobium paulinellae sp. nov. and Sphingobium algicola sp. nov., isolated from a freshwater green alga Paulinella chromatophora.	Lee Y, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.002435	2017

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 )
#44083	Yunho Lee and Che Ok Jeon: Sphingobium paulinellae sp. nov. and Sphingobium algicola sp. nov., isolated from a freshwater green alga Paulinella chromatophora. IJSEM 67: 5165 - 5171 2017 ( DOI 10.1099/ijsem.0.002435 , PubMed 29056116 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Sphingobium limneticum (KACC 19283, JCM 32054, Pch-B)

Name and taxonomic classification