Sphingopyxis panaciterrae (DSM 27164, KCTC 12580, LMG 24003)

Name: Sphingopyxis panaciterrae (DSM 27164, KCTC 12580, LMG 24003)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23283

Type strain

Culture col. no. DSM 27164 KCTC 12580 LMG 24003 Gsoil 124

NCBI tax ID(s) 363841

Special Collections DSMZ KCTC

Links

Sphingopyxis panaciterrae DSM 27164 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from soil of ginseng field.

Gram-negative aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 408026

KCTC 12580,DSM 27164

@ref 20215

Last LPSN update 2025-12-16 09:52:37

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingopyxis

Species Sphingopyxis panaciterrae

Full scientific name Sphingopyxis panaciterrae Lee et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Confidence
67771	negative
125438	negative	95.828
125439	negative	98.1

Multimedia

@ref:	19123
multimedia content:	DSM_27164.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_27164.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19123	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
19123	positive	growth	28	mesophilic
67771	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	aerobe	95.9

Spore formation

@ref	Spore formation	Confidence
125438		90.474
125439		96.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
19123	soil of ginseng field	Pocheon Province	Republic of Korea	KOR	Asia
67771	From soil of ginseng field	Pocheon Province	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB245353 (>99% sequence identity) for Sphingopyxis from Microbeatlas

Aquatic Samples	362
Soil Samples	407
Animal Samples	572
Plant Samples	284
Total Samples	1625

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19123	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1176212v1 assembly for Sphingopyxis panaciterrae DSM 27164	contig	GCA_011762125	363841.3	2828390859	363841	69.01

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19123	Sphingopyxis panaciterrae gene for 16S rRNA, partial sequence, strain: Gsoil 124	AB245353	1449		363841

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingopyxis panaciterrae DSM 27164
NCBI: GCA_011762125

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.60	no
125439	motility	BacteriaNetⓘ	yes	64.30	no
125439	gram_stain	BacteriaNetⓘ	negative	98.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	95.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingopyxis panaciterrae strain DSM 27164
PATRIC: 363841.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.83	yes
125438	anaerobic	anaerobicⓘ	no	95.32	yes
125438	spore-forming	spore-formingⓘ	no	90.47	no
125438	aerobic	aerobicⓘ	yes	88.28	yes
125438	thermophilic	thermophileⓘ	no	97.34	no
125438	flagellated	motile2+ⓘ	yes	65.30	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Ecological shifts in soil microbiota and root rot disease progress during ginseng monoculture.	Cho G, Kim DR, Kwak YS.	Front Microbiol	10.3389/fmicb.2024.1442208	2024
	Rooting for Success: The Role of Microorganisms in Promoting Growth and Resilience in Black Alder Seedlings.	Striganaviciute G, Vaitiekunaite D, Silanskiene M, Sirgedaite-Seziene V.	Environ Microbiol Rep	10.1111/1758-2229.70060	2024
Genetics	Extra benefit of microalgae in raw piggery wastewater treatment: pathogen reduction.	Lee SA, Kim M, Kim HS, Ahn CY.	Microbiome	10.1186/s40168-022-01339-3	2022
Metabolism	Secondary compound hypothesis revisited: Selected plant secondary metabolites promote bacterial degradation of cis-1,2-dichloroethylene (cDCE).	Fraraccio S, Strejcek M, Dolinova I, Macek T, Uhlik O.	Sci Rep	10.1038/s41598-017-07760-1	2017
Phylogeny	Sphingopyxis fribergensis sp. nov., a soil bacterium with the ability to degrade styrene and phenylacetic acid.	Oelschlagel M, Ruckert C, Kalinowski J, Schmidt G, Schlomann M, Tischler D	Int J Syst Evol Microbiol	10.1099/ijs.0.000371	2015
Phylogeny	Sphingopyxis italica sp. nov., isolated from Roman catacombs.	Alias-Villegas C, Jurado V, Laiz L, Saiz-Jimenez C	Int J Syst Evol Microbiol	10.1099/ijs.0.046573-0	2012
Phylogeny	Sphingopyxis panaciterrae sp. nov., isolated from soil from ginseng field.	Lee HW, Ten IL, Jung HM, Liu QM, Im WT, Lee ST	J Microbiol Biotechnol	7422	2008

References

#19123	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27164
#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 )
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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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Sphingopyxis panaciterrae (DSM 27164, KCTC 12580, LMG 24003)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_011762125

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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