Sphingobacterium yanglingense (DSM 28353, ACCC 19328, JCM 30166)

Name: Sphingobacterium yanglingense (DSM 28353, ACCC 19328, JCM 30166)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130661

Type strain

Strain Designation CCNWSP36-1

Culture col. no. DSM 28353 ACCC 19328 JCM 30166 CCNWSP36-1

NCBI tax ID(s) 1437280

Special Collections DSMZ JCM

History DSMZ <- P. Shi, Northwest A&F Univ., Yangling, China; CCNWSP36-1 JCM <-- S. Peng; Northwest A&F Univ., China; CCNWSP36-1.

Links

Sphingobacterium yanglingense CCNWSP36-1 is a bacterium that was isolated from root nodule surface of soybean Merrill) cultivar Zhonghuang 13.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 405434

JCM 30166,DSM 28353

@ref 20215

Last LPSN update 2026-05-29 08:37:25

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Sphingobacterium

Species Sphingobacterium yanglingense

Full scientific name Sphingobacterium yanglingense Peng et al. 2014

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.604
125439	negative	98.646

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21780	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
21780	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)		Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21780	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		99.852

Observation

67770

Observationquinones: MK-7

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root nodule

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
21780	root nodule surface of soybean (Glycine max (L.) Merrill) cultivar Zhonghuang 13	Glycine max	Shaanxi Province, Yangling (34° 16' N 108° 4' E)	China	CHN	Asia	34.2667	108.067 34.2667/108.067
67770	Nodule surface of soybean [Glycine max (L.) Merrill]	Glycine max

Taxonmaps

69479

Global distribution of 16S sequence KF735812 (>99% sequence identity) for Sphingobacterium from Microbeatlas

Aquatic Samples	257
Soil Samples	648
Animal Samples	951
Plant Samples	89
Total Samples	1945

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21780	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM436324v1 assembly for Sphingobacterium yanglingense DSM 28353	scaffold	GCA_004363245	1437280.3	2734482083	1437280	69.49

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21780	Sphingobacterium yanglingense strain CCNWSP36-1 16S ribosomal RNA gene, partial sequence	KF735812	1418		1437280

GC content

@ref	GC-content (mol%)	Method
21780	41.1	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: ASM436324v1 assembly for Sphingobacterium yanglingense DSM 28353
BV-BRC: 1437280.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	55.25	no
125439	gram_stain	BacteriaNetⓘ	negative	98.65	no
125439	motility	BacteriaNetⓘ	no	66.58	no
125439	spore_formation	BacteriaNetⓘ	no	99.85	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingobacterium yanglingense strain DSM 28353
PATRIC: 1437280.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.60	no
125438	anaerobic	anaerobicⓘ	no	96.63	no
125438	spore-forming	spore-formingⓘ	no	88.01	no
125438	aerobic	aerobicⓘ	yes	84.35	no
125438	thermophilic	thermophileⓘ	no	99.00	yes
125438	flagellated	motile2+ⓘ	no	86.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobacterium yanglingense sp. nov., isolated from the nodule surface of soybean.	Peng S, Hong DD, Xin YB, Jun LM, Hong WG	Int J Syst Evol Microbiol	10.1099/ijs.0.068254-0	2014
Phylogeny	Sphingobacterium jejuense sp. nov., with ginsenoside-converting activity, isolated from compost.	Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT, Aslam Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.001370	2016

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 )
#21780	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28353
#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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Sphingobacterium yanglingense (DSM 28353, ACCC 19328, JCM 30166)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004363245

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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