Sphingobacterium allocomposti (DSM 18850, KACC 11313, 4M24)

Name: Sphingobacterium allocomposti (DSM 18850, KACC 11313, 4M24)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14128

Type strain

Strain Designation 4M24

Culture col. no. DSM 18850 KACC 11313 4M24 NBRC 106383 JCM 16391

NCBI tax ID(s) 415956

Special Collections DSMZ JCM Literature strains

History <- S.-W. Kwon, KACC <- Yoo et al.; 4M24 KACC 11313 <-- H.-Y. Weon 4M24.

Links

Sphingobacterium allocomposti 4M24 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from cotton waste compost.

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

Name and taxonomic classification

SI-ID 402190

JCM 16391,NBRC 106383,DSM 18850

@ref 20215

Last LPSN update 2026-02-09 11:21:20

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Sphingobacterium

Species Sphingobacterium allocomposti

Full scientific name Sphingobacterium allocomposti Goo and Li 2024

Synonyms (1)

Sphingobacterium composti

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32089	negative	1.5 µm	0.55 µm	rod-shaped
125438	negative				98.104
125439	negative				97.8

Pigmentation

32089

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7741	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)
7741	positive	growth	28
32089	positive	growth	10-45
32089	positive	optimum	27.5
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
32089	positive	optimum	7.5
32089	positive	growth	06-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

32089

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
32089
125438		91.615
125439		95.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32089	NaCl	positive	growth	0-5 %
32089	NaCl	positive	optimum	2.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32089	22599 ChEBI	arabinose	+	carbon source
32089	17057 ChEBI	cellobiose	+	carbon source
32089	28757 ChEBI	fructose	+	carbon source
32089	33984 ChEBI	fucose	+	carbon source
32089	28260 ChEBI	galactose	+	carbon source
32089	17234 ChEBI	glucose	+	carbon source
32089	17716 ChEBI	lactose	+	carbon source
32089	17306 ChEBI	maltose	+	carbon source
32089	37684 ChEBI	mannose	+	carbon source
32089	28053 ChEBI	melibiose	+	carbon source
32089	506227 ChEBI	N-acetylglucosamine	+	carbon source
32089	16634 ChEBI	raffinose	+	carbon source
32089	17814 ChEBI	salicin	+	carbon source
32089	17992 ChEBI	sucrose	+	carbon source
32089	27082 ChEBI	trehalose	+	carbon source
32089	53424 ChEBI	tween 20	+	carbon source
32089	53426 ChEBI	tween 80	+	carbon source
32089	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32089	acid phosphatase	+	3.1.3.2
32089	alkaline phosphatase	+	3.1.3.1
32089	catalase	+	1.11.1.6
32089	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	-
#Engineered	#Biodegradation	#Composting
#Engineered	#Waste	#Solid plant waste
#Host	#Plants	#Shrub (Scrub)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
7741	cotton waste compost	Republic of Korea	KOR	Asia
67770	Cotton-waste composts	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF122436 (>99% sequence identity) for Sphingobacterium composti subclade from Microbeatlas

Aquatic Samples	360
Soil Samples	427
Animal Samples	989
Plant Samples	218
Total Samples	1994

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM812488v1 assembly for Sphingobacterium allocomposti DSM 18850	scaffold	GCA_008124885	415956.3	2700988711	415956	63.15

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
32089	Sphingobacterium composti Yoo et al. 2007 strain 4M24 16S ribosomal RNA gene, partial sequence	EF122436	1487		415956
124043	Sphingobacterium composti Yoo et al. 2007 gene for 16S rRNA, partial sequence, strain: NBRC 106383.	AB682399	1453		415956

GC content

@ref	GC-content (mol%)	Method
32089	42.3
67770	42.3	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: Sphingobacterium composti Yoo et al. 2007 non Ten et al. 2007 DSM 18850
NCBI: GCA_008124885

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.90	no
125439	motility	BacteriaNetⓘ	no	60.30	no
125439	gram_stain	BacteriaNetⓘ	negative	97.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	74.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingobacterium composti Yoo et al. 2007 non Ten et al. 2007 strain DSM 18850
PATRIC: 415956.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.10	no
125438	anaerobic	anaerobicⓘ	no	96.21	yes
125438	spore-forming	spore-formingⓘ	no	91.62	yes
125438	aerobic	aerobicⓘ	yes	84.98	yes
125438	thermophilic	thermophileⓘ	no	97.48	yes
125438	flagellated	motile2+ⓘ	no	86.63	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobacterium gobiense sp. nov., isolated from soil of the Gobi Desert.	Zhao P, Zhou Z, Chen M, Lin W, Zhang W, Wei G	Int J Syst Evol Microbiol	10.1099/ijs.0.064246-0	2014
Phylogeny	Sphingobacterium arenae sp. nov., isolated from sandy soil.	Jiang S, Chen M, Su S, Yang M, Li A, Zhang C, Lin M, Zhang W, Luo X	Int J Syst Evol Microbiol	10.1099/ijs.0.051706-0	2013
Phylogeny	Sphingobacterium anhuiense sp. nov., isolated from forest soil.	Wei W, Zhou Y, Wang X, Huang X, Lai R	Int J Syst Evol Microbiol	10.1099/ijs.0.65864-0	2008
Phylogeny	Sphingobacterium composti sp. nov., isolated from cotton-waste composts.	Yoo SH, Weon HY, Jang HB, Kim BY, Kwon SW, Go SJ, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.64948-0	2007

References

#7741	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18850
#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 )
#28335	IJSEM 1590 2007 ( DOI 10.1099/ijs.0.64948-0 , PubMed 17625199 )
#32089	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28335
#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 .
#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 )

Rate our new design

Content

About us

Sphingobacterium allocomposti (DSM 18850, KACC 11313, 4M24)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_008124885

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media