Name: Sphingobacterium allocomposti 4M24
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 14128

Type strain:

Species: Sphingobacterium allocomposti

Strain Designation: 4M24

Culture col. no.: DSM 18850, KACC 11313, JCM 16391, NBRC 106383

Strain history: KACC 11313 <-- H.-Y. Weon 4M24.

NCBI tax ID(s): 363260 (species)

Special Collections

Section

When using BacDive for research please cite our paper

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Sphingobacterium*
	Species	**Sphingobacterium allocomposti**
	Full Scientific Name (LPSN)	Sphingobacterium allocomposti Goo and Li 2024

Synonym

Sphingobacterium composti

Information on morphological and physiological properties Morphology

[Ref.: #32089]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %98.104
[Ref.: #125439]	Gram stain	negative Confidence in %97.8

[Ref.: #32089]	Cell length	1.5 µm

[Ref.: #32089]	Cell width	0.55 µm

[Ref.: #32089]	Cell shape	rod-shaped

[Ref.: #32089]	Motility	no

[Ref.: #32089]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7741]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #7741]

Culture medium growth

[Ref.: #7741]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7741]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7741]	growth	28 °C
[Ref.: #32089]	growth	10-45 °C
[Ref.: #32089]	optimum	27.5 °C
[Ref.: #67770]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #32089]			optimum	7.5
[Ref.: #32089]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32089]

Oxygen tolerance

aerobe

[Ref.: #32089]	Ability of spore formation	no
[Ref.: #125438]	Ability of spore formation	no Confidence in %91.615
[Ref.: #125439]	Ability of spore formation	no Confidence in %95.9

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32089]		NaCl		growth	0-5	%
[Ref.: #32089]		NaCl		optimum	2.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32089]	arabinose ChEBI	+	carbon source
[Ref.: #32089]	cellobiose ChEBI	+	carbon source
[Ref.: #32089]	fructose ChEBI	+	carbon source
[Ref.: #32089]	fucose ChEBI	+	carbon source
[Ref.: #32089]	galactose ChEBI	+	carbon source
[Ref.: #32089]	glucose ChEBI	+	carbon source
[Ref.: #32089]	lactose ChEBI	+	carbon source
[Ref.: #32089]	maltose ChEBI	+	carbon source
[Ref.: #32089]	mannose ChEBI	+	carbon source
[Ref.: #32089]	melibiose ChEBI	+	carbon source
[Ref.: #32089]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #32089]	raffinose ChEBI	+	carbon source
[Ref.: #32089]	salicin ChEBI	+	carbon source
[Ref.: #32089]	sucrose ChEBI	+	carbon source
[Ref.: #32089]	trehalose ChEBI	+	carbon source
[Ref.: #32089]	tween 20 ChEBI	+	carbon source
[Ref.: #32089]	tween 80 ChEBI	+	carbon source
[Ref.: #32089]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #32089]	acid phosphatase	+	3.1.3.2
[Ref.: #32089]	alkaline phosphatase	+	3.1.3.1
[Ref.: #32089]	catalase	+	1.11.1.6
[Ref.: #32089]	cytochrome oxidase	+	1.9.3.1

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7741]	Sample type/isolated from	cotton waste compost
[Ref.: #7741]	Country	Republic of Korea
[Ref.: #7741]	Country ISO 3 Code	KOR
[Ref.: #7741]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Cotton-waste composts
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #32089]	Sphingobacterium composti Yoo et al. 2007 strain 4M24 16S ribosomal RNA gene, partial sequence	EF122436	1487	GenBank ENA	415956 tax ID
[Ref.: #124043]	Sphingobacterium composti Yoo et al. 2007 gene for 16S rRNA, partial sequence, strain: NBRC 106383.	AB682399	1453	GenBank ENA	415956 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Sphingobacterium composti Yoo et al. 2007 non Ten et al. 2007 DSM 18850	GCA_008124885	scaffold	GenBank ENA	415956 tax ID
[Ref.: #66792]	Sphingobacterium composti Yoo et al. 2007 non Ten et al. 2007 strain DSM 18850	415956.3	wgs	PATRIC	415956 tax ID	*
[Ref.: #66792]	Sphingobacterium composti DSM 18850	2700988711	draft	JGI IMG/M	415956 tax ID	*

[Ref.: #32089]	GC-content	42.3 mol%
[Ref.: #67770]	GC-content	42.3 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	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.: #125438]	gram-positive	gram-positiveⓘ	no	98.104	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.211	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	91.615	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	84.975	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.479	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	86.625	yes

	Model	Trait	Prediction	Confidence in %
	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.: #125439]	BacteriaNet	spore_formationⓘ	no	95.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	60.3
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	97.8
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	facultative aerobe	74.4

Availability in culture collections External links

[Ref.: #7741]

Culture collection no.

DSM 18850, KACC 11313, JCM 16391, NBRC 106383

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 )

#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 (see below)

#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) .

#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 .

#28335

IJSEM 1590 2007 ( DOI 10.1099/ijs.0.64948-0 , PubMed 17625199 )

* These data were automatically processed and therefore are not curated

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Sphingobacterium composti Yoo et al. 2007 non Ten et al. 2007 strain DSM 18850

Sphingobacterium composti Yoo et al. 2007 non Ten et al. 2007 DSM 18850

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