Name: Allosphingosinicella vermicomposti YC7378
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 14296

Type strain:

Species: Allosphingosinicella vermicomposti

Strain Designation: YC7378

Culture col. no.: DSM 21593, KCTC 22446

Strain history: <- YR Chung, Kyeongsang Univ.

NCBI tax ID(s): 614671 (species)

SI-ID 398273

DSM 21593

Special Collections

Section

Allosphingosinicella vermicomposti YC7378 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from vermicompost.

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

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Allosphingosinicella*
	Species	**Allosphingosinicella vermicomposti**
	Full Scientific Name (LPSN)	Allosphingosinicella vermicomposti (Yasir et al. 2010) Hördt et al. 2020

Synonym

Sphingosinicella vermicomposti

Information on morphological and physiological properties Morphology

[Ref.: #29315]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %94.828

[Ref.: #29315]	Cell length	1.3 µm

[Ref.: #29315]	Cell width	0.45 µm

[Ref.: #29315]	Cell shape	rod-shaped

[Ref.: #29315]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15833]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #15833]

Culture medium growth

[Ref.: #15833]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15833]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15833]	growth	28 °C
[Ref.: #29315]	growth	10-37 °C
[Ref.: #29315]	optimum	30 °C
[Ref.: #67771]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #29315]			optimum	7.5
[Ref.: #29315]			growth	06-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29315]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #29315]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %91.253
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29315]		NaCl		growth	0-1.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #29315]	alanine ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #29315]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #29315]	L-alaninamide ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #29315]	malate ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #29315]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #29315]	acid phosphatase	+	3.1.3.2
[Ref.: #29315]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #29315]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #15833]	23253	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+

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

[Ref.: #15833]	Sample type/isolated from	vermicompost
[Ref.: #15833]	Geographic location (country and/or sea, region)	Mansan, farm
[Ref.: #15833]	Country	Republic of Korea
[Ref.: #15833]	Country ISO 3 Code	KOR
[Ref.: #15833]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From vermicompost
[Ref.: #67771]	Geographic location (country and/or sea, region)	Masan
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered

#Biodegradation

#Composting

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ442859 (>99% sequence identity) for Allosphingosinicella vermicomposti subclade from Microbeatlas

Aquatic Samples	8
Soil Samples	2
Animal Samples	1
Plant Samples
Total Samples	11

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #15833]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #15833]	Sphingosinicella vermicomposti strain YC7378 16S ribosomal RNA gene, partial sequence	FJ442859	1315	GenBank ENA	614671 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Allosphingosinicella vermicomposti KCTC 22446	GCA_003012815	contig	GenBank ENA	614671 tax ID	*
[Ref.: #66792]	Sphingosinicella vermicomposti strain KCTC 22446	614671.3	wgs	PATRIC	614671 tax ID	*
[Ref.: #66792]	Allosphingosinicella vermicomposti KCTC 22446	2832661309	draft	JGI IMG/M	614671 tax ID	*

[Ref.: #15833]	GC-content	59.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29315]	GC-content	59.4 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Sphingosinicella vermicomposti strain KCTC 22446 PATRIC: 614671.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingosinicella vermicomposti strain KCTC 22446 PATRIC: 614671.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	94.828	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	93.416	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	91.253	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	82.521	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	92.888	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	58.414	no

Availability in culture collections External links

[Ref.: #15833]

Culture collection no.

DSM 21593, KCTC 22446

[Ref.: #83449]

SI-ID 398273

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingosinicella humi sp. nov., isolated from arsenic-contaminated farmland soil and emended description of the genus Sphingosinicella.	Qiao Z, Cao M, Wang D, Liao S, Wang G	Int J Syst Evol Microbiol	10.1099/ijsem.0.003186	2018	*
Phylogeny	Sphingomonas deserti sp. nov., isolated from Mu Us Sandy Land soil.	Liu L, Hui N, Liang L, Zhang X, Sun Q, Li L	Int J Syst Evol Microbiol	10.1099/ijsem.0.003168	2018	*
Phylogeny	Sphingomonas montis sp. nov., Isolated from Forest Soil of Low-Altitude Mountain.	Chaudhary DK, Dahal RH, Kim J	Curr Microbiol	10.1007/s00284-018-1524-y	2018	*
Phylogeny	Sphingomonas colocasiae sp. nov., isolated from taro (Colocasia esculanta).	Lin SY, Hameed A, Hsu YH, Liu YC, Hung MH, Lai WA, Young CC	Int J Syst Evol Microbiol	10.1099/ijsem.0.002471	2017	*
Phylogeny	Sphingomonas faucium sp. nov., isolated from canyon soil.	Liu D, Jin X, Sun X, Song Y, Feng L, Wang G, Li M	Int J Syst Evol Microbiol	10.1099/ijsem.0.001064	2016	*
Phylogeny	Sphingosinicella cucumeris sp. nov., isolated from soil of a cucumber garden.	Akter S, Du J, Won K, Yin CS, Kook M, Yi TH	Antonie Van Leeuwenhoek	10.1007/s10482-015-0572-6	2015	*
Phylogeny	Sphingosinicella ginsenosidimutans sp. nov., with ginsenoside converting activity.	Kim JK, Kang MS, Park SC, Kim KM, Choi K, Yoon MH, Im WT	J Microbiol	10.1007/s12275-015-5087-3	2015	*
Phylogeny	Sphingomonas indica sp. nov., isolated from hexachlorocyclohexane (HCH)-contaminated soil.	Niharika N, Jindal S, Kaur J, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.033845-0	2012	*
Phylogeny	Sphingosinicella vermicomposti sp. nov., isolated from vermicompost, and emended description of the genus Sphingosinicella.	Yasir M, Aslam Z, Song GC, Jeon CO, Chung YR	Int J Syst Evol Microbiol	10.1099/ijs.0.010777-0	2009	*

References

#15833

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21593

#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 )

#29315

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 #25728 (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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68369

Automatically annotated from API 20NE .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#83449

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID398273.1 )

#25728

IJSEM 580 2010 ( DOI 10.1099/ijs.0.010777-0 , PubMed 19654337 )

* These data were automatically processed and therefore are not curated

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Sphingosinicella vermicomposti strain KCTC 22446

Sphingosinicella vermicomposti strain KCTC 22446

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