Allosphingosinicella vermicomposti (DSM 21593, KCTC 22446, YC7378)

Name: Allosphingosinicella vermicomposti (DSM 21593, KCTC 22446, YC7378)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14296

Type strain

Strain Designation YC7378

Culture col. no. DSM 21593 KCTC 22446 YC7378

NCBI tax ID(s) 614671

Special Collections DSMZ KCTC Literature strains

History DSMZ <- Y. R. Chung, Gyeongsang Nat. Univ. (GSNU), Jinju, Korea; YC7378 <- M. Yasir KCTC <- YR Chung, Kyeongsang Univ.

Links

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

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

Name and taxonomic classification

SI-ID 398273

KCTC 22446,DSM 21593

@ref 20215

Last LPSN update 2026-05-29 08:28:15

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Allosphingosinicella

Species Allosphingosinicella vermicomposti

Full scientific name Allosphingosinicella vermicomposti (Yasir et al. 2010) Hördt et al. 2020

Synonyms (1)

Sphingosinicella vermicomposti

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29315	negative	1.3 µm	0.45 µm	rod-shaped
67771	negative
125439	negative				93.39
125438	negative				94.828

Pigmentation

29315

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15833	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
15833	positive	growth	28
29315	positive	growth	10-37
29315	positive	optimum	30
67771	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
29315	positive	optimum	7.5
29315	positive	growth	06-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29315	aerobe
67771	aerobe
125439	aerobe	93.508

Spore formation

@ref	Spore formation	Confidence
29315
125438		91.253
125439		97.588

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29315	NaCl	positive	growth	0-1.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
29315	16449 ChEBI	alanine	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
29315	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
29315	21217 ChEBI	L-alaninamide	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
29315	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
29315	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
29315	acid phosphatase	+	3.1.3.2
29315	alkaline phosphatase	+	3.1.3.1
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
29315	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
15833	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Composting

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15833	vermicompost	Mansan, farm	Republic of Korea	KOR	Asia
67771	From vermicompost	Masan	Republic of Korea	KOR	Asia

Taxonmaps

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	0
Total Samples	11

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15833	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	ASM301281v1 assembly for Allosphingosinicella vermicomposti KCTC 22446	contig	GCA_003012815	614671.3	2832661309	614671	75.77

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15833	Sphingosinicella vermicomposti strain YC7378 16S ribosomal RNA gene, partial sequence	FJ442859	1315		614671
124043	Sphingosinicella vermicomposti strain DSM 21593 16S ribosomal RNA gene, partial sequence.	KU133480	1453		614671

GC content

@ref	GC-content (mol%)	Method
15833	59.4	high performance liquid chromatography (HPLC)
29315	59.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM301281v1 assembly for Allosphingosinicella vermicomposti KCTC 22446
NCBI: GCA_003012815

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	93.51	no
125439	gram_stain	BacteriaNetⓘ	negative	93.39	no
125439	motility	BacteriaNetⓘ	yes	48.81	no
125439	spore_formation	BacteriaNetⓘ	no	97.59	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingosinicella vermicomposti strain KCTC 22446
PATRIC: 614671.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.83	no
125438	anaerobic	anaerobicⓘ	no	93.42	yes
125438	spore-forming	spore-formingⓘ	no	91.25	no
125438	aerobic	aerobicⓘ	yes	82.52	no
125438	thermophilic	thermophileⓘ	no	92.89	yes
125438	flagellated	motile2+ⓘ	yes	58.41	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
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 )
#25728	IJSEM 580 2010 ( DOI 10.1099/ijs.0.010777-0 , PubMed 19654337 )
#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
#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 .
#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 )

Content

About us

Allosphingosinicella vermicomposti (DSM 21593, KCTC 22446, YC7378)

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

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003012815

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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