Name: Sphingobium abikonense DDA 109
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14191

Type strain:

Species: Sphingobium abikonense

Strain Designation: DDA 109

Culture col. no.: DSM 23268, IAM 12404, JCM 20554, KCTC 2864, NBRC 16140, CCUG 54779, IFO 16140

Strain history: IAM 12404 <-- S. Yamada DDA 109.

NCBI tax ID(s): 1219036 (strain), 86193 (species)

Section

Sphingobium abikonense DDA 109 is a mesophilic, Gram-negative bacterium that was isolated from oil-contaminated soil.

Gram-negative
mesophilic
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	*Sphingobium*
	Species	**Sphingobium abikonense**
	Full Scientific Name (LPSN)	Sphingobium abikonense Kumari et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.994

Multimedia content

[Ref.: #16768]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #67770]			growth	25 °C

[Ref.: #67770]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.991

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

[Ref.: #16768]	Sample type/isolated from	oil-contaminated soil
[Ref.: #16768]	Geographic location (country and/or sea, region)	Lucknow
[Ref.: #16768]	Country	India
[Ref.: #16768]	Country ISO 3 Code	IND
[Ref.: #16768]	Continent	Asia

[Ref.: #60327]	Sample type/isolated from	Oil soaked soil

[Ref.: #67770]	Sample type/isolated from	Oil-soaked soil
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	#Oil (Fuel)
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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

[Ref.: #16768]

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.: #16768]	Sphingobium abikonense gene for 16S rRNA, strain: IAM 12404	AB021416	1477	ENA	86193 tax ID
[Ref.: #20218]	Sphingobium abikonense gene for 16S rRNA, partial sequence, strain: NBRC 16140	AB681054	1412	ENA	86193 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Sphingobium abikonense NBRC 16140	GCA_001598335	contig	GenBank	1219036 tax ID
[Ref.: #66792]	Sphingobium abikonense NBRC 16140	1219036.3	wgs	PATRIC	1219036 tax ID	*
[Ref.: #66792]	Sphingobium abikonense NBRC 16140	2731957697	draft	JGI IMG/M	1219036 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Sphingobium abikonense NBRC 16140 PATRIC: 1219036.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingobium abikonense NBRC 16140 PATRIC: 1219036.3
[Ref.: #69480]	motile	yes	57.414	no
[Ref.: #69480]	gram-positive	no	97.057	no
[Ref.: #69480]	anaerobic	no	99.266	no
[Ref.: #69480]	aerobic	yes	93.353	no
[Ref.: #69480]	halophile	no	93.415	no
[Ref.: #69480]	spore-forming	no	95.03	no
[Ref.: #69480]	thermophile	no	96.053	yes
[Ref.: #69480]	glucose-util	yes	90.283	no
[Ref.: #69480]	flagellated	no	87.865	no
[Ref.: #69480]	glucose-ferment	no	93.531	no

Availability in culture collections External links

[Ref.: #16768]

Culture collection no.

DSM 23268, IAM 12404, JCM 20554, KCTC 2864, NBRC 16140, CCUG 54779, IFO 16140

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobium aquiterrae sp. nov., a toluene, meta- and para-xylene-degrading bacterium isolated from petroleum hydrocarbon-contaminated groundwater.	Revesz F, Toth EM, Kriszt B, Boka K, Benedek T, Sarkany O, Nagy Z, Tancsics A	Int J Syst Evol Microbiol	10.1099/ijsem.0.002898	2018	*
Phylogeny	Sphingobium naphthae sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil.	Chaudhary DK, Jeong SW, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002064	2017	*
Phylogeny	Sphingobium soli sp. nov. isolated from rhizosphere soil of a rose.	Du J, Singh H, Yang JE, Yin CS, Kook M, Yu H, Yi TH	Antonie Van Leeuwenhoek	10.1007/s10482-015-0562-8	2015	*
Phylogeny	Sphingobium cupriresistens sp. nov., a copper-resistant bacterium isolated from copper mine soil, and emended description of the genus Sphingobium.	Li L, Liu H, Shi Z, Wang G	Int J Syst Evol Microbiol	10.1099/ijs.0.040865-0	2012	*
Phylogeny	Sphingobium lactosutens sp. nov., isolated from a hexachlorocyclohexane dump site and Sphingobium abikonense sp. nov., isolated from oil-contaminated soil.	Kumari H, Gupta SK, Jindal S, Katoch P, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.004739-0	2009	*

References

#16768

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23268

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#60327 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54779

#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;

#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 )

* These data were automatically processed and therefore are not curated

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Sphingobium abikonense NBRC 16140

Sphingobium abikonense NBRC 16140

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