Sphingobium indicum (DSM 16412, CCM 7286, MTCC 6364)

Name: Sphingobium indicum (DSM 16412, CCM 7286, MTCC 6364)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14184

Type strain

Strain Designation B90A

Culture col. no. DSM 16412 CCM 7286 MTCC 6364 B90A CIP 108929

NCBI tax ID(s) 332055

Special Collections DSMZ CIP

History <- R. Lal, Univ. New Delhi; B90A <- N. Sethunathan CIP <- 2005, CCM <- 2005, R. Lal, Dehli Univ., Delhi, India: strain B90A

Links

Sphingobium indicum B90A is a facultative anaerobe, Gram-negative, rod-shaped bacterium that was isolated from sugarcane rhizosphere soil.

Gram-negative rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 265629

MTCC 6364,CCM 7286,DSM 16412,CIP 108929

@ref 20215

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

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingobium

Species Sphingobium indicum

Full scientific name Sphingobium indicum Pal et al. 2005

Synonyms (4)

Sphingobium chinhatense
Sphingobium lucknowense
Sphingobium francense
Sphingobium japonicum

BacDive ID	Other strains from **Sphingobium indicum** (2)	Type strain
14185	S. indicum UT26, DSM 16413, CCM 7287, MTCC 6362, CIP ...
23269	S. indicum Sp+, DSM 26779, CCM 7288, MTCC 6363, CCUG ...

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
120083	negative	rod-shaped
125439	negative			96.7

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
38370	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120083	CIP Medium 72			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
38370	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
120083	facultative anaerobe
125439	aerobe	96.7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
120083	17632 ChEBI	nitrate	+	reduction
120083	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120083	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120083	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120083	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
120083	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120083	ornithine decarboxylase	-	4.1.1.17
120083	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
120083	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
120083	-	+	+	-	-	+	+	-	+	+	+	+	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6438	sugarcane rhizosphere soil	Cuttack	India	IND	Asia
120083	Environment, Rice rhizosphere	Cuttack	India	IND	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6438	1	Risk group (German classification) According to TRBA 466
120083	1	Risk group (French 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	ASM26494v2 assembly for Sphingobium indicum B90A	complete	GCA_000264945	861109.21	2775507255	861109	97.35
66792	Sphingobium indicum B90A	contig		861109.3		861109	46.8

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6438	Sphingobium indicum strain B90A 16S ribosomal RNA gene, partial sequence	AY519129	1452		861109

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingobium indicum B90A
NCBI: GCA_000264945

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	89.20	no
125439	motility	BacteriaNetⓘ	yes	52.10	no
125439	gram_stain	BacteriaNetⓘ	negative	96.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	96.70	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Markerless gene deletion system for sphingomonads.	Kaczmarczyk A, Vorholt JA, Francez-Charlot A.	Appl Environ Microbiol	10.1128/aem.07347-11	2012
Metabolism	Cumate-inducible gene expression system for sphingomonads and other Alphaproteobacteria.	Kaczmarczyk A, Vorholt JA, Francez-Charlot A.	Appl Environ Microbiol	10.1128/aem.02296-13	2013
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	Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov.	Pal R, Bala S, Dadhwal M, Kumar M, Dhingra G, Prakash O, Prabagaran SR, Shivaji S, Cullum J, Holliger C, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.63201-0	2005

References

#6438	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16412
#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 )
#38370	; Curators of the CIP;
#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) .
#68382	Automatically annotated from API zym .
#120083	Collection of Institut Pasteur ; Curators of the CIP; CIP 108929
#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 )

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Sphingobium indicum (DSM 16412, CCM 7286, MTCC 6364)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000264945

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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