Novosphingobium indicum (DSM 23608, CGMCC 1.6784, LMG 24713)

Name: Novosphingobium indicum (DSM 23608, CGMCC 1.6784, LMG 24713)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14165

Type strain

Strain Designation H25

Culture col. no. DSM 23608 CGMCC 1.6784 LMG 24713 MCCC 1A01080 H25

NCBI tax ID(s) 462949

Special Collections DSMZ Literature strains

Links

Novosphingobium indicum H25 is a mesophilic, Gram-negative, rod-shaped prokaryote that was isolated from Deep-sea water.

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

Name and taxonomic classification

SI-ID 351957

DSM 23608,LMG 24628,LMG 24713,CGMCC 1.6784

@ref 20215

Last LPSN update 2025-12-16 09:50:16

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Erythrobacteraceae

Genus Novosphingobium

Species Novosphingobium indicum

Full scientific name Novosphingobium indicum Yuan et al. 2009

Synonyms (1)

Pseudonovosphingobium indicum

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
28970	negative	1.25 µm	0.65 µm	rod-shaped
125439	negative
125438	negative

Pigmentation

28970

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17300	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
17300	positive	growth	28	mesophilic
28970	positive	growth	10-41
28970	positive	optimum	27.5	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	95.1

Spore formation

@ref	Spore formation	Confidence
125439		99.5

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
28970	28644 ChEBI	2-oxopentanoate	+	carbon source
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
28970	16449 ChEBI	alanine	+	carbon source
28970	40585 ChEBI	alpha-cyclodextrin	+	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
28970	23652 ChEBI	dextrin	+	carbon source
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
28970	17234 ChEBI	glucose	+	carbon source
28970	29987 ChEBI	glutamate	+	carbon source
28970	28087 ChEBI	glycogen	+	carbon source
28970	21217 ChEBI	L-alaninamide	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
28970	25017 ChEBI	leucine	+	carbon source
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
28970	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
28970	37684 ChEBI	mannose	+	carbon source
28970	51850 ChEBI	methyl pyruvate	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
28970	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
28970	26271 ChEBI	proline	+	carbon source
28970	30031 ChEBI	succinate	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
28970	53423 ChEBI	tween 40	+	carbon source
28970	53426 ChEBI	tween 80	+	carbon source
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
28970	acid phosphatase	+	3.1.3.2
28970	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
28970	catalase	+	1.11.1.6
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
17300	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17300	Deep-sea water	Indian Ocean	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF549586 (>99% sequence identity) for Novosphingobium from Microbeatlas

Aquatic Samples	1021
Soil Samples	233
Animal Samples	222
Plant Samples	49
Total Samples	1525

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17300	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	ASM1464519v1 assembly for Novosphingobium indicum CGMCC 1.6784	scaffold	GCA_014645195	462949.3	8069047553	462949	54.89

Genome browser: GCA_014645195

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17300	Novosphingobium indicum strain H25 16S ribosomal RNA gene, partial sequence	EF549586	1456		462949

GC content

28970

GC-content (mol%)62

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Novosphingobium indicum CGMCC 1.6784
NCBI: GCA_014645195

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	yes	83.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	95.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Novosphingobium indicum CGMCC 1.6784
NCBI: GCA_014645195.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.30	yes
125438	anaerobic	anaerobicⓘ	no	93.45	no
125438	aerobic	aerobicⓘ	yes	85.72	no
125438	spore-forming	spore-formingⓘ	no	87.99	no
125438	thermophilic	thermophileⓘ	no	98.07	no
125438	flagellated	motile2+ⓘ	yes	67.72	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Novosphingobium marinum sp. nov., isolated from seawater.	Huo YY, You H, Li ZY, Wang CS, Xu XW	Int J Syst Evol Microbiol	10.1099/ijs.0.070433-0	2014
Phylogeny	Novosphingobium malaysiense sp. nov. isolated from mangrove sediment.	Lee LH, Azman AS, Zainal N, Eng SK, Fang CM, Hong K, Chan KG	Int J Syst Evol Microbiol	10.1099/ijs.0.059014-0	2014
Phylogeny	Novosphingobium indicum sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from a deep-sea environment.	Yuan J, Lai Q, Zheng T, Shao Z	Int J Syst Evol Microbiol	10.1099/ijs.0.002873-0	2009

References

#17300	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23608
#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 )
#28970	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 #25406 (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) .
#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 .
#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 )

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Novosphingobium indicum (DSM 23608, CGMCC 1.6784, LMG 24713)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

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_014645195

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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