Novosphingobium kunmingense (DSM 25975, CGMCC 1.12274, 18-11HK)

Name: Novosphingobium kunmingense (DSM 25975, CGMCC 1.12274, 18-11HK)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130665

Type strain

Strain Designation 18-11HK

Culture col. no. DSM 25975 CGMCC 1.12274 18-11HK

NCBI tax ID(s) 1211806

Special Collections DSMZ

History DSMZ <- F. Xie, Henan Key Laboratory of Microbial Eng., Zhengzhou, China; 18-11HK

Links

Novosphingobium kunmingense 18-11HK is a bacterium that was isolated from phosphate rock powder from a phosphate-mining field.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 398635

DSM 25975

@ref 20215

Last LPSN update 2026-05-29 08:37:26

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Erythrobacteraceae

Genus Novosphingobium

Species Novosphingobium kunmingense

Full scientific name Novosphingobium kunmingense Xie et al. 2014

Synonyms (1)

Paranovosphingobium kunmingense

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	96.302
125439	negative	95.143

Multimedia

@ref:	21701
multimedia content:	DSM_25975.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_25975.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21701	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21701	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.909

Spore formation

@ref	Spore formation	Confidence
125439		98.551

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
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
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
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
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	valine metabolism	100	9 of 9
66794	L-lactaldehyde degradation	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	phenylmercury acetate degradation	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	methylglyoxal degradation	100	5 of 5
66794	octane oxidation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	vitamin B12 metabolism	88.24	30 of 34
66794	propanol degradation	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	phenol degradation	85	17 of 20
66794	leucine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	starch degradation	80	8 of 10
66794	propionate fermentation	80	8 of 10
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	3-phenylpropionate degradation	80	12 of 15
66794	gallate degradation	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	glutathione metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	purine metabolism	75.53	71 of 94
66794	glycogen biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	toluene degradation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	histidine metabolism	72.41	21 of 29
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	tryptophan metabolism	68.42	26 of 38
66794	lipid metabolism	67.74	21 of 31
66794	cyanate degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	pyrimidine metabolism	64.44	29 of 45
66794	tyrosine metabolism	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	cysteine metabolism	61.11	11 of 18
66794	glycolysis	58.82	10 of 17
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	non-pathway related	57.89	22 of 38
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	degradation of sugar alcohols	56.25	9 of 16
66794	degradation of sugar acids	56	14 of 25
66794	lysine metabolism	54.76	23 of 42
66794	polyamine pathway	52.17	12 of 23
66794	pantothenate biosynthesis	50	3 of 6
66794	myo-inositol biosynthesis	50	5 of 10
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	carnitine metabolism	50	4 of 8
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	vitamin E metabolism	50	2 of 4
66794	arginine metabolism	50	12 of 24
66794	quinate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	sulfate reduction	46.15	6 of 13
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	ascorbate metabolism	45.45	10 of 22
66794	metabolism of disaccharids	45.45	5 of 11
66794	degradation of hexoses	44.44	8 of 18
66794	nitrate assimilation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	carotenoid biosynthesis	40.91	9 of 22
66794	factor 420 biosynthesis	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	hydrogen production	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	oxidative phosphorylation	39.56	36 of 91
66794	degradation of pentoses	39.29	11 of 28
66794	arachidonic acid metabolism	38.89	7 of 18
66794	d-xylose degradation	36.36	4 of 11
66794	methane metabolism	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	lactate fermentation	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	catecholamine biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4

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
21701	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Environmental	#Terrestrial	#Geologic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
21701	phosphate rock powder from a phosphate-mining field	Yunnan Province, suburb of Kunming	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21701	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM281324v1 assembly for Novosphingobium kunmingense CGMCC 1.12274	contig	GCA_002813245	1211806.3	2718217687	1211806	74.38

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21701	Novosphingobium kunmingense strain 18-11HK 16S ribosomal RNA gene, partial sequence	JQ246446	1453		1211806

GC content

@ref	GC-content (mol%)	Method
21701	65.3	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM281324v1 assembly for Novosphingobium kunmingense CGMCC 1.12274
BV-BRC: 1211806.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.91	no
125439	motility	BacteriaNetⓘ	yes	46.50	no
125439	gram_stain	BacteriaNetⓘ	negative	95.14	no
125439	spore_formation	BacteriaNetⓘ	no	98.55	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Novosphingobium kunmingense strain CGMCC 1.12274
PATRIC: 1211806.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.30	no
125438	anaerobic	anaerobicⓘ	no	93.63	no
125438	spore-forming	spore-formingⓘ	no	89.18	no
125438	aerobic	aerobicⓘ	yes	87.44	no
125438	thermophilic	thermophileⓘ	no	93.91	no
125438	flagellated	motile2+ⓘ	no	61.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Novosphingobium naphthae sp. nov., from oil-contaminated soil.	Chaudhary DK, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001164	2016
Phylogeny	Novosphingobium kunmingense sp. nov., isolated from a phosphate mine.	Xie F, Quan S, Liu D, He W, Wang Y, Ma H, Chen G, Chao Y, Qian S	Int J Syst Evol Microbiol	10.1099/ijs.0.057273-0	2014

References

#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 )
#21701	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25975
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#68369	Automatically annotated from API 20NE .
#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 kunmingense (DSM 25975, CGMCC 1.12274, 18-11HK)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002813245

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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