Name: Novosphingobium barchaimii LL02
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 23265

Type strain:

Species: Novosphingobium barchaimii

Strain Designation: LL02

Culture col. no.: DSM 25411, CCM 7980

Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; LL02 <- J. Damborsky, Masaryk Univ., Faculty of Science, Brno, Czech Republic

NCBI tax ID(s): 1420591 (species)

SI-ID 401713

DSM 25411

Special Collections

Section

Novosphingobium barchaimii LL02 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from hexachlorocyclohexane contaminated soil besides lindane producing plant.

Gram-negative
rod-shaped
aerobe
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	*Erythrobacteraceae*
	Genus	*Novosphingobium*
	Species	**Novosphingobium barchaimii**
	Full Scientific Name (LPSN)	Novosphingobium barchaimii Niharika et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30604]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %95.797

[Ref.: #30604]	Cell length	1 µm

[Ref.: #30604]	Cell width	1 µm

[Ref.: #30604]	Cell shape	rod-shaped

[Ref.: #30604]	Motility	no

[Ref.: #30604]

Pigment production

yes

Multimedia content

[Ref.: #19229]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19229]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #19229]

Culture medium growth

[Ref.: #19229]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19229]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #19229]	growth	28 °C
[Ref.: #30604]	growth	28-37 °C
[Ref.: #30604]	optimum	28 °C

	pH	Kind of pH		pH
[Ref.: #30604]			optimum	7
[Ref.: #30604]			growth	05-07

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30604]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30604]		NaCl		growth	0-3	%
[Ref.: #30604]		NaCl		optimum	1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30604]	esculin ChEBI	+	hydrolysis
[Ref.: #30604]	glucose ChEBI	+	carbon source
[Ref.: #30604]	nitrate ChEBI	+	reduction
[Ref.: #30604]	rhamnose ChEBI	+	carbon source
[Ref.: #30604]	sucrose ChEBI	+	carbon source
[Ref.: #30604]	tween 20 ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30604]		gelatinase	+
[Ref.: #30604]		urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	purine metabolism	68.09	64 of 94
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	pyrimidine metabolism	60	27 of 45
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	58.82	10 of 17
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	53.85	7 of 13
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	oxidative phosphorylation	50.55	46 of 91
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #19229]	Sample type/isolated from	hexachlorocyclohexane contaminated soil besides lindane producing plant
[Ref.: #19229]	Country	Czech Republic
[Ref.: #19229]	Country ISO 3 Code	CZE
[Ref.: #19229]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Engineered	#Industrial	#Plant (Factory)
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JN695619 (>99% sequence identity) for Novosphingobium barchaimii from Microbeatlas

Aquatic Samples	120
Soil Samples	125
Animal Samples	298
Plant Samples	57
Total Samples	600

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

[Ref.: #19229]

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.: #19229]	Novosphingobium barchaimii LL02 16S ribosomal RNA gene, partial sequence	JN695619	1405	GenBank ENA	1114963 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Novosphingobium barchaimii LL02	GCA_001046635	scaffold	GenBank ENA	1114963 tax ID	*
[Ref.: #66792]	Novosphingobium barchaimii LL02	1114963.3	wgs	PATRIC	1114963 tax ID	*
[Ref.: #66792]	Novosphingobium barchaimii LL02	2654587500	draft	JGI IMG/M	1114963 tax ID	*

[Ref.: #19229]	GC-content	67.72 mol%	fluorimetric
[Ref.: #30604]	GC-content	67.72 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Novosphingobium barchaimii LL02 LL02 NCBI: GCA_001046635.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	95.797	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.187	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	88.969	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	85.153	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.885	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	60.331	no

Availability in culture collections External links

[Ref.: #19229]

Culture collection no.

DSM 25411, CCM 7980

[Ref.: #87488]

SI-ID 401713

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Novosphingobium profundi sp. nov. isolated from a deep-sea seamount.	Zhang DC, Liu YX, Huang HJ	Antonie Van Leeuwenhoek	10.1007/s10482-016-0769-3	2016	*
Phylogeny	Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum.	Kampfer P, Martin K, McInroy JA, Glaeser SP	Int J Syst Evol Microbiol	10.1099/ijs.0.000339	2015	*
Phylogeny	Novosphingobium barchaimii sp. nov., isolated from hexachlorocyclohexane-contaminated soil.	Niharika N, Moskalikova H, Kaur J, Sedlackova M, Hampl A, Damborsky J, Prokop Z, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.039826-0	2012	*

References

#19229

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25411

#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 )

#30604

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 #26935 (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) .

#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 )

#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 .

#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) .

#87488

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID401713.1 )

#26935

IJSEM 667 2013 ( DOI 10.1099/ijs.0.039826-0 , PubMed 22544801 )

* These data were automatically processed and therefore are not curated

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Novosphingobium barchaimii LL02 LL02

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