Name: Novosphingobium mathurense SM117
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14162

Type strain:

Species: Novosphingobium mathurense

Strain Designation: SM117

Culture col. no.: DSM 23374, CCM 7473, MTCC 9020

Strain history: <- CCM <- MTCC; SM117 <- R. Lal, Univ. Delhi, Dept. Zoology, India

NCBI tax ID(s): 428990 (species)

Section

Novosphingobium mathurense SM117 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from oil-contaminated soil.

Gram-negative
motile
rod-shaped
aerobe
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	*Erythrobacteraceae*
	Genus	*Novosphingobium*
	Species	**Novosphingobium mathurense**
	Full Scientific Name (LPSN)	Novosphingobium mathurense Gupta et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #32592]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.988

[Ref.: #32592]	Cell length	1.4 µm

[Ref.: #32592]	Cell width	0.8 µm

[Ref.: #32592]	Cell shape	rod-shaped

[Ref.: #32592]	Motility	yes

[Ref.: #32592]

Pigment production

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #32592]			growth	28-37 °C
[Ref.: #32592]			optimum	32.5 °C

[Ref.: #32592]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #32592]			optimum	7.2

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32592]

Oxygen tolerance

aerobe

[Ref.: #32592]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.991

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32592]	arabinose ChEBI	+	carbon source
[Ref.: #32592]	esculin ChEBI	+	hydrolysis
[Ref.: #32592]	fructose ChEBI	+	carbon source
[Ref.: #32592]	galactose ChEBI	+	carbon source
[Ref.: #32592]	glucose ChEBI	+	carbon source
[Ref.: #32592]	lactose ChEBI	+	carbon source
[Ref.: #32592]	maltose ChEBI	+	carbon source
[Ref.: #32592]	mannose ChEBI	+	carbon source
[Ref.: #32592]	raffinose ChEBI	+	carbon source
[Ref.: #32592]	rhamnose ChEBI	+	carbon source
[Ref.: #32592]	trehalose ChEBI	+	carbon source
[Ref.: #32592]	tween 80 ChEBI	+	carbon source
[Ref.: #32592]	xylose ChEBI	+	carbon source
	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.: #16714]	Sample type/isolated from	oil-contaminated soil
[Ref.: #16714]	Geographic location (country and/or sea, region)	Mathura
[Ref.: #16714]	Country	India
[Ref.: #16714]	Country ISO 3 Code	IND
[Ref.: #16714]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF424403 (>99% sequence identity) for Novosphingobium from Microbeatlas

Aquatic Samples	1963
Soil Samples	623
Animal Samples	828
Plant Samples	663
Total Samples	4077

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

[Ref.: #16714]

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.: #16714]	Novosphingobium mathurense strain SM117 16S ribosomal RNA gene, partial sequence	EF424403	1381	ENA	428990 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Novosphingobium mathurense SM117	GCA_900168325	scaffold	GenBank	428990 tax ID	*
[Ref.: #66792]	Novosphingobium mathurense SM117	2706795032	draft	JGI IMG/M	428990 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: Novosphingobium mathurense SM117 NCBI: GCA_900168325.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Novosphingobium mathurense SM117 NCBI: GCA_900168325.1
[Ref.: #69480]	motile	yes	65.219	yes
[Ref.: #69480]	flagellated	no	82.638	no
[Ref.: #69480]	gram-positive	no	97.647	yes
[Ref.: #69480]	anaerobic	no	98.323	yes
[Ref.: #69480]	aerobic	yes	88.407	yes
[Ref.: #69480]	halophile	no	90.764	no
[Ref.: #69480]	spore-forming	no	95.055	yes
[Ref.: #69480]	thermophile	no	97.554	yes
[Ref.: #69480]	glucose-util	yes	93.844	yes
[Ref.: #69480]	glucose-ferment	no	91.098	no

Availability in culture collections External links

[Ref.: #16714]

Culture collection no.

DSM 23374, CCM 7473, MTCC 9020

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Novosphingobium aureum sp. nov., a marine bacterium isolated from salt flat sediment.	Yoo Y, Kim D, Lee H, Khim JS, Kim B, Yang D, Pathiraja D, Choi IG, Kim JJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004930	2021	*
Phylogeny	Novosphingobium aquimarinum sp. nov., isolated from seawater.	Le VV, Ko SR, Lee SA, Jin L, Ahn CY, Oh HM	Int J Syst Evol Microbiol	10.1099/ijsem.0.004493	2020	*
Phylogeny	Novosphingobium ipomoeae sp. nov., isolated from a water convolvulus field.	Chen WM, Huang CW, Chen JC, Chen ZH, Sheu SY	Int J Syst Evol Microbiol	10.1099/ijsem.0.002174	2017	*
Phylogeny	Novosphingobium fontis sp. nov., isolated from a spring.	Sheu SY, Liu LP, Young CC, Chen WM	Int J Syst Evol Microbiol	10.1099/ijsem.0.001973	2017	*
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 naphthae sp. nov., from oil-contaminated soil.	Chaudhary DK, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001164	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 lindaniclasticum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite.	Saxena A, Anand S, Dua A, Sangwan N, Khan F, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.045443-0	2012	*
Phylogeny	Novosphingobium panipatense sp. nov. and Novosphingobium mathurense sp. nov., from oil-contaminated soil.	Gupta SK, Lal D, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.65743-0	2009	*

References

#16714

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23374

#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 )

#32592

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 #28805 (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) .

#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) .

#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 )

#28805

IJSEM 156 2009 ( DOI 10.1099/ijs.0.65743-0 , PubMed 19126741 )

* These data were automatically processed and therefore are not curated

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