Name: Novosphingobium sediminicola HU1-AH51
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 23264

Type strain:

Species: Novosphingobium sediminicola

Strain Designation: HU1-AH51

Culture col. no.: DSM 27057, KCTC 22311, LMG 24320

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 563162 (species)

SI-ID 319132

LMG 24320, KCTC 22311, DSM 27057

Special Collections

DSMZ
KCTC

Section

Novosphingobium sediminicola HU1-AH51 is an aerobe, Gram-negative bacterium that was isolated from freshwater sediment from littoral zone.

Gram-negative
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 sediminicola**
	Full Scientific Name (LPSN)	Novosphingobium sediminicola Baek et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %95

Multimedia content

[Ref.: #19124]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19124]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #19124]

Culture medium growth

[Ref.: #19124]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19124]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #19124]			growth	28 °C
[Ref.: #67771]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %98

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

[Ref.: #19124]	Sample type/isolated from	freshwater sediment from littoral zone
[Ref.: #19124]	Geographic location (country and/or sea, region)	Lake Hakha
[Ref.: #19124]	Country	Republic of Korea
[Ref.: #19124]	Country ISO 3 Code	KOR
[Ref.: #19124]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From freshwater sediment
[Ref.: #67771]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ177534 (>99% sequence identity) for Novosphingobium sediminicola from Microbeatlas

Aquatic Samples	24
Soil Samples	2
Animal Samples	4
Plant Samples	11
Total Samples	41

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

[Ref.: #19124]

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.: #19124]	Novosphingobium sediminicola strain HU1-AH51 16S ribosomal RNA gene, partial sequence	FJ177534	1387	GenBank ENA	563162 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Novosphingobium sediminicola DSM 27057	GCA_014196525	scaffold	GenBank ENA	563162 tax ID	*
[Ref.: #66792]	Novosphingobium sediminicola strain DSM 27057	563162.3	wgs	PATRIC	563162 tax ID	*
[Ref.: #66792]	Novosphingobium sediminicola DSM 27057	2829917985	draft	JGI IMG/M	563162 tax ID	*

[Ref.: #19124]

GC-content

62.6 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Novosphingobium sediminicola DSM 27057 NCBI: GCA_014196525.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	98	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Novosphingobium sediminicola DSM 27057 NCBI: GCA_014196525.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	95	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	89.413	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	84.589	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	87.434	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.385	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	73.942	no

Availability in culture collections External links

[Ref.: #19124]

Culture collection no.

DSM 27057, KCTC 22311, LMG 24320

[Ref.: #87487]

SI-ID 319132

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Novosphingobium lotistagni sp. nov., isolated from a lotus pond.	Ngo HTT, Trinh H, Kim JH, Yang JE, Won KH, Kim JH, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001418	2016	*
Phylogeny	Novosphingobium sediminicola sp. nov. isolated from freshwater sediment.	Baek SH, Lim JH, Jin L, Lee HG, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.024307-0	2010	*
Phylogeny	Novosphingobium humi sp. nov., isolated from soil of a military shooting range.	Hyeon JW, Kim K, Son AR, Choi E, Lee SK, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.002089	2017	*
Phylogeny	Novosphingobium oryzae sp. nov., a potential plant-promoting endophytic bacterium isolated from rice roots.	Zhang L, Gao JS, Kim SG, Zhang CW, Jiang JQ, Ma XT, Zhang J, Zhang XX	Int J Syst Evol Microbiol	10.1099/ijsem.0.000718	2015	*

References

#19124

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27057

#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 )

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#87487

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-ID319132.1 )

* These data were automatically processed and therefore are not curated

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Novosphingobium sediminicola DSM 27057

Novosphingobium sediminicola DSM 27057

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