Name: Silvanigrella paludirubra SP-Ram-0.45-NSY-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 164430

Type strain:

Species: Silvanigrella paludirubra

Strain Designation: SP-Ram-0.45-NSY-1, SP-Ram- 0.45-NSY-1

Culture col. no.: JCM 32975, DSM 107809

Strain history: <- M. Hahn, University of Innsbruck,Research Institute for Limnology; SP-Ram-0.45-NSY-1 <- S. Pitt

NCBI tax ID(s): 2499159 (species)

SI-ID 406629

DSM 107809

Section

Silvanigrella paludirubra SP-Ram-0.45-NSY-1 is a psychrophilic, Gram-negative bacterium that was isolated from Small pond in Schönramer Moor.

Gram-negative
psychrophilic
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	*Oligoflexia*
	Order	*Silvanigrellales*
	Family	*Silvanigrellaceae*
	Genus	*Silvanigrella*
	Species	**Silvanigrella paludirubra**
	Full Scientific Name (LPSN)	Silvanigrella paludirubra Pitt et al. 2020

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.979

Information on culture and growth conditions Culture and growth conditions

[Ref.: #68960]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #68960]

Culture medium growth

[Ref.: #68960]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #68960]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #68960]

Culture medium growth

[Ref.: #68960]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #67770]	growth	20 °C
[Ref.: #68960]	growth	25 °C
[Ref.: #69598]	growth	36 °C

[Ref.: #67770]	Temperature range	psychrophilic
[Ref.: #68960]	Temperature range	mesophilic
[Ref.: #69598]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.989
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #69598]		NaCl		growth	1.1	%(w/v)

[Ref.: #67770]	Observation	quinones: MK-8
[Ref.: #69598]	Observation	The polar lipids are phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, two unidentified glycolipids, two unidentified lipids and one aminolipid.

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #69598]	(-)-quinic acid ChEBI	-	assimilation
[Ref.: #69598]	(S)-lactate ChEBI	-	assimilation
[Ref.: #69598]	2-oxobutanoate ChEBI	-	assimilation
[Ref.: #69598]	2-oxoglutarate ChEBI	+	assimilation
[Ref.: #69598]	3-methylglucose ChEBI	-	assimilation
[Ref.: #69598]	4-hydroxyphenylacetic acid ChEBI	-	assimilation
[Ref.: #69598]	acetic acid ChEBI	-	assimilation
[Ref.: #69598]	acetoacetate ChEBI	+	assimilation
[Ref.: #69598]	alpha-D-glucose ChEBI	+	assimilation
[Ref.: #69598]	alpha-hydroxybutyrate	-	assimilation
[Ref.: #69598]	bromosuccinate ChEBI	-	assimilation
[Ref.: #69598]	cellobiose ChEBI	-	assimilation
[Ref.: #69598]	citrate ChEBI	-	assimilation
[Ref.: #69598]	D-arabitol ChEBI	-	assimilation
[Ref.: #69598]	D-aspartate ChEBI	-	assimilation
[Ref.: #69598]	D-fructose ChEBI	+	assimilation
[Ref.: #69598]	D-fructose 6-phosphate ChEBI	-	assimilation
[Ref.: #69598]	D-fucose ChEBI	+	assimilation
[Ref.: #69598]	D-galactose ChEBI	+	assimilation
[Ref.: #69598]	D-galacturonic acid ChEBI	-	assimilation
[Ref.: #69598]	D-gluconate ChEBI	-	assimilation
[Ref.: #69598]	D-glucose 6-phosphate ChEBI	+	assimilation
[Ref.: #69598]	D-glucuronate ChEBI	-	assimilation
[Ref.: #69598]	D-malate ChEBI	-	assimilation
[Ref.: #69598]	D-mannitol ChEBI	-	assimilation
[Ref.: #69598]	D-mannose ChEBI	-	assimilation
[Ref.: #69598]	D-saccharate ChEBI	-	assimilation
[Ref.: #69598]	D-salicin ChEBI	-	assimilation
[Ref.: #69598]	D-serine ChEBI	-	assimilation
[Ref.: #69598]	D-sorbitol ChEBI	-	assimilation
[Ref.: #69598]	dextrin ChEBI	-	assimilation
[Ref.: #69598]	formate ChEBI	-	assimilation
[Ref.: #69598]	galactarate ChEBI	-	assimilation
[Ref.: #69598]	gamma-aminobutyric acid ChEBI	-	assimilation
[Ref.: #69598]	gelatin ChEBI	-	assimilation
[Ref.: #69598]	gentiobiose ChEBI	-	assimilation
[Ref.: #69598]	glycerol ChEBI	-	assimilation
[Ref.: #69598]	glycyl-L-proline ChEBI	-	assimilation
[Ref.: #69598]	inosine ChEBI	-	assimilation
[Ref.: #69598]	L-alanine ChEBI	-	assimilation
[Ref.: #69598]	L-arginine ChEBI	-	assimilation
[Ref.: #69598]	L-aspartate ChEBI	-	assimilation
[Ref.: #69598]	L-fucose ChEBI	-	assimilation
[Ref.: #69598]	L-galactonate ChEBI	-	assimilation
[Ref.: #69598]	L-glutamate ChEBI	+	assimilation
[Ref.: #69598]	L-histidine ChEBI	+	assimilation
[Ref.: #69598]	L-malate ChEBI	-	assimilation
[Ref.: #69598]	L-pyroglutamic acid 2-naphthylamide ChEBI	-	assimilation
[Ref.: #69598]	L-rhamnose ChEBI	-	assimilation
[Ref.: #69598]	L-serine ChEBI	-	assimilation
[Ref.: #69598]	lactose ChEBI	-	assimilation
[Ref.: #69598]	maltose ChEBI	-	assimilation
[Ref.: #69598]	melibiose ChEBI	-	assimilation
[Ref.: #69598]	methyl (R)-lactate ChEBI	-	assimilation
[Ref.: #69598]	methyl beta-D-glucopyranoside ChEBI	-	assimilation
[Ref.: #69598]	methyl pyruvate ChEBI	-	assimilation
[Ref.: #69598]	myo-inositol ChEBI	-	assimilation
[Ref.: #69598]	N-acetyl-beta-D-mannosamine ChEBI	-	assimilation
[Ref.: #69598]	n-acetyl-D-galactosamine ChEBI	-	assimilation
[Ref.: #69598]	N-acetyl-D-glucosamine ChEBI	-	assimilation
[Ref.: #69598]	n-acetyl-neuraminic acid	-	assimilation
[Ref.: #69598]	pectin ChEBI	-	assimilation
[Ref.: #69598]	propionate ChEBI	-	assimilation
[Ref.: #69598]	raffinose ChEBI	-	assimilation
[Ref.: #69598]	stachyose ChEBI	-	assimilation
[Ref.: #69598]	sucrose ChEBI	-	assimilation
[Ref.: #69598]	trehalose ChEBI	-	assimilation
[Ref.: #69598]	turanose ChEBI	-	assimilation
[Ref.: #69598]	tween 40 ChEBI	+	assimilation
	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.: #67770]	Sample type/isolated from	Small pond in Schönramer Moor
[Ref.: #67770]	Geographic location (country and/or sea, region)	Bavaria
[Ref.: #67770]	Country	Germany
[Ref.: #67770]	Country ISO 3 Code	DEU
[Ref.: #67770]	Continent	Europe

[Ref.: #68960]	Sample type/isolated from	freshwater
[Ref.: #68960]	Geographic location (country and/or sea, region)	Schönramer Moorsee
[Ref.: #68960]	Country	Germany
[Ref.: #68960]	Country ISO 3 Code	DEU
[Ref.: #68960]	Continent	Europe
[Ref.: #68960]	Geographic location	47.8980°/12.8508°

[Ref.: #69598]	Sample type/isolated from	a small pond located in Schönramer Moor, Bavaria, Germany.
[Ref.: #69598]	Geographic location (country and/or sea, region)	Schönramer Moor,Bavaria
[Ref.: #69598]	Country	Germany
[Ref.: #69598]	Country ISO 3 Code	DEU
[Ref.: #69598]	Continent	Europe
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence MN565732 (>99% sequence identity) for Silvanigrella aquatica subclade from Microbeatlas

Aquatic Samples	4923
Soil Samples	579
Animal Samples	395
Plant Samples	45
Total Samples	5942

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.: #69598]	16S rRNA gene sequence	WFLM00000000		ENA
[Ref.: #67770]	Silvanigrella sp. strain SP-Ram-0.45-NSY-1 16S ribosomal RNA gene, partial sequence	MN565732	1417	ENA	2499159 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Silvanigrella paludirubra SP-Ram-0.45-NSY-1	GCA_009208775	scaffold	GenBank	2499159 tax ID
[Ref.: #69598]	genome sequence	MN565732		GenBank	2499159 tax ID

[Ref.: #69598]

GC-content

29.3 mol%

genome sequence analysis

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: Silvanigrella paludirubra SP-Ram-0.45-NSY-1 NCBI: GCA_009208775.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Silvanigrella paludirubra SP-Ram-0.45-NSY-1 NCBI: GCA_009208775.1
[Ref.: #69480]	flagellated	no	72.712	no
[Ref.: #69480]	gram-positive	no	98.151	no
[Ref.: #69480]	anaerobic	no	95.881	no
[Ref.: #69480]	aerobic	yes	70.113	no
[Ref.: #69480]	halophile	no	86.396	no
[Ref.: #69480]	spore-forming	no	89.12	no
[Ref.: #69480]	thermophile	no	98.511	yes
[Ref.: #69480]	glucose-util	yes	60.48	no
[Ref.: #69480]	motile	yes	80.758	no
[Ref.: #69480]	glucose-ferment	no	83.222	no

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 32975, DSM 107809

[Ref.: #114164]

SI-ID 406629

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Fluviispira multicolorata gen. nov., sp. nov. and Silvanigrella paludirubra sp. nov., isolated from freshwater habitats.	Pitt A, Koll U, Schmidt J, Hahn MW	Int J Syst Evol Microbiol	10.1099/ijsem.0.003947	2020	*

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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68960

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 107809

#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 )

#69598

Alexandra Pitt, Ulrike Koll, Johanna Schmidt and Martin W. Hahn: Fluviispira multicolorata gen. nov., sp. nov. and Silvanigrella paludirubra sp. nov., isolated from freshwater habitats. IJSEM 70: 2020 ( DOI 10.1099/ijsem.0.003947 )

#114164

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-ID406629.1 )

* These data were automatically processed and therefore are not curated

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