Name: Rouxiella silvae 213
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140277

Type strain:

Species: Rouxiella silvae

Strain Designation: 213

Culture col. no.: DSM 103735, CIP 111154

Strain history: CIP <- 2016, A. Le Flèche, Inst. Pasteur, Paris, France: strain 213 <- Inst. Process Eng. Life Sci., Karlsruhe, Germany

NCBI tax ID(s): 1646373 (species)

SI-ID 402375

DSM 103735, CIP 111154

Section

Rouxiella silvae 213 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from swampy meadow soil.

Gram-negative
rod-shaped
facultative anaerobe
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	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Yersiniaceae*
	Genus	*Rouxiella*
	Species	**Rouxiella silvae**
	Full Scientific Name (LPSN)	Rouxiella silvae Le Flèche-Matéos et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43210]	Gram stain	negative
[Ref.: #122606]	Gram stain	negative

[Ref.: #43210]	Cell shape	rod-shaped
[Ref.: #122606]	Cell shape	rod-shaped

[Ref.: #122606]	Motility	no

[Ref.: #43210]	Colony color	white
[Ref.: #43210]	Cultivation medium used	solid medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43210]

Culture medium

solid medium

[Ref.: #43210]

Culture medium growth

[Ref.: #42884]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #42884]

Culture medium growth

[Ref.: #42884]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42884]

Culture medium composition

expand / minimize

[Ref.: #122606]

Culture medium

CIP Medium 72

[Ref.: #122606]

Culture medium growth

[Ref.: #122606]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #42884]		growth	28 °C
[Ref.: #43210]	no	growth	37 °C
[Ref.: #43210]		growth	4-30 °C

[Ref.: #42884]	Temperature range	mesophilic
[Ref.: #43210]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43210]

Oxygen tolerance

facultative anaerobe

[Ref.: #42884]

Name of produced compound

surfactant

[Ref.: #43210]

Observation

produces surfactant

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	amygdalin ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #43210]	D-arabitol ChEBI	+	builds acid from
[Ref.: #43210]	D-fucose ChEBI	+	builds acid from
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #43210]	D-lyxose ChEBI	+	builds acid from
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #43210]	glycerol ChEBI	-	builds acid from
[Ref.: #68368]	L-arabinose ChEBI	+	fermentation	* from API 20E
[Ref.: #43210]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #68368]	L-rhamnose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #43210]	maltose ChEBI	+	builds acid from
[Ref.: #43210]	melezitose ChEBI	+	builds acid from
[Ref.: #68368]	melibiose ChEBI	+	fermentation	* from API 20E
[Ref.: #43210]	methyl D-glucoside ChEBI	-	builds acid from
[Ref.: #68368]	myo-inositol ChEBI	+	fermentation	* from API 20E
[Ref.: #43210]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #43210]	nitrate ChEBI	-	reduction
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #43210]	raffinose ChEBI	+	builds acid from
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #43210]	sucrose ChEBI	+	builds acid from
[Ref.: #68368]	sucrose ChEBI	+	fermentation	* from API 20E
[Ref.: #43210]	trehalose ChEBI	+	builds acid from
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #43210]	turanose ChEBI	+	builds acid from
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
[Ref.: #43210]	xylitol ChEBI	+	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #68368]	acetoin ChEBI	yes	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	+		* from API 20E
[Ref.: #68368]		indole ChEBI		-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	+	3.2.1.23	* from API 20E
[Ref.: #68368]	cytochrome oxidase	-	1.9.3.1	* from API 20E
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #42884]	17667	+	-	-	-	+	-	-	-	-	+	-	+	+	+	-	+	+	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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

[Ref.: #42884]	Sample type/isolated from	swampy meadow soil
[Ref.: #42884]	Geographic location (country and/or sea, region)	northern part of Black Forest
[Ref.: #42884]	Country	Germany
[Ref.: #42884]	Country ISO 3 Code	DEU
[Ref.: #42884]	Continent	Europe
[Ref.: #42884]	Geographic location	48.7190°/8.4640°

[Ref.: #43210]	Sample type/isolated from	swampy meadow
[Ref.: #43210]	Geographic location (country and/or sea, region)	Kaltenbronn, northern Black Forest, Baden-Württemberg
[Ref.: #43210]	Country	Germany
[Ref.: #43210]	Country ISO 3 Code	DEU
[Ref.: #43210]	Continent	Europe

[Ref.: #122606]	Sample type/isolated from	Environment, Meadow
[Ref.: #122606]	Geographic location (country and/or sea, region)	Black forest
[Ref.: #122606]	Country	Germany
[Ref.: #122606]	Country ISO 3 Code	DEU
[Ref.: #122606]	Continent	Europe
[Ref.: #122606]	Isolation date	2011-07-19
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Meadow
#Environmental	#Terrestrial	#Soil
#Environmental	#Terrestrial	#Wetland (Swamp)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX784908 (>99% sequence identity) for Yersiniaceae from Microbeatlas

Aquatic Samples	1026
Soil Samples	175
Animal Samples	1056
Plant Samples	530
Total Samples	2787

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

[Ref.: #42884]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122606]	Biosafety level	1	Risk group (French classification)

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.: #42884]	Rouxiella silvae strain 213 16S ribosomal RNA gene, partial sequence	KX784908	1357	ENA	1646373 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rouxiella silvae 213	GCA_002093625	scaffold	GenBank	1646373 tax ID	*
[Ref.: #66792]	Rouxiella silvae 213	2832085192	draft	JGI IMG/M	1646373 tax ID	*

[Ref.: #43210]	GC-content	51 mol%
[Ref.: #42884]	GC-content	51 mol%	sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rouxiella silvae 213 NCBI: GCA_002093625.1
[Ref.: #69480]	flagellated	no	93.984	no
[Ref.: #69480]	gram-positive	no	97.598	yes
[Ref.: #69480]	anaerobic	no	99.181	yes
[Ref.: #69480]	halophile	no	84.206	no
[Ref.: #69480]	spore-forming	no	96.218	no
[Ref.: #69480]	glucose-util	yes	95.933	no
[Ref.: #69480]	aerobic	yes	56.281	yes
[Ref.: #69480]	thermophile	no	99.552	yes
[Ref.: #69480]	motile	no	61.634	no
[Ref.: #69480]	glucose-ferment	yes	89.352	yes

Availability in culture collections External links

[Ref.: #42884]

Culture collection no.

DSM 103735, CIP 111154

[Ref.: #96583]

SI-ID 402375

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rouxiella badensis sp. nov. and Rouxiella silvae sp. nov. isolated from peat bog soil and emendation description of the genus Rouxiella.	Le Fleche-Mateos A, Kugler JH, Hansen SH, Syldatk C, Hausmann R, Lomprez F, Vandenbogaert M, Manuguerra JC, Grimont PAD	Int J Syst Evol Microbiol	10.1099/ijsem.0.001794	2017	*

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 )

#42884

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103735

#43210

Anne Le Fleche-Mateos, Johannes H. Kügler, Silla H. Hansen, Christoph Syldatk, Rudolf Hausmann, Fabienne Lomprez, Mathias Vandenbogaert, Jean-Claude Manuguerra, Patrick A.D. Grimont: Rouxiella badensis sp. nov. and Rouxiella silvae sp. nov. Isolated from peat bog soil and emendation description of the genus Rouxiella. IJSEM 67: 1255 - 1259 2017 ( DOI 10.1099/ijsem.0.001794 , PubMed 28100296 )

#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) .

#68368

Automatically annotated from API 20E .

#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) .

#96583

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-ID402375.1 )

#122606 Collection of Institut Pasteur ; Curators of the CIP; CIP 111154
* These data were automatically processed and therefore are not curated

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