Propionispira raffinosivorans SH2 | Type strain | DSM 20765, ATCC 49691, VTT E-90406 | BacDiveID:17187

Strain identifier

BacDive ID: 17187

Type strain:

Species: Propionispira raffinosivorans

Strain Designation: SH2

Culture col. no.: DSM 20765, ATCC 49691, VTT E-90406

Strain history: <- H. Seidel, SH2

NCBI tax ID(s): 1123511 (strain), 86959 (species)

SI-ID 45236

ATCC 49691, DSM 20765, VTT E-90406

Other strains from Propionispira raffinosivorans

P. raffinosivorans OW8, DSM 7198
P. raffinosivorans RG2, DSM 7199

Section

Propionispira raffinosivorans SH2 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from pitching yeast.

Gram-negative
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	*Bacillota*
	Class	*Negativicutes*
	Order	*Selenomonadales*
	Family	*Selenomonadaceae*
	Genus	*Propionispira*
	Species	**Propionispira raffinosivorans**
	Full Scientific Name (LPSN)	Propionispira raffinosivorans (Schleifer et al. 1990) Ueki et al. 2014

Synonym

Zymophilus raffinosivorans

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.807

Incubation period

3-7 days

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

Culture medium

BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

Culture medium

MRS pre-reduced (DSMZ Medium 11b)

Culture medium growth

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #9072]			growth	28 °C

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #9072]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %98.386

[Ref.: #69481]	Ability of spore formation	no Confidence in %91
[Ref.: #69480]	Ability of spore formation	no Confidence in %93.638

[Ref.: #9072]	Murein short key	A31
[Ref.: #9072]	Murein types	A1gamma m-Dpm-direct

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]		arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #68367]		cellobiose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]		D-glucose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]		D-mannitol ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]		D-mannose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68380]		D-mannose ChEBI	+	fermentation	* from API rID32A
[Ref.: #68367]		D-xylose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]		esculin ChEBI	+	hydrolysis	* from API 20A
[Ref.: #68367]		gelatin ChEBI	-	hydrolysis	* from API 20A
[Ref.: #68367]		glycerol ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]		L-arabinose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68380]		L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #68367]		L-rhamnose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]		lactose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]		maltose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]		melezitose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68380]		nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #68367]		raffinose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68380]		raffinose ChEBI	+	fermentation	* from API rID32A
[Ref.: #68367]		salicin ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]		sorbitol ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]		sucrose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]		trehalose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]		tryptophan ChEBI	-	energy source	* from API 20A, API rID32A
[Ref.: #68367]		urea ChEBI	-	hydrolysis	* from API 20A, API rID32A
		Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68367]		indole ChEBI	no	* from API 20A, API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A, API 20A

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #68380]		alanine arylamidase	-	3.4.11.2	* from API rID32A
[Ref.: #68380]		alkaline phosphatase	-	3.1.3.1	* from API rID32A
[Ref.: #68380]		alpha-fucosidase	-	3.2.1.51	* from API rID32A
[Ref.: #68380]		alpha-galactosidase	+	3.2.1.22	* from API rID32A
[Ref.: #68380]		alpha-glucosidase	+	3.2.1.20	* from API rID32A
[Ref.: #68380]		arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #68380]		beta-galactosidase	+	3.2.1.23	* from API rID32A
[Ref.: #68380]		beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]		beta-glucosidase	+	3.2.1.21	* from API rID32A, API 20A
[Ref.: #68380]		beta-glucuronidase	-	3.2.1.31	* from API rID32A
[Ref.: #9072]		catalase	-	1.11.1.6
[Ref.: #9072]		cytochrome-c oxidase	-	1.9.3.1
[Ref.: #68367]		gelatinase	-		* from API 20A
[Ref.: #68380]		glutamate decarboxylase	-	4.1.1.15	* from API rID32A
[Ref.: #68380]		glutamyl-glutamate arylamidase	-		* from API rID32A
[Ref.: #68380]		glycin arylamidase	-		* from API rID32A
[Ref.: #68380]		histidine arylamidase	-		* from API rID32A
[Ref.: #68380]		L-arginine arylamidase	-		* from API rID32A
[Ref.: #68380]		leucine arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]		leucyl glycin arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]		phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]		proline-arylamidase	-	3.4.11.5	* from API rID32A
[Ref.: #68380]		pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32A
[Ref.: #68380]		serine arylamidase	-		* from API rID32A
[Ref.: #68380]		tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #68380]		tyrosine arylamidase	-		* from API rID32A
[Ref.: #68380]		urease	-	3.5.1.5	* from API rID32A, API 20A
		Only first 10 entries are displayed. Click here to see all.

API® 20A:

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

	API ID	Indole productionIND	Urease/urea hydrolysisURE	Acid from D-glucoseGLU	Acid from D-mannitolMAN	Acid from lactoseLAC	Acid from sucroseSAC	Acid from maltoseMAL	Acid from salicinSAL	Acid from D-xyloseXYL	Acid from L-arabinoseARA	Gelatinase/gelatin hydrolysisGEL	Esculin hydrolysis/beta-glucosidaseESC	Acid from glycerolGLY	Acid from cellobioseCEL	Acid from D-mannoseMNE	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from sorbitolSOR	Acid from L-rhamnoseRHA	Acid from trehaloseTRE	CatalaseCAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
[Ref.: #9072]	2056	-	-	+	+	+	+	+	+	+	+	-	+	+	+	+	-	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API® rID32A:

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

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #9072]	12382	-	-	+	+	-	+	+	+	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
[Ref.: #9072]	12381	-	-	+	+	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #9072]	Sample type/isolated from	pitching yeast
[Ref.: #9072]	Geographic location (country and/or sea, region)	Freising
[Ref.: #9072]	Country	Germany
[Ref.: #9072]	Country ISO 3 Code	DEU
[Ref.: #9072]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Food production	#Starter culture
#Host	#Yeast	-

What are isolation sources categories?

Global distribution of 16S sequence DQ217599 (>99% sequence identity) for Propionispira from Microbeatlas

Aquatic Samples	2518
Soil Samples	510
Animal Samples	1023
Plant Samples	35
Total Samples	4086

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

Biosafety level

1

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.: #9072]	Zymophilus raffinosivorans strain VTT E-90406 16S ribosomal RNA gene, partial sequence	DQ217599	1448	ENA	1123511 tax ID
[Ref.: #20218]	Zymophilus raffinosivorans DNA, 16S/23S rRNA intergenic spacer region	AB022068	591	ENA	1123511 tax ID	*
[Ref.: #20218]	Zymophilus raffinosivorans DNA, 16S/23S rRNA intergenic spacer region	AB022093	376	ENA	1123511 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Propionispira raffinosivorans DSM 20765	GCA_000381065	scaffold	GenBank	1123511 tax ID	*
[Ref.: #66792]	Zymophilus raffinosivorans DSM 20765	1123511.3	wgs	PATRIC	1123511 tax ID	*
[Ref.: #66792]	Propionispira raffinosivorans DSM 20765	2518645621	draft	JGI IMG/M	1123511 tax ID	*

[Ref.: #9072]	GC-content	41.0 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #9072]	GC-content	39.9 mol%	high performance liquid chromatography (HPLC)

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: Propionispira raffinosivorans DSM 20765 DSM 20765 NCBI: GCA_000381065.1
[Ref.: #69481]	spore-forming	no	91	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Propionispira raffinosivorans DSM 20765 DSM 20765 NCBI: GCA_000381065.1
[Ref.: #69480]	motile	yes	85.721	no
[Ref.: #69480]	flagellated	no	71.237	no
[Ref.: #69480]	gram-positive	no	92.485	no
[Ref.: #69480]	anaerobic	yes	96.29	no
[Ref.: #69480]	aerobic	no	94.783	no
[Ref.: #69480]	halophile	no	96.469	no
[Ref.: #69480]	spore-forming	no	65.325	no
[Ref.: #69480]	thermophile	no	95.917	yes
[Ref.: #69480]	glucose-util	yes	88.542	no
[Ref.: #69480]	glucose-ferment	no	54.768	no

Availability in culture collections External links

Culture collection no.

DSM 20765, ATCC 49691, VTT E-90406

SI-ID 45236

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description of Propionispira arcuata sp. nov., isolated from a methanogenic reactor of cattle waste, reclassification of Zymophilus raffinosivorans and Zymophilus paucivorans as Propionispira raffinosivorans comb. nov. and Propionispira paucivorans comb. nov. and emended description of the genus Propionispira.	Ueki A, Watanabe M, Ohtaki Y, Kaku N, Ueki K	Int J Syst Evol Microbiol	10.1099/ijs.0.063875-0	2014	*

References

#9072

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20765

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#68367

Automatically annotated from API 20A .

#68380

Automatically annotated from API rID32A .

#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 )

#86186

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-ID45236.1 )

* These data were automatically processed and therefore are not curated

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