Propionispira raffinosivorans (DSM 20765, ATCC 49691, VTT E-90406)

Name: Propionispira raffinosivorans (DSM 20765, ATCC 49691, VTT E-90406)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17187

Type strain

Strain Designation SH2

Culture col. no. DSM 20765 ATCC 49691 VTT E-90406 SH2

NCBI tax ID(s) 1123511 86959

Special Collections DSMZ

History <- H. Seidel, SH2

Links

Propionispira raffinosivorans SH2 is an anaerobe bacterium that was isolated from pitching yeast.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 45236

ATCC 49691,DSM 20765,VTT E-90406

@ref 20215

Last LPSN update 2026-02-09 11:22:09

Domain Bacteria

Phylum Bacillota

Class Negativicutes

Order Selenomonadales

Family Selenomonadaceae

Genus Propionispira

Species Propionispira raffinosivorans

Full scientific name Propionispira raffinosivorans (Schleifer et al. 1990) Ueki et al. 2014

Synonyms (1)

Zymophilus raffinosivorans

BacDive ID	Other strains from **Propionispira raffinosivorans** (2)	Type strain
17185	P. raffinosivorans OW8, DSM 7198
17186	P. raffinosivorans RG2, DSM 7199

Morphology

Colony morphology

9072

Incubation period3-7 days

Multimedia

@ref:	66793
multimedia content:	EM_DSM_20765_1.jpg
multimedia.multimedia content:	EM_DSM_20765_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_20765_2.jpg
multimedia.multimedia content:	EM_DSM_20765_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_20765_3.jpg
multimedia.multimedia content:	EM_DSM_20765_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_20765_4.jpg
multimedia.multimedia content:	EM_DSM_20765_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_20765_5.jpg
multimedia.multimedia content:	EM_DSM_20765_5.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
9072	FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)	Medium recipe at MediaDive	Name: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water
9072	BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)	Medium recipe at MediaDive	Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water
9072	MRS pre-reduced (DSMZ Medium 11b)	Medium recipe at MediaDive	Name: MRS pre-reduced (DSMZ Medium 11b) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Resazurin 0.001 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
9072	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
9072	anaerobe
125439	anaerobe	91.5

Murein

@ref	Murein short key	Type
9072	A31	A1gamma m-Dpm-direct

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68367	17057 ChEBI	cellobiose	+	builds acid from	from API 20A
68367	17634 ChEBI	D-glucose	+	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	+	builds acid from	from API 20A
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
68367	16024 ChEBI	D-mannose	+	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	+	builds acid from	from API 20A
68367	4853 ChEBI	esculin	+	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
68367	17754 ChEBI	glycerol	+	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	+	builds acid from	from API 20A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68367	62345 ChEBI	L-rhamnose	+	builds acid from	from API 20A
68367	17716 ChEBI	lactose	+	builds acid from	from API 20A
68367	17306 ChEBI	maltose	+	builds acid from	from API 20A
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	+	fermentation	from API rID32A
68367	16634 ChEBI	raffinose	+	builds acid from	from API 20A
68367	17814 ChEBI	salicin	+	builds acid from	from API 20A
68367	30911 ChEBI	sorbitol	+	builds acid from	from API 20A
68367	17992 ChEBI	sucrose	+	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	-	builds acid from	from API 20A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A
68367	35581 ChEBI	indole		from API 20A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A
68367	35581 ChEBI	indole	-	from API 20A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	+	3.2.1.21	from API rID32A
68367	beta-glucosidase	+	3.2.1.21	from API 20A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
9072	catalase	-	1.11.1.6
9072	cytochrome-c oxidase	-	1.9.3.1
68367	gelatinase	-		from API 20A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A
68367	urease	-	3.5.1.5	from API 20A

API 20A

@ref	IND	URE	GLU	MAN	LAC	SAC	MAL	SAL	XYL	ARA	GEL	ESC	GLY	CEL	MNE	MLZ	RAF	SOR	RHA	TRE	CAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
9072	-	-	+	+	+	+	+	+	+	+	-	+	+	+	+	-	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
9072	-	-	+	+	-	+	+	+	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
9072	-	-	+	+	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Starter culture
#Host	#Yeast	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
9072	pitching yeast	Freising	Germany	DEU	Europe

Taxonmaps

69479

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
9072	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM38106v1 assembly for Propionispira raffinosivorans DSM 20765	scaffold	GCA_000381065	1123511.3	2518645621	1123511	62.6

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Zymophilus raffinosivorans DNA, 16S/23S rRNA intergenic spacer region	AB022068	591	1123511
20218	Zymophilus raffinosivorans DNA, 16S/23S rRNA intergenic spacer region	AB022093	376	1123511
9072	Zymophilus raffinosivorans strain VTT E-90406 16S ribosomal RNA gene, partial sequence	DQ217599	1448	1123511

GC content

@ref	GC-content (mol%)	Method
9072	41.0	thermal denaturation, midpoint method (Tm)
9072	39.9	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Propionispira raffinosivorans DSM 20765
NCBI: GCA_000381065

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	61.70	no
125439	motility	BacteriaNetⓘ	no	62.50	no
125439	gram_stain	BacteriaNetⓘ	positive	88.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	91.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Propionispira raffinosivorans DSM 20765 DSM 20765
NCBI: GCA_000381065.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	83.42	no
125438	anaerobic	anaerobicⓘ	yes	78.93	yes
125438	aerobic	aerobicⓘ	no	88.91	yes
125438	spore-forming	spore-formingⓘ	no	56.49	no
125438	thermophilic	thermophileⓘ	no	87.89	no
125438	flagellated	motile2+ⓘ	yes	72.94	no

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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Propionispira raffinosivorans (DSM 20765, ATCC 49691, VTT E-90406)

Name and taxonomic classification

Morphology

Colony morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Murein

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20A

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000381065

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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