Pseudoscardovia radai (DSM 24742, CCM 7943, DPVI-TET3)

Name: Pseudoscardovia radai (DSM 24742, CCM 7943, DPVI-TET3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130216

Type strain

Strain Designation DPVI-TET3

Culture col. no. DSM 24742 CCM 7943 DPVI-TET3

NCBI tax ID(s) 987066

Special Collections DSMZ

History DSMZ <- J. Killer, Inst. Animal Physiol. and Genetics, Czech Acad. Sci., Prague; DPVI-TET3

Links

Pseudoscardovia radai DPVI-TET3 is an anaerobe bacterium that was isolated from digestive tract of a wild pig Sus scrofa scrofa.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 406237

DSM 24742

@ref 20215

Last LPSN update 2026-05-29 08:37:19

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Pseudoscardovia

Species Pseudoscardovia radai

Full scientific name Pseudoscardovia radai Killer et al. 2014

Morphology

Cell morphology

@ref	Confidence	Gram stain
125438	93.5
125439	92.017
125439	96.497	positive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22094	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

Culture temp

@ref	Growth	Type	Temperature (°C)
22094	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
22094	anaerobe
125439	facultative anaerobe	91.633

Spore formation

@ref	Spore formation	Confidence
125438		91.266

Murein

@ref	Murein short key	Type
22094	A21.12	A4ß L-Orn-D-Ser-D-Glu

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
22094	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	+/-	+	+/-	-	-	+/-	+	+	-	-	-	-	-	-	-	-	-	-	-	-
22094	-	-	-	-	-	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	+	-	-	+	+	+	-	+	-	+	+	-	-	-	+	+	+	-	-	+	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Suidae (Pig,Swine)
#Host Body-Site	#Gastrointestinal tract	-

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
22094	digestive tract of a wild pig Sus scrofa scrofa	Sus scrofa scrofa	Central Bohemia, Brzina	Czech Republic	CZE	Europe

Taxonmaps

69479

Global distribution of 16S sequence HQ842704 (>99% sequence identity) for Pseudoscardovia radai subclade from Microbeatlas

Aquatic Samples	18
Soil Samples	53
Animal Samples	2431
Plant Samples	16
Total Samples	2518

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22094	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM225960v1 assembly for Pseudoscardovia radai DSM 24742	contig	GCA_002259605	987066.3	2788500239	987066	68.16

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22094	Pseudoscardovia radai strain DPVI-TET3 16S ribosomal RNA gene, partial sequence	HQ842704	1395		987066
124043	Pseudoscardovia suis strain DPTE5 16S-23S ribosomal RNA intergenic spacer, partial sequence.	JQ363653	470		987066

GC content

@ref	GC-content (mol%)	Method
22094	53.4	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: ASM225960v1 assembly for Pseudoscardovia radai DSM 24742
NCBI: GCA_002259605

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	91.63	no
125439	gram_stain	BacteriaNetⓘ	positive	96.50	no
125439	motility	BacteriaNetⓘ	no	92.02	no
125439	spore_formation	BacteriaNetⓘ	no	83.87	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudoscardovia radai strain DSM 24742
PATRIC: 987066.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.44	no
125438	anaerobic	anaerobicⓘ	yes	84.80	yes
125438	aerobic	aerobicⓘ	no	90.33	no
125438	spore-forming	spore-formingⓘ	no	91.27	no
125438	thermophilic	thermophileⓘ	no	93.99	yes
125438	flagellated	motile2+ⓘ	no	93.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family.	Lugli GA, Milani C, Turroni F, Duranti S, Mancabelli L, Mangifesta M, Ferrario C, Modesto M, Mattarelli P, Jiri K, van Sinderen D, Ventura M.	BMC Genomics	10.1186/s12864-017-3955-4	2017
Phylogeny	Pseudoscardovia radai sp. nov., another representative of a new genus within the family Bifidobacteriaceae isolated from the digestive tract of a wild pig ( Sus scrofa scrofa ).	Killer J, Havlik J, Bunesova V, Vlkova E, Benada O	Int J Syst Evol Microbiol	10.1099/ijs.0.063230-0	2014

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 )
#22094	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24742
#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) .
#68371	Automatically annotated from API 50CH acid .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

Content

About us

Pseudoscardovia radai (DSM 24742, CCM 7943, DPVI-TET3)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Murein

Metabolite utilization

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002259605

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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