Pseudoscardovia suis (DSM 24744, CCM 7942, KCTC 15323)

Name: Pseudoscardovia suis (DSM 24744, CCM 7942, KCTC 15323)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23793

Type strain

Strain Designation DPTE4

Culture col. no. DSM 24744 CCM 7942 KCTC 15323 DPTE4

NCBI tax ID(s) 987063

Special Collections DSMZ KCTC

History DSMZ <- J. Killer, Inst. Animal Physiol. and Genetics, Czech Acad. Sci., Prague; DPTE4 KCTC <- DSM <- J Killer, Inst. Animal Physiol and Genetics, Czech Acad Sci, Prague, DPTE4

Links

Pseudoscardovia suis DPTE4 is an anaerobe, rod-shaped bacterium that was isolated from digestive tract of wild pig Sus scrofa.

rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 400360

KCTC 15323,DSM 24744

@ref 20215

Last LPSN update 2026-05-29 08:30:30

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Pseudoscardovia

Species Pseudoscardovia suis

Full scientific name Pseudoscardovia suis Killer et al. 2014

Morphology

Cell morphology

@ref	Cell shape	Gram stain	Confidence
67771	rod-shaped
67771	curved-shaped
67771		positive
125439			96.307
125439		positive	96.47
125438			93.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19240	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)
19240	positive	growth	37
67771	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
19240	anaerobe
67771	anaerobe
125439	facultative anaerobe	93.058

Spore formation

@ref	Spore formation	Confidence
67771
125439		99.334
125438		91.79

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	peptidoglycan biosynthesis	93.33	14 of 15
66794	starch degradation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	photosynthesis	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	pentose phosphate pathway	81.82	9 of 11
66794	glycogen metabolism	80	4 of 5
66794	lipoate biosynthesis	80	4 of 5
66794	serine metabolism	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	palmitate biosynthesis	77.27	17 of 22
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	phenylalanine metabolism	69.23	9 of 13
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	pyrimidine metabolism	60	27 of 45
66794	glycolysis	58.82	10 of 17
66794	methionine metabolism	57.69	15 of 26
66794	purine metabolism	57.45	54 of 94
66794	propanol degradation	57.14	4 of 7
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	d-mannose degradation	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	d-xylose degradation	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	oxidative phosphorylation	53.85	49 of 91
66794	cysteine metabolism	50	9 of 18
66794	glycogen biosynthesis	50	2 of 4
66794	degradation of sugar alcohols	50	8 of 16
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	coenzyme A metabolism	50	2 of 4
66794	citric acid cycle	50	7 of 14
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	tryptophan metabolism	47.37	18 of 38
66794	flavin biosynthesis	46.67	7 of 15
66794	arginine metabolism	45.83	11 of 24
66794	vitamin B6 metabolism	45.45	5 of 11
66794	metabolism of disaccharids	45.45	5 of 11
66794	proline metabolism	45.45	5 of 11
66794	alanine metabolism	44.83	13 of 29
66794	non-pathway related	44.74	17 of 38
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	lysine metabolism	42.86	18 of 42
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	glycine metabolism	40	4 of 10
66794	Entner Doudoroff pathway	40	4 of 10
66794	lipid metabolism	38.71	12 of 31
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	ketogluconate metabolism	37.5	3 of 8
66794	tyrosine metabolism	35.71	5 of 14
66794	glutathione metabolism	35.71	5 of 14
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	urea cycle	30.77	4 of 13
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	propionate fermentation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of pentoses	28.57	8 of 28
66794	degradation of hexoses	27.78	5 of 18
66794	ascorbate metabolism	27.27	6 of 22
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	CMP-KDO biosynthesis	25	1 of 4
66794	sulfate reduction	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9

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
19240	digestive tract of wild pig Sus scrofa	Sus scrofa	South Bohemia	Czech Republic	CZE	Europe
67771	From digestive tract of wild pigs, `Sus scrofa`		South Bohemia	Czech Republic	CZE	Europe

Taxonmaps

69479

Global distribution of 16S sequence HQ842701 (>99% sequence identity) for Pseudoscardovia suis subclade from Microbeatlas

Aquatic Samples	128
Soil Samples	233
Animal Samples	8688
Plant Samples	91
Total Samples	9140

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19240	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	ASM279787v1 assembly for Pseudoscardovia suis DSM 24744	contig	GCA_002797875	987063.4	2731639185	987063	70.58
66792	ASM225971v1 assembly for Pseudoscardovia suis DSM 24744	contig	GCA_002259715	987063.3	2802429515	987063	69.34

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19240	Pseudoscardovia suis strain DPTE4 16S ribosomal RNA gene, partial sequence	HQ842701	1360		987063
124043	Pseudoscardovia suis strain DPTE4 16S-23S ribosomal RNA intergenic spacer, partial sequence.	JQ363651	470		987063

GC content

19240

GC-content (mol%)51.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM279787v1 assembly for Pseudoscardovia suis DSM 24744
BV-BRC: 987063.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	93.06	no
125439	motility	BacteriaNetⓘ	no	96.31	no
125439	gram_stain	BacteriaNetⓘ	positive	96.47	no
125439	spore_formation	BacteriaNetⓘ	no	99.33	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudoscardovia suis strain DSM 24744
PATRIC: 987063.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	86.66	no
125438	anaerobic	anaerobicⓘ	yes	86.73	yes
125438	aerobic	aerobicⓘ	no	91.43	no
125438	spore-forming	spore-formingⓘ	no	91.79	no
125438	thermophilic	thermophileⓘ	no	93.00	yes
125438	flagellated	motile2+ⓘ	no	93.50	yes

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 suis gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of wild pigs (Sus scrofa).	Killer J, Mrazek J, Bunesova V, Havlik J, Koppova I, Benada O, Rada V, Kopecny J, Vlkova E	Syst Appl Microbiol	10.1016/j.syapm.2012.09.001	2012
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

#19240	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24744
#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 )
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 )

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Pseudoscardovia suis (DSM 24744, CCM 7942, KCTC 15323)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002797875

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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