Name: Pseudoscardovia suis DPTE4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23793

Type strain:

Species: Pseudoscardovia suis

Strain Designation: DPTE4

Culture col. no.: DSM 24744, CCM 7942, KCTC 15323

Strain history: <- DSM <- J Killer, Inst. Animal Physiol and Genetics, Czech Acad Sci, Prague, DPTE4

NCBI tax ID(s): 987063 (species)

SI-ID 400360

DSM 24744

Section

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

rod-shaped
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Bifidobacteriales*
	Family	*Bifidobacteriaceae*
	Genus	*Pseudoscardovia*
	Species	**Pseudoscardovia suis**
	Full Scientific Name (LPSN)	Pseudoscardovia suis Killer et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %99.999

[Ref.: #67771]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	curved-shaped

[Ref.: #67771]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %91.014

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19240]

Culture medium

BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)

[Ref.: #19240]

Culture medium growth

[Ref.: #19240]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19240]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #19240]			growth	37 °C
[Ref.: #67771]			growth	37 °C

[Ref.: #19240]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #19240]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %98.971

[Ref.: #67771]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

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

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

[Ref.: #19240]	Sample type/isolated from	digestive tract of wild pig Sus scrofa
[Ref.: #19240]	Host species	Sus scrofa
[Ref.: #19240]	Geographic location (country and/or sea, region)	South Bohemia
[Ref.: #19240]	Country	Czech Republic
[Ref.: #19240]	Country ISO 3 Code	CZE
[Ref.: #19240]	Continent	Europe

[Ref.: #67771]	Sample type/isolated from	From digestive tract of wild pigs, `Sus scrofa`
[Ref.: #67771]	Geographic location (country and/or sea, region)	South Bohemia
[Ref.: #67771]	Country	Czech Republic
[Ref.: #67771]	Country ISO 3 Code	CZE
[Ref.: #67771]	Continent	Europe
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #19240]

Biosafety level

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.: #19240]	Pseudoscardovia suis strain DPTE4 16S ribosomal RNA gene, partial sequence	HQ842701	1360	ENA	987063 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudoscardovia suis DSM 24744	GCA_002797875	contig	GenBank	987063 tax ID	*
[Ref.: #66792]	Pseudoscardovia suis DSM 24744	GCA_002259715	contig	GenBank	987063 tax ID	*
[Ref.: #66792]	Pseudoscardovia suis strain DSM 24744	987063.3	wgs	PATRIC	987063 tax ID	*
[Ref.: #66792]	Pseudoscardovia suis strain DSM 24744	987063.4	wgs	PATRIC	987063 tax ID	*
[Ref.: #66792]	Pseudoscardovia suis DSM 24744	2731639185	draft	JGI IMG/M	987063 tax ID	*
[Ref.: #66792]	Pseudoscardovia suis DSM 24744	2802429515	draft	JGI IMG/M	987063 tax ID	*

[Ref.: #19240]

GC-content

51.8 mol%

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: Pseudoscardovia suis strain DSM 24744 PATRIC: 987063.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudoscardovia suis strain DSM 24744 PATRIC: 987063.3
[Ref.: #69480]	motile	no	91.885	yes
[Ref.: #69480]	flagellated	no	95.91	yes
[Ref.: #69480]	gram-positive	yes	91.516	yes
[Ref.: #69480]	anaerobic	yes	98.024	yes
[Ref.: #69480]	halophile	no	64.636	no
[Ref.: #69480]	spore-forming	no	95.739	yes
[Ref.: #69480]	glucose-util	yes	86.485	no
[Ref.: #69480]	aerobic	no	97.039	yes
[Ref.: #69480]	thermophile	no	95.622	yes
[Ref.: #69480]	glucose-ferment	yes	80.176	no

Availability in culture collections External links

[Ref.: #19240]

Culture collection no.

DSM 24744, CCM 7942, KCTC 15323

[Ref.: #87824]

SI-ID 400360

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#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 )

#87824

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-ID400360.1 )

* These data were automatically processed and therefore are not curated

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Pseudoscardovia suis strain DSM 24744

Pseudoscardovia suis strain DSM 24744

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