Parascardovia denticolens (DSM 10105, B3028, VTT E-991434)

Name: Parascardovia denticolens (DSM 10105, B3028, VTT E-991434)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1761

Type strain

Strain Designation B3028

Culture col. no. DSM 10105 B3028 VTT E-991434 NCTC 12936 LMG 18312 6 more

NCBI tax ID(s) 864564 78258

Special Collections DSMZ CCUG JCM KCTC

Links

Parascardovia denticolens B3028 is an anaerobe, mesophilic prokaryote that was isolated from human dental caries.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 9633

LMG 17241,CCUG 35728,DSM 10105,LMG 18312,AS 1.2280,CCUG 36886,JCM 12538,NCTC 12936,CGMCC 1.2280,VTT E-991434

@ref 20215

Last LPSN update 2025-12-16 09:47:11

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Parascardovia

Species Parascardovia denticolens

Full scientific name Parascardovia denticolens (Crociani et al. 1996) Jian and Dong 2002

Synonyms (1)

Bifidobacterium denticolens

BacDive ID	Other strains from **Parascardovia denticolens** (1)	Type strain
1762	P. denticolens B3047, DSM 10106, CCUG 44927

Morphology

Cell morphology

@ref	Motility	Confidence
125438		95

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3798	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)	Range
3798	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
3798	anaerobe
125439	anaerobe	99.5

Spore formation

@ref	Spore formation	Confidence
125439		92.9

Murein

@ref	Murein short key	Type
3798	A11.32	A4alpha L-Lys(L-Orn)-D-Asp

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	12936 ChEBI	D-galactose	+	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	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	+	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	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		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	+	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	+	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	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	denitrification	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	cardiolipin biosynthesis	100	7 of 7
66794	cyanate degradation	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	aspartate and asparagine metabolism	100	9 of 9
66794	starch degradation	90	9 of 10
66794	palmitate biosynthesis	86.36	19 of 22
66794	photosynthesis	85.71	12 of 14
66794	pentose phosphate pathway	81.82	9 of 11
66794	glycogen metabolism	80	4 of 5
66794	ppGpp biosynthesis	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	metabolism of disaccharids	63.64	7 of 11
66794	phenylalanine metabolism	61.54	8 of 13
66794	NAD metabolism	61.11	11 of 18
66794	Entner Doudoroff pathway	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	purine metabolism	58.51	55 of 94
66794	oxidative phosphorylation	56.04	51 of 91
66794	serine metabolism	55.56	5 of 9
66794	d-mannose degradation	55.56	5 of 9
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	degradation of pentoses	53.57	15 of 28
66794	pyrimidine metabolism	53.33	24 of 45
66794	lipid metabolism	51.61	16 of 31
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	coenzyme A metabolism	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	vitamin B1 metabolism	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	d-xylose degradation	45.45	5 of 11
66794	degradation of hexoses	44.44	8 of 18
66794	cysteine metabolism	44.44	8 of 18
66794	tetrahydrofolate metabolism	42.86	6 of 14
66794	propanol degradation	42.86	3 of 7
66794	alanine metabolism	41.38	12 of 29
66794	cellulose degradation	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	glutamate and glutamine metabolism	39.29	11 of 28
66794	isoleucine metabolism	37.5	3 of 8
66794	arginine metabolism	37.5	9 of 24
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
66794	non-pathway related	36.84	14 of 38
66794	vitamin B6 metabolism	36.36	4 of 11
66794	glutathione metabolism	35.71	5 of 14
66794	octane oxidation	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	sphingosine metabolism	33.33	2 of 6
66794	lipid A biosynthesis	33.33	3 of 9
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of sugar alcohols	31.25	5 of 16
66794	methionine metabolism	30.77	8 of 26
66794	myo-inositol biosynthesis	30	3 of 10
66794	threonine metabolism	30	3 of 10
66794	glycine metabolism	30	3 of 10
66794	tryptophan metabolism	28.95	11 of 38
66794	citric acid cycle	28.57	4 of 14
66794	mevalonate metabolism	28.57	2 of 7
66794	ubiquinone biosynthesis	28.57	2 of 7
66794	tyrosine metabolism	28.57	4 of 14
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	flavin biosynthesis	26.67	4 of 15
66794	degradation of aromatic, nitrogen containing compounds	25	3 of 12
66794	lactate fermentation	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	histidine metabolism	24.14	7 of 29
66794	degradation of sugar acids	24	6 of 25
66794	sulfate reduction	23.08	3 of 13
66794	isoprenoid biosynthesis	23.08	6 of 26
66794	leucine metabolism	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9
66794	arachidonic acid metabolism	22.22	4 of 18
66794	valine metabolism	22.22	2 of 9
66794	lysine metabolism	21.43	9 of 42

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
3798	-	-	-	-	+	+	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	+/-	+	+	+	+	+/-	+	+	-	+	-	+	+	+	-	-	+/-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body-Site	#Oral cavity and airways	#Tooth
#Host Body-Site	#Other	#Wound

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
3798	human dental caries	Bologna	Italy	ITA	Europe
67770	Human dental caries

Taxonmaps

69479

Global distribution of 16S sequence LC383835 (>99% sequence identity) for Parascardovia denticolens subclade from Microbeatlas

Aquatic Samples	417
Soil Samples	132
Animal Samples	18923
Plant Samples	65
Total Samples	19537

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
3798	yes, in single cases	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	ASM104267v1 assembly for Parascardovia denticolens DSM 10105 = JCM 12538	complete	GCA_001042675	864564.6	2811994997	864564	98.06
66792	ASM19178v1 assembly for Parascardovia denticolens DSM 10105 = JCM 12538	chromosome	GCA_000191785	864564.3	649989980	864564	87.77
66792	Paras_denticolens_F0305 assembly for Parascardovia denticolens F0305	scaffold	GCA_000163835	641144.3	647533193	641144	73.09

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Parascardovia denticolens gene for 16S rRNA, partial sequence, strain: DSM 10105	D89331	1518		864564
67770	Parascardovia denticolens JCM 12538 gene for 16S ribosomal RNA, partial sequence	LC383835	1466		864564

GC content

@ref	GC-content (mol%)	Method
3798	55	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Parascardovia denticolens DSM 10105 = JCM 12538
NCBI: GCA_001042675

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	92.90	no
125439	motility	BacteriaNetⓘ	no	67.50	no
125439	gram_stain	BacteriaNetⓘ	positive	83.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Parascardovia denticolens DSM 10105 = JCM 12538 JCM 12538
NCBI: GCA_001042675.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	83.91	no
125438	anaerobic	anaerobicⓘ	yes	74.38	yes
125438	aerobic	aerobicⓘ	no	93.26	yes
125438	spore-forming	spore-formingⓘ	no	89.86	no
125438	thermophilic	thermophileⓘ	no	94.96	no
125438	flagellated	motile2+ⓘ	no	95.00	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
Transcriptome	Investigating the Campylobacter jejuni Transcriptional Response to Host Intestinal Extracts Reveals the Involvement of a Widely Conserved Iron Uptake System.	Liu MM, Boinett CJ, Chan ACK, Parkhill J, Murphy MEP, Gaynor EC.	mBio	10.1128/mbio.01347-18	2018
Phylogeny	Genomic encyclopedia of type strains of the genus Bifidobacterium.	Milani C, Lugli GA, Duranti S, Turroni F, Bottacini F, Mangifesta M, Sanchez B, Viappiani A, Mancabelli L, Taminiau B, Delcenserie V, Barrangou R, Margolles A, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.02308-14	2014
Cultivation	Acidogenicity of dual-species biofilms of bifidobacteria and Streptococcus mutans.	de Matos BM, Brighenti FL, Do T, Beighton D, Koga-Ito CY	Clin Oral Investig	10.1007/s00784-016-1958-1	2016
Genetics	Complete Genome Sequence of Parascardovia denticolens JCM 12538T, Isolated from Human Dental Caries.	Oshima K, Hayashi J, Toh H, Nakano A, Shindo C, Komiya K, Morita H, Honda K, Hattori M	Genome Announc	10.1128/genomeA.00485-15	2015
Phylogeny	Alloscardovia omnicolens gen. nov., sp. nov., from human clinical samples.	Huys G, Vancanneyt M, D'Haene K, Falsen E, Wauters G, Vandamme P	Int J Syst Evol Microbiol	10.1099/ijs.0.64812-0	2007
Phylogeny	Bifidobacterium inopinatum sp. nov. and Bifidobacterium denticolens sp. nov., two new species isolated from human dental caries.	Crociani F, Biavati B, Alessandrini A, Chiarini C, Scardovi V	Int J Syst Bacteriol	10.1099/00207713-46-2-564	1996

References

#3798	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 10105
#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) .
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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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Parascardovia denticolens (DSM 10105, B3028, VTT E-991434)

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

Pathway annotation

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001042675

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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