Name: Scardovia inopinata B3109
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1763

Type strain:

Species: Scardovia inopinata

Strain Designation: B3109

Culture col. no.: DSM 10107, JCM 12537, CCUG 35729, CGMCC 1.2187, LMG 17242, LMG 18313, NCTC 12937, VTT E-991435

Strain history: AS 1.2187 <-- DSM 10107 <-- B. Biavati <-- F. Crociani B3109.

NCBI tax ID(s): 1150468 (strain), 78259 (species)

SI-ID 9642

LMG 17242, CCUG 35729, DSM 10107, LMG 18313, AS 1.2187, JCM 12537, NCTC 12937, CGMCC 1.2187, VTT E-991435, CCUG 36887

Other strains from Scardovia inopinata

S. inopinata B3067, DSM 10108

Section

Scardovia inopinata B3109 is an anaerobe, mesophilic human pathogen that was isolated from human dental caries.

anaerobe
human pathogen
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	*Scardovia*
	Species	**Scardovia inopinata**
	Full Scientific Name (LPSN)	Scardovia inopinata (Crociani et al. 1996) Jian and Dong 2002

Synonym

Bifidobacterium inopinatum

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %99.719

[Ref.: #69480]	Motility	no Confidence in %91.044

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3800]

Culture medium

BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)

[Ref.: #3800]

Culture medium growth

[Ref.: #3800]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3800]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #3800]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #3800]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #3800]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %98.65

[Ref.: #69481]	Ability of spore formation	no Confidence in %91
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #3800]	14272	-	-	-	-	-	+	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	+	+	+	+	-	+	-	+	+	-	-	-	+	+	+	-	+	+	-	-	-	-	-	-	-	-	-

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

[Ref.: #3800]	Sample type/isolated from	human dental caries
[Ref.: #3800]	Geographic location (country and/or sea, region)	Bologna
[Ref.: #3800]	Country	Italy
[Ref.: #3800]	Country ISO 3 Code	ITA
[Ref.: #3800]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Human dental caries
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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

[Ref.: #3800]	Pathogenicity (human)	yes, in single cases
[Ref.: #3800]	Biosafety level	1	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.: #3800]	Scardovia inopinata gene for 16S rRNA, partial sequence, strain: DSM 10107	D89332	1532	ENA	1150468 tax ID
[Ref.: #67770]	Scardovia inopinata JCM 12537 gene for 16S ribosomal RNA, partial sequence	LC383834	1480	ENA	1150468 tax ID
[Ref.: #20218]	Bifidobacterium inopinatum gene for 16S rRNA	AB029087	1557	ENA	1150468 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]	Scardovia inopinata JCM 12537	GCA_001042695	complete	GenBank	1150468 tax ID	*
[Ref.: #66792]	Scardovia inopinata NCTC12937	GCA_900445765	contig	GenBank	78259 tax ID	*
[Ref.: #66792]	Parascardovia denticolens strain NCTC12937	78258.9	wgs	PATRIC	78258 tax ID	*
[Ref.: #66792]	Scardovia inopinata F0304	641146.3	wgs	PATRIC	641146 tax ID	*
[Ref.: #66792]	Scardovia inopinata JCM 12537	1150468.4	complete	PATRIC	1150468 tax ID	*
[Ref.: #66792]	Parascardovia denticolens NCTC 12937	2811995288	draft	JGI IMG/M	78258 tax ID	*

[Ref.: #3800]	GC-content	54 mol%	high performance liquid chromatography (HPLC)
[Ref.: #3800]	GC-content	45 mol%	thermal denaturation, midpoint method (Tm)

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: Scardovia inopinata JCM 12537 JCM 12537 NCBI: GCA_001042695.1
[Ref.: #69481]	spore-forming	no	91	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Scardovia inopinata JCM 12537 JCM 12537 NCBI: GCA_001042695.1
[Ref.: #69480]	motile	no	95.968	no
[Ref.: #69480]	flagellated	no	97.329	no
[Ref.: #69480]	gram-positive	yes	89.363	no
[Ref.: #69480]	anaerobic	yes	94.704	no
[Ref.: #69480]	aerobic	no	98.208	no
[Ref.: #69480]	halophile	no	61.433	no
[Ref.: #69480]	spore-forming	no	96.228	no
[Ref.: #69480]	thermophile	no	92.765	no
[Ref.: #69480]	glucose-util	yes	84.295	no
[Ref.: #69480]	glucose-ferment	yes	82.261	no

Availability in culture collections External links

[Ref.: #3800]

Culture collection no.

DSM 10107, JCM 12537, CCUG 35729, CGMCC 1.2187, LMG 17242, LMG 18313, NCTC 12937, VTT E-991435

[Ref.: #71410]

SI-ID 9642

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 Scardovia inopinata JCM 12537T, Isolated from Human Dental Caries.	Oshima K, Hayashi J, Toh H, Nakano A, Omori E, Hattori Y, Morita H, Honda K, Hattori M	Genome Announc	10.1128/genomeA.00481-15	2015	*
Phylogeny	Scardovia wiggsiae sp. nov., isolated from the human oral cavity and clinical material, and emended descriptions of the genus Scardovia and Scardovia inopinata.	Downes J, Mantzourani M, Beighton D, Hooper S, Wilson MJ, Nicholson A, Wade WG	Int J Syst Evol Microbiol	10.1099/ijs.0.019752-0	2010	*
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

#3800

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 10107

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68371

Automatically annotated from API 50CH acid .

#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 )

#71410

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-ID9642.1 )

* These data were automatically processed and therefore are not curated

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Scardovia inopinata JCM 12537 JCM 12537

Scardovia inopinata JCM 12537 JCM 12537

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