Scardovia inopinata (DSM 10107, B3109, VTT E-991435)

Name: Scardovia inopinata (DSM 10107, B3109, VTT E-991435)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1763

Type strain

Strain Designation B3109

Culture col. no. DSM 10107 B3109 VTT E-991435 NCTC 12937 LMG 18313 4 more

NCBI tax ID(s) 1150468 78259

Special Collections DSMZ CCUG JCM

History <- B. Biavati <- F. Crociani, B3109 AS 1.2187 <-- DSM 10107 <-- B. Biavati <-- F. Crociani B3109.

Links

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

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

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

@ref 20215

Last LPSN update 2026-02-09 11:18:10

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Scardovia

Species Scardovia inopinata

Full scientific name Scardovia inopinata (Crociani et al. 1996) Jian and Dong 2002

Synonyms (1)

Bifidobacterium inopinatum

BacDive ID	Other strains from **Scardovia inopinata** (1)	Type strain
1764	S. inopinata B3067, DSM 10108

Morphology

Cell morphology

@ref	Motility	Confidence
125438		95.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3800	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
3800	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

3800

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.3
125438		91.543

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	+	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	+	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	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	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	32528 ChEBI	turanose	+	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
3800	-	-	-	-	-	+	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	+	+	+	+	-	+	-	+	+	-	-	-	+	+	+	-	+	+	-	-	-	-	-	-	-	-	-

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
3800	human dental caries	Bologna	Italy	ITA	Europe
67770	Human dental caries

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
3800	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	ASM104269v1 assembly for Scardovia inopinata JCM 12537	complete	GCA_001042695	1150468.4		1150468	94.66
66792	53618_F01 assembly for Scardovia inopinata NCTC12937	contig	GCA_900445765	78258.9	2811995288	78259	74.68
66792	ASM16375v1 assembly for Scardovia inopinata F0304	scaffold	GCA_000163755	641146.3	647533207	641146	73.03

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Bifidobacterium inopinatum gene for 16S rRNA	AB029087	1557	1150468
3800	Scardovia inopinata gene for 16S rRNA, partial sequence, strain: DSM 10107	D89332	1532	1150468
67770	Scardovia inopinata JCM 12537 gene for 16S ribosomal RNA, partial sequence	LC383834	1480	1150468

GC content

@ref	GC-content (mol%)	Method
3800	54	high performance liquid chromatography (HPLC)
3800	45	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: Scardovia inopinata JCM 12537
PATRIC: 1150468.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	80.30	no
125439	gram_stain	BacteriaNetⓘ	positive	59.50	no
125439	motility	BacteriaNetⓘ	no	86.90	no
125439	spore_formation	BacteriaNetⓘ	no	98.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Scardovia inopinata JCM 12537 JCM 12537
NCBI: GCA_001042695.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	83.28	no
125438	anaerobic	anaerobicⓘ	yes	69.42	no
125438	aerobic	aerobicⓘ	no	94.12	yes
125438	spore-forming	spore-formingⓘ	no	91.54	no
125438	thermophilic	thermophileⓘ	no	95.98	yes
125438	flagellated	motile2+ⓘ	no	95.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Exploring the biodiversity of Bifidobacterium asteroides among honey bee microbiomes.	Lugli GA, Fontana F, Tarracchini C, Mancabelli L, Milani C, Turroni F, Ventura M.	Environ Microbiol	10.1111/1462-2920.16223	2022
Enzymology	Selective Isolation of Bifidobacterium From Human Faeces Using Pangenomics, Metagenomics, and Enzymology.	Yang S, Xie X, Ma J, He X, Li Y, Du M, Li L, Yang L, Wu Q, Chen W, Zhang J.	Front Microbiol	10.3389/fmicb.2021.649698	2021
Genetics	Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches.	Lugli GA, Milani C, Duranti S, Alessandri G, Turroni F, Mancabelli L, Tatoni D, Ossiprandi MC, van Sinderen D, Ventura M.	Genome Biol	10.1186/s13059-019-1711-6	2019
Genetics	Tracking the Taxonomy of the Genus Bifidobacterium Based on a Phylogenomic Approach.	Lugli GA, Milani C, Duranti S, Mancabelli L, Mangifesta M, Turroni F, Viappiani A, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.02249-17	2018
	Genetic insights into the dark matter of the mammalian gut microbiota through targeted genome reconstruction.	Lugli GA, Alessandri G, Milani C, Viappiani A, Fontana F, Tarracchini C, Mancabelli L, Argentini C, Ruiz L, Margolles A, van Sinderen D, Turroni F, Ventura M.	Environ Microbiol	10.1111/1462-2920.15559	2021
Transcriptome	Gene expression of bacterial collagenolytic proteases in root caries.	Dame-Teixeira N, Parolo CCF, Maltz M, Rup AG, Devine DA, Do T.	J Oral Microbiol	10.1080/20002297.2018.1424475	2018
	Associations between stool micro-transcriptome, gut microbiota, and infant growth.	Carney MC, Zhan X, Rangnekar A, Chroneos MZ, Craig SJC, Makova KD, Paul IM, Hicks SD.	J Dev Orig Health Dis	10.1017/s2040174420001324	2021
Genetics	Assessing the Genomic Variability of Gardnerella vaginalis through Comparative Genomic Analyses: Evolutionary and Ecological Implications.	Tarracchini C, Lugli GA, Mancabelli L, Milani C, Turroni F, Ventura M.	Appl Environ Microbiol	10.1128/aem.02188-20	2020
	The genus bifidobacterium: From genomics to functionality of an important component of the mammalian gut microbiota running title: Bifidobacterial adaptation to and interaction with the host.	Alessandri G, van Sinderen D, Ventura M.	Comput Struct Biotechnol J	10.1016/j.csbj.2021.03.006	2021
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
	Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae.	Estrada-de Los Santos P, Palmer M, Chavez-Ramirez B, Beukes C, Steenkamp ET, Briscoe L, Khan N, Maluk M, Lafos M, Humm E, Arrabit M, Crook M, Gross E, Simon MF, Dos Reis Junior FB, Whitman WB, Shapiro N, Poole PS, Hirsch AM, Venter SN, James EK.	Genes (Basel)	10.3390/genes9080389	2018
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 .
#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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Scardovia inopinata (DSM 10107, B3109, VTT E-991435)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001042695

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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