Bifidobacterium apri (DSM 100238, CCM 8605, LMG 28779)

Name: Bifidobacterium apri (DSM 100238, CCM 8605, LMG 28779)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140310

Type strain

Strain Designation RP115

Culture col. no. DSM 100238 CCM 8605 LMG 28779 RP115

NCBI tax ID(s) 1769423

Special Collections DSMZ Literature strains

History DSMZ <- J. Killer, Inst. Animal Physiol. and Genetics, Czech Acad. Sci., Prague; RP115 <- R. Pechar

Links

Bifidobacterium apri RP115 is an anaerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from large intestine contents of a wild boar .

Gram-positive rod-shaped colony-forming anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 405771

LMG 28779,DSM 100238

@ref 20215

Last LPSN update 2026-05-29 08:39:41

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Bifidobacterium

Species Bifidobacterium apri

Full scientific name Bifidobacterium apri Pechar et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
43284	positive	1.5-6.0 µm	0.3-0.8 µm	rod-shaped
125438					93
125439					90.104

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43284	1.4-2.8 mm	creamy white	circular	3 days	TPY agar

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
43284	TPY agar
42917	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)
42917	positive	growth	37
43284	positive	optimum	37
43284	positive	growth	10-49

Culture pH

@ref	Ability	Type	PH	PH range
43284	positive	optimum	6.5
43284	positive	growth	3.5-7.5	acidophile

Physiology and metabolism

Oxygen tolerance

43284

Oxygen toleranceanaerobe

Spore formation

@ref	Type of spore	Spore formation	Confidence
43284	spore
125439			97.299

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43284	27613 ChEBI	amygdalin	+	builds acid from
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
43284	18305 ChEBI	arbutin	+	fermentation
43284	18305 ChEBI	arbutin	+	builds acid from
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
43284	17057 ChEBI	cellobiose	-	builds acid from
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
43284	17108 ChEBI	D-arabinose	-	builds acid from
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
43284	18333 ChEBI	D-arabitol	-	builds acid from
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
43284	15824 ChEBI	D-fructose	+	fermentation
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
43284	28847 ChEBI	D-fucose	-	builds acid from
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
43284		D-galactose	+	fermentation
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
43284	17634 ChEBI	D-glucose	+	fermentation
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
43284	62318 ChEBI	D-lyxose	-	builds acid from
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
43284	16899 ChEBI	D-mannitol	-	builds acid from
43284	16899 ChEBI	D-mannitol	-	fermentation
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
43284	16024 ChEBI	D-mannose	-	builds acid from
43284	16024 ChEBI	D-mannose	-	fermentation
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
43284	16988 ChEBI	D-ribose	-	builds acid from
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
43284	17924 ChEBI	D-sorbitol	-	builds acid from
43284	17924 ChEBI	D-sorbitol	-	fermentation
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
43284	16443 ChEBI	D-tagatose	-	builds acid from
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
43284	65327 ChEBI	D-xylose	-	builds acid from
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
43284	17113 ChEBI	erythritol	-	builds acid from
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
43284	4853 ChEBI	esculin	+	fermentation
43284	4853 ChEBI	esculin	+	builds acid from
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
43284	16813 ChEBI	galactitol	-	builds acid from
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
43284	28066 ChEBI	gentiobiose	-	builds acid from
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
43284	17754 ChEBI	glycerol	-	builds acid from
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
43284	28087 ChEBI	glycogen	+	fermentation
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
43284	15443 ChEBI	inulin	-	builds acid from
43284	15443 ChEBI	inulin	-	fermentation
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
43284	30849 ChEBI	L-arabinose	-	builds acid from
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
43284	18403 ChEBI	L-arabitol	-	builds acid from
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
43284	18287 ChEBI	L-fucose	-	builds acid from
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
43284	62345 ChEBI	L-rhamnose	-	builds acid from
43284	62345 ChEBI	L-rhamnose	-	fermentation
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
43284	17266 ChEBI	L-sorbose	-	builds acid from
43284	17266 ChEBI	L-sorbose	-	fermentation
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
43284	65328 ChEBI	L-xylose	-	builds acid from
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
43284	17716 ChEBI	lactose	+/-	builds acid from
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
43284	17306 ChEBI	maltose	+	fermentation
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
43284	6731 ChEBI	melezitose	+	builds acid from
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
43284	28053 ChEBI	melibiose	+	fermentation
68371	28053 ChEBI	melibiose	+	builds acid from	from API 50CH acid
43284	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from	from API 50CH acid
43284	43943 ChEBI	methyl alpha-D-mannoside	+	builds acid from
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
43284	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
43284	17268 ChEBI	myo-inositol	-	builds acid from
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
43284	506227 ChEBI	N-acetylglucosamine	-	builds acid from
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
43284	17632 ChEBI	nitrate	-	reduction
43284		potassium 2-dehydro-D-gluconate	-	builds acid from
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
43284		potassium 5-dehydro-D-gluconate	-	builds acid from
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
43284	32032 ChEBI	potassium gluconate	-	builds acid from
43284	16634 ChEBI	raffinose	+	fermentation
68371	16634 ChEBI	raffinose	+	builds acid from	from API 50CH acid
43284	15963 ChEBI	ribitol	-	builds acid from
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
43284	17814 ChEBI	salicin	+	fermentation
43284	17814 ChEBI	salicin	+	builds acid from
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
43284	28017 ChEBI	starch	+	fermentation
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
43284	17992 ChEBI	sucrose	+	fermentation
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
43284	27082 ChEBI	trehalose	+	builds acid from
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
43284	32528 ChEBI	turanose	+	fermentation
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid
43284	17151 ChEBI	xylitol	-	builds acid from
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43284	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43284	6-phospho-beta-galactosidase	-	3.2.1.85
43284	acid phosphatase	+	3.1.3.2
43284	alanine arylamidase	+	3.4.11.2
43284	alkaline phosphatase	-	3.1.3.1
43284	alpha-arabinosidase	-	3.2.1.55
43284	alpha-chymotrypsin	-	3.4.21.1
43284	alpha-fucosidase	-	3.2.1.51
43284	alpha-galactosidase	+	3.2.1.22
43284	alpha-mannosidase	-	3.2.1.24
43284	arginine arylamidase	+
43284	arginine dihydrolase	-	3.5.3.6
43284	beta-galactosidase	+	3.2.1.23
43284	beta-glucosidase	+	3.2.1.21
43284	beta-glucuronidase	-	3.2.1.31
43284	catalase	-	1.11.1.6
43284	cystine arylamidase	-	3.4.11.3
43284	cytochrome oxidase	-	1.9.3.1
43284	esterase (C 4)	+
43284	esterase Lipase (C 8)	-
43284	fructose-6-phosphate phosphoketolase	+	4.1.2.22
43284	glutamate decarboxylase	+	4.1.1.15
43284	glutamyl-glutamate arylamidase	-
43284	glycin arylamidase	+
43284	histidine arylamidase	-
43284	leucine arylamidase	+	3.4.11.1
43284	leucyl glycin arylamidase	+	3.4.11.1
43284	lipase (C 14)	-
43284	N-acetyl-beta-glucosaminidase	-	3.2.1.52
43284	naphthol-AS-BI-phosphohydrolase	+
43284	phenylalanine arylamidase	-
43284	proline-arylamidase	+	3.4.11.5
43284	pyroglutamic acid arylamidase	-
43284	serine arylamidase	+
43284	trypsin	-	3.4.21.4
43284	tyrosine arylamidase	+
43284	urease	-	3.5.1.5
43284	valine arylamidase	+/-

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
42917	-	-	-	-	-	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	+	-	-	+	+	+	-	+	-	+	+	-	-	-	+	+	+	-	-	+	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Suidae (Pig,Swine)
#Host Body-Site	#Gastrointestinal tract	#Large intestine

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
42917	large intestine contents of a wild boar (Sus scrofa scrofa)	Sus scrofa scrofa	Central Bohemia, Prague-Divoká Šárka	Czech Republic	CZE	Europe
43284	Fresh samples of intestinal contents of three wild pigs		Prague-Divok a Sárka, Czech Republic	Czech Republic	CZE	Europe

Taxonmaps

69479

Global distribution of 16S sequence KT343145 (>99% sequence identity) for Bifidobacterium apri subclade from Microbeatlas

Aquatic Samples	194
Soil Samples	121
Animal Samples	14593
Plant Samples	83
Total Samples	14991

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42917	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM929948v1 assembly for Bifidobacterium apri DSM 100238	contig	GCA_009299485	1769423.3	2996697445	1769423	70.1
124043	ASM4243255v1 assembly for Bifidobacterium apri CCM 8605	scaffold	GCA_042432555			1769423	56.56

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
43284	Bifidobacterium apri strain RP115 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequence	KT343137	440		1769423
42917	Bifidobacterium apri strain RP115 16S ribosomal RNA gene, partial sequence	KT343145	1396		1769423

GC content

@ref	GC-content (mol%)	Method
42917	59.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM929948v1 assembly for Bifidobacterium apri DSM 100238
NCBI: GCA_009299485

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	81.12	no
125439	motility	BacteriaNetⓘ	no	90.10	no
125439	gram_stain	BacteriaNetⓘ	positive	81.29	no
125439	spore_formation	BacteriaNetⓘ	no	97.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bifidobacterium apri strain DSM 100238
PATRIC: 1769423.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.72	yes
125438	anaerobic	anaerobicⓘ	yes	82.18	yes
125438	spore-forming	spore-formingⓘ	no	89.77	yes
125438	thermophilic	thermophileⓘ	no	91.97	yes
125438	aerobic	aerobicⓘ	no	93.99	no
125438	flagellated	motile2+ⓘ	no	93.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Probiotic bacteria of wild boar origin intended for piglets - An in vitro study.	Kostovova I, Kavanova K, Moravkova M, Gebauer J, Leva L, Vicenova M, Babak V, Faldyna M, Crhanova M.	Vet Med (Praha)	10.17221/35/2024-vetmed	2024
	Expanding the biosynthesis spectrum of hydroxy fatty acids: unleashing the potential of novel bacterial fatty acid hydratases.	Heng YC, Wong GWJ, Kittelmann S.	Biotechnol Biofuels Bioprod	10.1186/s13068-024-02578-2	2024
Phylogeny	Bifidobacterium apri sp. nov., a thermophilic actinobacterium isolated from the digestive tract of wild pigs (Sus scrofa).	Pechar R, Killer J, Salmonova H, Geigerova M, Svejstil R, Svec P, Sedlacek I, Rada V, Benada O	Int J Syst Evol Microbiol	10.1099/ijsem.0.001956	2017

References

#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 )
#42917	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100238
#43284	R. Pechar, J. Killer, H. Salmonová, M. Geigerová, R. vejstil, P. vec, I. Sedlácek, V. Rada and O. Benada: Bifidobacterium apri sp. nov., a thermophilic actinobacterium isolated from the digestive tract of wild pigs (Sus scrofa). IJSEM 67: 2349 - 2356 2017 ( DOI 10.1099/ijsem.0.001956 , PubMed 28714841 )
#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) .
#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 .
#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 )

Content

About us

Bifidobacterium apri (DSM 100238, CCM 8605, LMG 28779)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Enzymes

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_009299485

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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