Name: Bifidobacterium apri RP115
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140310

Type strain:

Species: Bifidobacterium apri

Strain Designation: RP115

Culture col. no.: DSM 100238, CCM 8605, LMG 28779

Strain history: <- J. Killer, Inst. Animal Physiol. and Genetics, Czech Acad. Sci., Prague; RP115 <- R. Pechar

NCBI tax ID(s): 1769423 (species)

SI-ID 405771

DSM 100238

Section

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

colony-forming
Gram-positive
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	*Bifidobacterium*
	Species	**Bifidobacterium apri**
	Full Scientific Name (LPSN)	Bifidobacterium apri Pechar et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43284]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #43284]	Cell length	1.5-6.0 µm

[Ref.: #43284]	Cell width	0.3-0.8 µm

[Ref.: #43284]	Cell shape	rod-shaped

[Ref.: #43284]	Motility	no

[Ref.: #43284]	Colony size	1.4-2.8 mm
[Ref.: #43284]	Colony color	creamy white
[Ref.: #43284]	Colony shape	circular
[Ref.: #43284]	Incubation period	3 days
[Ref.: #43284]	Cultivation medium used	TPY agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43284]

Culture medium

TPY agar

[Ref.: #43284]

Culture medium growth

[Ref.: #42917]

Culture medium

BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)

[Ref.: #42917]

Culture medium growth

[Ref.: #42917]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42917]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #42917]	growth	37 °C
[Ref.: #43284]	optimum	37 °C
[Ref.: #43284]	growth	10-49 °C

[Ref.: #42917]	Temperature range	mesophilic
[Ref.: #43284]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43284]			optimum	6.5
[Ref.: #43284]			growth	3.5-7.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43284]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.15

[Ref.: #43284]	Type of spore	spore
[Ref.: #43284]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43284]	amygdalin ChEBI	+	builds acid from
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	arbutin ChEBI	+	fermentation
[Ref.: #43284]	arbutin ChEBI	+	builds acid from
[Ref.: #68371]	arbutin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #43284]	cellobiose ChEBI	-	builds acid from
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	D-arabinose ChEBI	-	builds acid from
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	D-arabitol ChEBI	-	builds acid from
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	D-fructose ChEBI	+	fermentation
[Ref.: #68371]	D-fructose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #43284]	D-fucose ChEBI	-	builds acid from
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	D-galactose	+	fermentation
[Ref.: #68371]	D-galactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #43284]	D-glucose ChEBI	+	fermentation
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #43284]	D-lyxose ChEBI	-	builds acid from
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	D-mannitol ChEBI	-	builds acid from
[Ref.: #43284]	D-mannitol ChEBI	-	fermentation
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	D-mannose ChEBI	-	builds acid from
[Ref.: #43284]	D-mannose ChEBI	-	fermentation
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	D-ribose ChEBI	-	builds acid from
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #43284]	D-sorbitol ChEBI	-	fermentation
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	D-tagatose ChEBI	-	builds acid from
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	D-xylose ChEBI	-	builds acid from
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	erythritol ChEBI	-	builds acid from
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	esculin ChEBI	+	fermentation
[Ref.: #43284]	esculin ChEBI	+	builds acid from
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #43284]	galactitol ChEBI	-	builds acid from
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	gentiobiose ChEBI	-	builds acid from
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	glycerol ChEBI	-	builds acid from
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	glycogen ChEBI	+	fermentation
[Ref.: #68371]	glycogen ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #43284]	inulin ChEBI	-	builds acid from
[Ref.: #43284]	inulin ChEBI	-	fermentation
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	L-arabinose ChEBI	-	builds acid from
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	L-arabitol ChEBI	-	builds acid from
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	L-fucose ChEBI	-	builds acid from
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #43284]	L-rhamnose ChEBI	-	fermentation
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	L-sorbose ChEBI	-	builds acid from
[Ref.: #43284]	L-sorbose ChEBI	-	fermentation
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	L-xylose ChEBI	-	builds acid from
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	lactose ChEBI	+/-	builds acid from
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	maltose ChEBI	+	fermentation
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #43284]	melezitose ChEBI	+	builds acid from
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	melibiose ChEBI	+	fermentation
[Ref.: #68371]	melibiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #43284]	methyl alpha-D-glucopyranoside ChEBI	+	builds acid from
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #43284]	methyl alpha-D-mannoside ChEBI	+	builds acid from
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	myo-inositol ChEBI	-	builds acid from
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	nitrate ChEBI	-	reduction
[Ref.: #43284]	potassium 2-dehydro-D-gluconate	-	builds acid from
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	potassium 5-dehydro-D-gluconate	-	builds acid from
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	potassium gluconate ChEBI	-	builds acid from
[Ref.: #43284]	raffinose ChEBI	+	fermentation
[Ref.: #68371]	raffinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #43284]	ribitol ChEBI	-	builds acid from
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	salicin ChEBI	+	fermentation
[Ref.: #43284]	salicin ChEBI	+	builds acid from
[Ref.: #68371]	salicin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #43284]	starch ChEBI	+	fermentation
[Ref.: #68371]	starch ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #43284]	sucrose ChEBI	+	fermentation
[Ref.: #68371]	sucrose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #43284]	trehalose ChEBI	+	builds acid from
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #43284]	turanose ChEBI	+	fermentation
[Ref.: #68371]	turanose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #43284]	xylitol ChEBI	-	builds acid from
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43284]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43284]	6-phospho-beta-galactosidase	-	3.2.1.85
[Ref.: #43284]	acid phosphatase	+	3.1.3.2
[Ref.: #43284]	alanine arylamidase	+	3.4.11.2
[Ref.: #43284]	alkaline phosphatase	-	3.1.3.1
[Ref.: #43284]	alpha-arabinosidase	-	3.2.1.55
[Ref.: #43284]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43284]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43284]	alpha-galactosidase	+	3.2.1.22
[Ref.: #43284]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43284]	arginine arylamidase	+
[Ref.: #43284]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43284]	beta-galactosidase	+	3.2.1.23
[Ref.: #43284]	beta-glucosidase	+	3.2.1.21
[Ref.: #43284]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43284]	catalase	-	1.11.1.6
[Ref.: #43284]	cystine arylamidase	-	3.4.11.3
[Ref.: #43284]	cytochrome oxidase	-	1.9.3.1
[Ref.: #43284]	esterase (C 4)	+
[Ref.: #43284]	esterase Lipase (C 8)	-
[Ref.: #43284]	fructose-6-phosphate phosphoketolase	+	4.1.2.22
[Ref.: #43284]	glutamate decarboxylase	+	4.1.1.15
[Ref.: #43284]	glutamyl-glutamate arylamidase	-
[Ref.: #43284]	glycin arylamidase	+
[Ref.: #43284]	histidine arylamidase	-
[Ref.: #43284]	leucine arylamidase	+	3.4.11.1
[Ref.: #43284]	leucyl glycin arylamidase	+	3.4.11.1
[Ref.: #43284]	lipase (C 14)	-
[Ref.: #43284]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43284]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43284]	phenylalanine arylamidase	-
[Ref.: #43284]	proline-arylamidase	+	3.4.11.5
[Ref.: #43284]	pyroglutamic acid arylamidase	-
[Ref.: #43284]	serine arylamidase	+
[Ref.: #43284]	trypsin	-	3.4.21.4
[Ref.: #43284]	tyrosine arylamidase	+
[Ref.: #43284]	urease	-	3.5.1.5
[Ref.: #43284]	valine arylamidase	+/-
	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.: #42917]	14881	-	-	-	-	-	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	+	-	-	+	+	+	-	+	-	+	+	-	-	-	+	+	+	-	-	+	-	-	-	-	-	-	-	-	-

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

[Ref.: #42917]	Sample type/isolated from	large intestine contents of a wild boar (Sus scrofa scrofa)
[Ref.: #42917]	Host species	Sus scrofa scrofa
[Ref.: #42917]	Geographic location (country and/or sea, region)	Central Bohemia, Prague-Divoká Šárka
[Ref.: #42917]	Country	Czech Republic
[Ref.: #42917]	Country ISO 3 Code	CZE
[Ref.: #42917]	Continent	Europe

[Ref.: #43284]	Sample type/isolated from	Fresh samples of intestinal contents of three wild pigs
[Ref.: #43284]	Geographic location (country and/or sea, region)	Prague-Divok a Sárka, Czech Republic
[Ref.: #43284]	Country	Czech Republic
[Ref.: #43284]	Country ISO 3 Code	CZE
[Ref.: #43284]	Continent	Europe
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #42917]

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.: #43284]	RP115 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene	KT343137	440	ENA	1769423 tax ID
[Ref.: #42917]	Bifidobacterium apri strain RP115 16S ribosomal RNA gene, partial sequence	KT343145	1396	ENA	1769423 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Bifidobacterium apri DSM 100238	GCA_009299485	contig	GenBank	1769423 tax ID	*
[Ref.: #66792]	Bifidobacterium apri strain DSM 100238	1769423.3	wgs	PATRIC	1769423 tax ID	*

[Ref.: #42917]

GC-content

59.4 mol%

high performance liquid chromatography (HPLC)

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: Bifidobacterium apri strain DSM 100238 PATRIC: 1769423.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Bifidobacterium apri strain DSM 100238 PATRIC: 1769423.3
[Ref.: #69480]	motile	no	93.29	yes
[Ref.: #69480]	gram-positive	yes	91.67	yes
[Ref.: #69480]	anaerobic	yes	98.127	no
[Ref.: #69480]	aerobic	no	98.211	no
[Ref.: #69480]	halophile	no	70.406	no
[Ref.: #69480]	spore-forming	no	95.846	yes
[Ref.: #69480]	thermophile	no	95.746	yes
[Ref.: #69480]	glucose-util	yes	87.916	no
[Ref.: #69480]	flagellated	no	95.607	yes
[Ref.: #69480]	glucose-ferment	yes	84.674	yes

Availability in culture collections External links

[Ref.: #42917]

Culture collection no.

DSM 100238, CCM 8605, LMG 28779

[Ref.: #96615]

SI-ID 405771

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#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 )

#96615

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-ID405771.1 )

* These data were automatically processed and therefore are not curated

Change proposal

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Bifidobacterium apri strain DSM 100238

Bifidobacterium apri strain DSM 100238

Change proposal

Change proposal