Name: Bifidobacterium cuniculi RA93
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1701

Type strain:

Species: Bifidobacterium cuniculi

Strain Designation: RA93

Culture col. no.: DSM 20435, ATCC 27916, CCUG 24610, JCM 1213, BCRC 14672, CGMCC 1.2239, CIP 103379, KCTC 3276, LMG 10738

Strain history: ATCC 27916 <-- V. Scardovi RA93.

NCBI tax ID(s): 1437601 (strain), 1688 (species)

Section

Bifidobacterium cuniculi RA93 is an anaerobe, mesophilic bacterium that was isolated from rabbit faeces.

anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Bifidobacteriales*
	Family	*Bifidobacteriaceae*
	Genus	*Bifidobacterium*
	Species	**Bifidobacterium cuniculi**
	Full Scientific Name (LPSN)	Bifidobacterium cuniculi Scardovi et al. 1979 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

[Ref.: #69480]

Gram stain

positive Confidence in %100

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8811]

Culture medium

BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)

[Ref.: #8811]

Culture medium growth

[Ref.: #8811]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8811]

Culture medium composition

expand / minimize

[Ref.: #34255]

Culture medium

MEDIUM 20 - for Anaerobic bacteria

[Ref.: #34255]

Culture medium growth

[Ref.: #34255]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8811]	growth	37 °C
[Ref.: #34255]	growth	37 °C
[Ref.: #47995]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #8811]	Temperature range	mesophilic
[Ref.: #34255]	Temperature range	mesophilic
[Ref.: #47995]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #8811]	Oxygen tolerance	anaerobe
[Ref.: #47995]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.292

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

[Ref.: #8811]	Murein short key	A11.21
[Ref.: #8811]	Murein types	A3alpha L-Lys(L-Orn)-L-Ala(L-Ser)-L-Ala₂

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	peptidoglycan biosynthesis	100	15 of 15
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	palmitate biosynthesis	77.27	17 of 22
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	purine metabolism	65.96	62 of 94
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	glutamate and glutamine metabolism	60.71	17 of 28
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	pyrimidine metabolism	60	27 of 45
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	alanine metabolism	55.17	16 of 29
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	oxidative phosphorylation	53.85	49 of 91
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	citric acid cycle	50	7 of 14
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	degradation of sugar alcohols	43.75	7 of 16
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	tryptophan metabolism	42.11	16 of 38
[Ref.: #66794]	non-pathway related	42.11	16 of 38
[Ref.: #66794]	lysine metabolism	40.48	17 of 42
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	flavin biosynthesis	33.33	5 of 15
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	propionate fermentation	30	3 of 10
[Ref.: #66794]	ubiquinone biosynthesis	28.57	2 of 7
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	lipid A biosynthesis	22.22	2 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #8811]	Sample type/isolated from	rabbit faeces

[Ref.: #47995]	Sample type/isolated from	Rabbit feces
[Ref.: #47995]	Sampling date	1989-05-02

[Ref.: #67770]	Sample type/isolated from	Feces of a rabbit
* marker position based on {}

Isolation sources categories

#Host	#Mammals	#Leporidae (Rabbit/Hare)
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC071801 (>99% sequence identity) for Bifidobacterium cuniculi subclade from Microbeatlas

Aquatic Samples	90
Soil Samples	140
Animal Samples	5399
Plant Samples	27
Total Samples	5656

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

[Ref.: #8811]

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:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Bifidobacterium cuniculi gene for 16S ribosomal RNA, partial sequence, strain: JCM 1213	LC071801	1429	ENA	1688 tax ID
[Ref.: #67770]	Bifidobacterium cuniculi gene for 16S rRNA, partial sequence	AB438223	1521	ENA	1688 tax ID
[Ref.: #8811]	Bifidobacterium cuniculi DSM 20435, whole genome shotgun sequencing project	JDUL00000000	264	ENA	1437601 tax ID
[Ref.: #20218]	Bifidobacterium cunniculi 16S ribosomal RNA	M58734	1487	ENA	1688 tax ID	*
[Ref.: #20218]	Bifidobacterium cuniculi ATCC 27916 16S-23S intergenic spacer, partial sequence	U09790	490	ENA	1688 tax ID	*
[Ref.: #20218]	Bifidobacterium cuniculi gene for 16S rRNA, partial sequence, strain: JCM 1213	AB116298	489	ENA	1688 tax ID	*
[Ref.: #20218]	Bifidobacterium cuniculi gene for 16S rRNA, partial sequence, strain: JCM 1213	AB507094	667	ENA	1688 tax ID	*
[Ref.: #20218]	Bifidobacterium cuniculi strain KCTC 3276 16S ribosomal RNA gene, partial sequence	GU361818	1492	ENA	1688 tax ID	*
[Ref.: #20218]	Bifidobacterium cuniculi strain LMG 10738 16S ribosomal RNA gene, partial sequence	JX986964	1481	ENA	1688 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.: #67770]	Bifidobacterium cuniculi DSM 20435 DSM 20435	GCA_000771465	contig	GenBank	1437601 tax ID
[Ref.: #67770]	Bifidobacterium cuniculi LMG 10738	GCA_000741575	contig	GenBank	1688 tax ID
[Ref.: #66792]	Bifidobacterium cuniculi DSM 20435	1437601.3	wgs	PATRIC	1437601 tax ID	*
[Ref.: #66792]	Bifidobacterium cuniculi strain LMG 10738	1688.3	wgs	PATRIC	1688 tax ID	*
[Ref.: #66792]	Bifidobacterium cuniculi LMG 10738	2597490228	draft	JGI IMG/M	1688 tax ID	*
[Ref.: #66792]	Bifidobacterium cuniculi DSM 20435	2671180748	draft	JGI IMG/M	1437601 tax ID	*

[Ref.: #8811]	GC-content	64.1 mol%
[Ref.: #67770]	GC-content	64.1 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 Diaspora project based on: Bifidobacterium cuniculi DSM 20435 PATRIC: 1437601.3
[Ref.: #69480]	gram-positive	yes	100	yes
[Ref.: #69480]	spore-forming	no	99.998	no
[Ref.: #69480]	anaerobic	yes	99.292	yes
[Ref.: #69480]	thermophile	no	99.756	yes
[Ref.: #69480]	motile	no	89.513	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Bifidobacterium cuniculi DSM 20435 PATRIC: 1437601.3
[Ref.: #69481]	spore-forming	no	100	no

Availability in culture collections External links

[Ref.: #8811]

Culture collection no.

DSM 20435, ATCC 27916, CCUG 24610, JCM 1213, BCRC 14672, CGMCC 1.2239, CIP 103379, KCTC 3276, LMG 10738

References

#8811

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20435

#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 )

#34255 ; Curators of the CIP;
#47995 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 24610

#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;

#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 )

* These data were automatically processed and therefore are not curated

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Bifidobacterium cuniculi DSM 20435

Bifidobacterium cuniculi DSM 20435

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