Bifidobacterium sp. (DSM 108971, Cla-CZ-59)

Name: Bifidobacterium sp. (DSM 108971, Cla-CZ-59)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 160370

Type strain

Strain Designation Cla-CZ-59

Culture col. no. DSM 108971 Cla-CZ-59

NCBI tax ID(s) 41200

Special Collections DSMZ Chicken DZIF

Links

Cla-CZ-59 is a mesophilic prokaryote that was isolated from chicken colon content, adult.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 397662

DSM 108971

@ref 20215

Last LPSN update 2025-12-16 10:08:28

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Bifidobacterium

Full scientific name Bifidobacterium Orla-Jensen 1924 (Approved Lists 1980)

Morphology

Cell morphology

@ref	Motility	Confidence
125438		93.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
67276	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
67276	positive	growth	37	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		91.1

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	+	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	+	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	+		from API rID32A
68380	proline-arylamidase	+	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
67276	-	-	+	+	-	+	+	+/-	-	-	-	+	-	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-
67276	-	-	+	+	-	+	+	+/-	-	-	-	+	-	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
67276	chicken colon content, adult	Dietramszell (Bavaria)	Germany	DEU	Europe	47.8589	11.5894 47.8589/11.5894

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	ASM1498300v1 assembly for Bifidobacterium pullorum subsp. saeculare DSM 108971	contig	GCA_014983005	78257.7	78257	72.08

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67276	Bifidobacterium pullorum subsp. saeculare strain ClaCZ59 16S ribosomal RNA gene, partial sequence	MN055938.1	1468		78257

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bifidobacterium pullorum subsp. saeculare DSM 108971
NCBI: GCA_014983005

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	91.10	no
125439	motility	BacteriaNetⓘ	no	62.10	no
125439	gram_stain	BacteriaNetⓘ	positive	89.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	89.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bifidobacterium saeculare strain DSM 108971
PATRIC: 78257.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	82.91	no
125438	anaerobic	anaerobicⓘ	yes	86.14	no
125438	aerobic	aerobicⓘ	no	96.61	no
125438	spore-forming	spore-formingⓘ	no	89.20	no
125438	thermophilic	thermophileⓘ	no	92.99	no
125438	flagellated	motile2+ⓘ	no	93.50	no

Literature

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 )
#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) .
#67276	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 108971
#68380	Automatically annotated from API rID32A .
#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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