Bifidobacterium bifidum (CIP 64.65, ATCC 15696, NCDO 2203)

Name: Bifidobacterium bifidum (CIP 64.65, ATCC 15696, NCDO 2203)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 137143

Type strain

Strain Designation S28a

Culture col. no. CIP 64.65 ATCC 15696 NCDO 2203 CCUG 45219 JCM 7004 5 more

NCBI tax ID(s) 1207542 1681

Special Collections CCUG JCM KCTC CIP

History T. Mitsuoka IV-4 <-- G. Reuter S28a (Variant b). CIP <- 1964, Lab. Ident. Inst. Pasteur, Paris, France <- M. Sebald, Inst. Pasteur, Paris, France <- H. Werner <- G. Reuter: strain S28a

Links

Bifidobacterium bifidum S28a is an anaerobe, mesophilic, Gram-positive prokaryote that was isolated from Intestine of infant.

Gram-positive rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 264229

LMG 10644,ATCC 15696,CCUG 17358,JCM 7004,LMG 13195,NCFB 2203,LMG 13209,NCDO 2203,CCUG 45219,CCRC 14614,NCIMB 702203,KCTC 3418,CIP 64.65,BCRC 14614,CGMCC 1.5043

@ref 20215

Last LPSN update 2026-02-09 11:32:49

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Bifidobacterium

Species Bifidobacterium bifidum

Full scientific name Bifidobacterium bifidum (Tissier 1900) Orla-Jensen 1924 (Approved Lists 1980)

Synonyms (2)

"Bacillus bifidus"
"Bacterium bifidum"

BacDive ID	Other strains from **Bifidobacterium bifidum** (23)	Type strain
1693	B. bifidum Ti, Tissier, DSM 20456, ATCC 29521, JCM 1255, ... (type strain)
1690	B. bifidum Hl 3, DSM 20215
1691	B. bifidum E319f (Variant a), 319f, DSM 20082, JCM 1254, ...
1692	B. bifidum 212A, DSM 20239, ATCC 11863, JCM 1209, NCDO ...
138906	B. bifidum Am, CIP 63.78, ATCC 11618
144562	B. bifidum CCUG 25687
151330	B. bifidum CCUG 43775
151925	B. bifidum CCUG 45218, CIP 64.64
155871	B. bifidum CCUG 59492
162513	B. bifidum JCM 19472
162514	B. bifidum JCM 19473
162515	B. bifidum JCM 19474
162516	B. bifidum JCM 19475
162518	B. bifidum JCM 19477
162519	B. bifidum JCM 19478
162520	B. bifidum JCM 19479
162522	B. bifidum JCM 19481
162523	B. bifidum JCM 19482
162524	B. bifidum JCM 19483
162525	B. bifidum JCM 19484
165447	B. bifidum JCM 7002
165448	B. bifidum JCM 7003
174364	B. bifidum HUN437, Calf96, DSM 115838

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125438			93.5
125439	positive		96.2
37007	positive	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
37007	MEDIUM 20 - for Anaerobic bacteria		Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
37007	CIP Medium 20			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
37007	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
37007	anaerobe
125439	obligate aerobe	92.4

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68381	40585 ChEBI	alpha-cyclodextrin	-	builds acid from	from API rID32STR
68381	29016 ChEBI	arginine	-	hydrolysis	from API rID32STR
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68381	18333 ChEBI	D-arabitol	-	builds acid from	from API rID32STR
68379	17634 ChEBI	D-glucose	+	fermentation	from API Coryne
68381	16899 ChEBI	D-mannitol	-	builds acid from	from API rID32STR
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68381	16988 ChEBI	D-ribose	-	builds acid from	from API rID32STR
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68381	16443 ChEBI	D-tagatose	-	builds acid from	from API rID32STR
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68381	28087 ChEBI	glycogen	-	builds acid from	from API rID32STR
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68381	606565 ChEBI	hippurate	-	hydrolysis	from API rID32STR
68381	30849 ChEBI	L-arabinose	-	builds acid from	from API rID32STR
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68381	17716 ChEBI	lactose	+	builds acid from	from API rID32STR
68379	17716 ChEBI	lactose	+	fermentation	from API Coryne
68381	17306 ChEBI	maltose	-	builds acid from	from API rID32STR
68379	17306 ChEBI	maltose	+	fermentation	from API Coryne
68381	6731 ChEBI	melezitose	-	builds acid from	from API rID32STR
68381	28053 ChEBI	melibiose	-	builds acid from	from API rID32STR
68381	320055 ChEBI	methyl beta-D-glucopyranoside	-	builds acid from	from API rID32STR
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
37007	17632 ChEBI	nitrate	-	reduction
37007	16301 ChEBI	nitrite	-	reduction
68381	27941 ChEBI	pullulan	-	builds acid from	from API rID32STR
68381	16634 ChEBI	raffinose	-	builds acid from	from API rID32STR
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68381	30911 ChEBI	sorbitol	-	builds acid from	from API rID32STR
68381	17992 ChEBI	sucrose	-	builds acid from	from API rID32STR
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68381	27082 ChEBI	trehalose	-	builds acid from	from API rID32STR
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68381	16199 ChEBI	urea	-	hydrolysis	from API rID32STR
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne

Metabolite production

@ref	Chebi-ID	Metabolite
68381	15688 ChEBI	acetoin	from API rID32STR
68380	35581 ChEBI	indole	from API rID32A
37007	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68381	15688 ChEBI	acetoin	-		from API rID32STR
68380	35581 ChEBI	indole		-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
68381	Alanyl-Phenylalanyl-Proline arylamidase	+		from API rID32STR
68381	alkaline phosphatase	-	3.1.3.1	from API rID32STR
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68381	alpha-galactosidase	+	3.2.1.22	from API rID32STR
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68381	arginine dihydrolase	-	3.5.3.6	from API rID32STR
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68381	beta-galactosidase	+	3.2.1.23	from API rID32STR
68382	beta-galactosidase	+	3.2.1.23	from API zym
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68379	beta-galactosidase	+	3.2.1.23	from API Coryne
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68382	beta-glucosidase	-	3.2.1.21	from API zym
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68381	beta-glucosidase	-	3.2.1.21	from API rID32STR
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68381	beta-glucuronidase	-	3.2.1.31	from API rID32STR
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68381	beta-mannosidase	-	3.2.1.25	from API rID32STR
37007	catalase	-	1.11.1.6
68379	catalase	-	1.11.1.6	from API Coryne
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
68379	gelatinase	-		from API Coryne
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	+		from API rID32A
68381	glycyl tryptophan arylamidase	-		from API rID32STR
68380	histidine arylamidase	+		from API rID32A
68380	L-arginine arylamidase	+		from API rID32A
68382	leucine arylamidase	+	3.4.11.1	from API zym
68380	leucine arylamidase	+	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68382	lipase (C 14)	-		from API zym
68381	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32STR
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
37007	oxidase	-
68380	phenylalanine arylamidase	+		from API rID32A
68380	proline-arylamidase	+	3.4.11.5	from API rID32A
68379	pyrazinamidase	+	3.5.1.B15	from API Coryne
68381	pyrrolidonyl arylamidase	+	3.4.19.3	from API rID32STR
68380	pyrrolidonyl arylamidase	+	3.4.19.3	from API rID32A
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68380	serine arylamidase	+		from API rID32A
68382	trypsin	-	3.4.21.4	from API zym
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	+		from API rID32A
68381	urease	-	3.5.1.5	from API rID32STR
37007	urease	-	3.5.1.5
68380	urease	-	3.5.1.5	from API rID32A
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	-		from API zym

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
65639	-	+	-	+	-	+	+	+	-	-	-	-	+	-	-	-	+	+	-	-	-

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
37007	-	-	-	-	-	+	-	-	-	-	+	+	-	+	-	-	-	+	-	-

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
65639	-	-	+	+	-	+	-	-	-	+	-	-	-	-	-	-	-	+	+	-	+	+	+	+	+	+	+	-	+

API rID32STR

@ref	ADH (Arg)	beta GLU	beta GAR	beta GUR	alpha GAL	PAL	RIB	MAN	SOR	LAC	TRE	RAF	SAC	LARA	DARL	Acid from alpha-cyclodextrinCDEX	Acetoin production (Voges Proskauer test)VP	Alanyl-Phenylalanyl-Proline arylamidaseAPPA	beta GAL	Pyrrolidonyl arylamidasePyrA	N-Acetyl-glucosaminidasebeta NAG	Glycyl-tryptophan arylamidaseGTA	HIP	GLYG	PUL	MAL	MEL	MLZ	Acidification of methyl beta-D-glucopyranosideMbeta DG	TAG	beta MAN	URE
65639	-	-	+	-	+	-	-	-	-	+	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type
67770	Intestine of infant
37007	Human, Infant, intestine

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
37007	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM357395v1 assembly for Bifidobacterium bifidum LMG 13195 JCM 7004	complete	GCA_003573955	1207542.9	2859461767	1207542	68.01

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
124043	Bifidobacterium bifidum gene for 16S rRNA, partial sequence, strain: JCM 7004.	AB116286	478		1207542
124043	Bifidobacterium bifidum gene for 16S rRNA, partial sequence, strain: JCM 7004.	AB507081	673		1207542

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bifidobacterium bifidum LMG 13195 JCM 7004
NCBI: GCA_003573955

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.40	no
125439	gram_stain	BacteriaNetⓘ	positive	96.20	no
125439	motility	BacteriaNetⓘ	no	82.80	no
125439	spore_formation	BacteriaNetⓘ	no	83.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bifidobacterium bifidum LMG 13195 JCM 7004
NCBI: GCA_003573955.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	84.91	no
125438	anaerobic	anaerobicⓘ	yes	77.39	yes
125438	aerobic	aerobicⓘ	no	91.11	yes
125438	spore-forming	spore-formingⓘ	no	89.17	no
125438	thermophilic	thermophileⓘ	no	94.97	yes
125438	flagellated	motile2+ⓘ	no	93.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Biochemical characterization of Bifidobacterium bifidum peptidoglycan d,l-endopeptidase BbMep that generates NOD2 ligands.	Kwan JMC, Feng S, Ng EWL, Qiao Y.	RSC Chem Biol	10.1039/d5cb00086f	2025
	Evaluation of the microbiota-sparing properties of the anti-staphylococcal antibiotic afabicin.	Nowakowska J, Cameron DR, De Martino A, Kuhn J, Le Fresne-Languille S, Leuillet S, Amouzou Y, Wittke F, Carton T, Le Vacon F, Chaves RL, Nicolas-Metral V, Vuagniaux G.	J Antimicrob Chemother	10.1093/jac/dkad181	2023
	Clinical Outcomes of Single vs. Two-Strain Probiotic Prophylaxis for Prevention of Necrotizing Enterocolitis in Preterm Infants.	Priyadarshi A, Lowe G, Saddi V, Trivedi A, Luig M, Tracy M.	Front Pediatr	10.3389/fped.2021.729535	2021
	Featured Prebiotic Agent: The Roles and Mechanisms of Direct and Indirect Prebiotic Activities of Lactoferrin and Its Application in Disease Control.	Liu ZS, Chen PW.	Nutrients	10.3390/nu15122759	2023
Genetics	Bifidobacterium bifidum: A Key Member of the Early Human Gut Microbiota.	Turroni F, Duranti S, Milani C, Lugli GA, van Sinderen D, Ventura M.	Microorganisms	10.3390/microorganisms7110544	2019
Genetics	Scarless gene disruption enabled by a dual-plasmid knockout platform in a clinical infant-derived Bifidobacterium breve strain.	Gao Z, Feng L.	Front Microbiol	10.3389/fmicb.2025.1653505	2025
Metabolism	Galacto- and Fructo-oligosaccharides Utilized for Growth by Cocultures of Bifidobacterial Species Characteristic of the Infant Gut.	Sims IM, Tannock GW.	Appl Environ Microbiol	10.1128/aem.00214-20	2020
	A Novel Major Pilin Subunit Protein FimM Is Involved in Adhesion of Bifidobacterium longum BBMN68 to Intestinal Epithelial Cells.	Xiong Y, Zhai Z, Lei Y, Xiao B, Hao Y.	Front Microbiol	10.3389/fmicb.2020.590435	2020
	The potential role of adherence factors in probiotic function in the gastrointestinal tract of adults and pediatrics: a narrative review of experimental and human studies.	Gorreja F, Walker WA.	Gut Microbes	10.1080/19490976.2022.2149214	2022
	Probiotics for Prevention of Severe Necrotizing Enterocolitis: Experience of New Zealand Neonatal Intensive Care Units.	Meyer MP, Chow SSW, Alsweiler J, Bourchier D, Broadbent R, Knight D, Lynn AM, Patel H.	Front Pediatr	10.3389/fped.2020.00119	2020
	Bifidobacterium bifidum in probiotic Edam cheese: influence on cheese ripening.	Sabikhi L, Kumar MH, Mathur BN.	J Food Sci Technol	10.1007/s13197-013-0945-7	2014
	How microbial glycosyl hydrolase activity in the gut mucosa initiates microbial cross-feeding.	Berkhout MD, Plugge CM, Belzer C.	Glycobiology	10.1093/glycob/cwab105	2022
	Necrotising enterocolitis and mortality in preterm infants after introduction of probiotics: a quasi-experimental study.	Samuels N, van de Graaf R, Been JV, de Jonge RC, Hanff LM, Wijnen RM, Kornelisse RF, Reiss IK, Vermeulen MJ.	Sci Rep	10.1038/srep31643	2016
Phylogeny	Probiotic Cocktail Identified by Microbial Network Analysis Inhibits Growth, Virulence Gene Expression, and Host Cell Colonization of Vancomycin-Resistant Enterococci.	Sun WS, Lee YJ, Tsai KN, Ho YH, Fang SB.	Microorganisms	10.3390/microorganisms8060816	2020
	Determining the metabolic fate of human milk oligosaccharides: it may just be more complex than you think?	Jackson PPJ, Wijeyesekera A, Rastall RA.	Gut Microbiome (Camb)	10.1017/gmb.2022.8	2022
	Prebiotic Potential and Chemical Composition of Seven Culinary Spice Extracts.	Lu QY, Summanen PH, Lee RP, Huang J, Henning SM, Heber D, Finegold SM, Li Z.	J Food Sci	10.1111/1750-3841.13792	2017
Enzymology	Quantitative detection of viable Bifidobacterium bifidum BF-1 cells in human feces by using propidium monoazide and strain-specific primers.	Fujimoto J, Watanabe K.	Appl Environ Microbiol	10.1128/aem.03294-12	2013
	Study of adhesion and survival of lactobacilli and bifidobacteria on table olives with the aim of formulating a new probiotic food.	Lavermicocca P, Valerio F, Lonigro SL, De Angelis M, Morelli L, Callegari ML, Rizzello CG, Visconti A.	Appl Environ Microbiol	10.1128/aem.71.8.4233-4240.2005	2005
	A Review on Adventitious Lactic Acid Bacteria from Table Olives.	Portilha-Cunha MF, Macedo AC, Malcata FX.	Foods	10.3390/foods9070948	2020
Enzymology	Genetic diversity of bile salt hydrolases among human intestinal bifidobacteria.	Jarocki P, Targonski Z.	Curr Microbiol	10.1007/s00284-013-0362-1	2013
Enzymology	Cloning and characterization of the bile salt hydrolase genes (bsh) from Bifidobacterium bifidum strains.	Kim GB, Miyamoto CM, Meighen EA, Lee BH.	Appl Environ Microbiol	10.1128/aem.70.9.5603-5612.2004	2004
	Technology and potential applications of probiotic encapsulation in fermented milk products.	Iravani S, Korbekandi H, Mirmohammadi SV.	J Food Sci Technol	10.1007/s13197-014-1516-2	2015
Metabolism	Isolation of a bifidogenic peptide from the pepsin hydrolysate of bovine lactoferrin.	Oda H, Wakabayashi H, Yamauchi K, Sato T, Xiao JZ, Abe F, Iwatsuki K.	Appl Environ Microbiol	10.1128/aem.03343-12	2013
	Transcription analysis of a lantibiotic gene cluster from Bifidobacterium longum DJO10A.	Lee JH, Li X, O'Sullivan DJ.	Appl Environ Microbiol	10.1128/aem.00571-11	2011
Enzymology	Specific identification and targeted characterization of Bifidobacterium lactis from different environmental isolates by a combined multiplex-PCR approach.	Ventura M, Reniero R, Zink R.	Appl Environ Microbiol	10.1128/aem.67.6.2760-2765.2001	2001
Metabolism	Bile Salts Modulate the Mucin-Activated Type VI Secretion System of Pandemic Vibrio cholerae.	Bachmann V, Kostiuk B, Unterweger D, Diaz-Satizabal L, Ogg S, Pukatzki S.	PLoS Negl Trop Dis	10.1371/journal.pntd.0004031	2015
	Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels.	Queipo-Ortuno MI, Seoane LM, Murri M, Pardo M, Gomez-Zumaquero JM, Cardona F, Casanueva F, Tinahones FJ.	PLoS One	10.1371/journal.pone.0065465	2013
	Antimicrobial Activity of Lactoferrin-Related Peptides and Applications in Human and Veterinary Medicine.	Bruni N, Capucchio MT, Biasibetti E, Pessione E, Cirrincione S, Giraudo L, Corona A, Dosio F.	Molecules	10.3390/molecules21060752	2016
Pathogenicity	Novel riboswitch-binding flavin analog that protects mice against Clostridium difficile infection without inhibiting cecal flora.	Blount KF, Megyola C, Plummer M, Osterman D, O'Connell T, Aristoff P, Quinn C, Chrusciel RA, Poel TJ, Schostarez HJ, Stewart CA, Walker DP, Wuts PG, Breaker RR.	Antimicrob Agents Chemother	10.1128/aac.01282-15	2015
Phylogeny	Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study.	Murri M, Leiva I, Gomez-Zumaquero JM, Tinahones FJ, Cardona F, Soriguer F, Queipo-Ortuno MI.	BMC Med	10.1186/1741-7015-11-46	2013
Enzymology	Structure of macroamphiphiles from several Bifidobacterium strains.	Iwasaki H, Araki Y, Ito E, Nagaoka M, Yokokura T.	J Bacteriol	10.1128/jb.172.2.845-852.1990	1990
Phylogeny	Identification of Bifidobacterium strains by rRNA gene restriction patterns.	Mangin I, Bourget N, Bouhnik Y, Bisetti N, Simonet JM, Decaris B.	Appl Environ Microbiol	10.1128/aem.60.5.1451-1458.1994	1994
	Growth promotion of Bifidobacterium species by whey and casein fractions from human and bovine milk.	Petschow BW, Talbott RD.	J Clin Microbiol	10.1128/jcm.28.2.287-292.1990	1990
Enzymology	Selective medium for isolation and enumeration of Bifidobacterium spp.	Munoa FJ, Pares R.	Appl Environ Microbiol	10.1128/aem.54.7.1715-1718.1988	1988
Enzymology	Species-specific oligonucleotide probes for five Bifidobacterium species detected in human intestinal microflora.	Yamamoto T, Morotomi M, Tanaka R.	Appl Environ Microbiol	10.1128/aem.58.12.4076-4079.1992	1992
Phylogeny	Rapid identification of Actinomycetaceae and related bacteria.	Kilian M.	J Clin Microbiol	10.1128/jcm.8.2.127-133.1978	1978
	Effectiveness of a probiotic combination on the neurodevelopment of the very premature infant.	Baucells BJ, Sebastiani G, Herrero-Aizpurua L, Andreu-Fernandez V, Navarro-Tapia E, Garcia-Algar O, Figueras-Aloy J.	Sci Rep	10.1038/s41598-023-37393-6	2023
Pathogenicity	Exploring the Potential of Novel Animal-Origin Probiotics as Key Players in One Health: Opportunities and Challenges.	Gorzelanna Z, Mamrot A, Bedkowska D, Bubak J, Miszczak M.	Int J Mol Sci	10.3390/ijms26115143	2025
Genetics	Neonatal microbiome dysbiosis decoded by mNGS: from mechanistic insights to precision interventions.	Huang F, Li J, Liu D, Li Y, Tang J.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1642072	2025
	Clinical NEC prevention practices drive different microbiome profiles and functional responses in the preterm intestine.	Neumann CJ, Mahnert A, Kumpitsch C, Kiu R, Dalby MJ, Kujawska M, Madl T, Kurath-Koller S, Urlesberger B, Resch B, Hall LJ, Moissl-Eichinger C.	Nat Commun	10.1038/s41467-023-36825-1	2023
	Probiotics to improve the gut microbiome in premature infants: are we there yet?	Mercer EM, Arrieta MC.	Gut Microbes	10.1080/19490976.2023.2201160	2023
	Late-onset sepsis treatment in very preterm infants alters longitudinal microbiome trajectory with lower abundance of Bifidobacterium despite probiotic supplementation.	Healy DB, Wang S, Patangia D, Grimaud G, Ross RP, Stanton C, Dempsey EM.	Gut Microbes	10.1080/19490976.2025.2523808	2025
	Microglia are necessary for probiotics supplementation to improve impaired fear extinction caused by pregnancy stress in adult offspring of rats.	Zeng R, Chen J, Peng Y, Xu W, Tao Y, Li M, Zhang R, Meng J, Li Z, Zeng L, Huang J.	Neurobiol Stress	10.1016/j.ynstr.2023.100591	2024
	Bioinformatics-Facilitated Identification of Novel Bacterial Sulfoglycosidases That Hydrolyze 6-Sulfo-N-acetylglucosamine.	Dong M, Chen Z, He Y, Zallot R, Jin Y.	ACS Bio Med Chem Au	10.1021/acsbiomedchemau.4c00088	2024
	Enzymatic Adaptation of Bifidobacterium bifidum to Host Glycans, Viewed from Glycoside Hydrolyases and Carbohydrate-Binding Modules.	Katoh T, Ojima MN, Sakanaka M, Ashida H, Gotoh A, Katayama T.	Microorganisms	10.3390/microorganisms8040481	2020
Metabolism	Comparative transcriptomics reveals key differences in the response to milk oligosaccharides of infant gut-associated bifidobacteria.	Garrido D, Ruiz-Moyano S, Lemay DG, Sela DA, German JB, Mills DA.	Sci Rep	10.1038/srep13517	2015
Genetics	A Transposon Mutagenesis System for Bifidobacterium longum subsp. longum Based on an IS3 Family Insertion Sequence, ISBlo11.	Sakanaka M, Nakakawaji S, Nakajima S, Fukiya S, Abe A, Saburi W, Mori H, Yokota A.	Appl Environ Microbiol	10.1128/aem.00824-18	2018
	Utilization of Host-Derived Glycans by Intestinal Lactobacillus and Bifidobacterium Species.	Zuniga M, Monedero V, Yebra MJ.	Front Microbiol	10.3389/fmicb.2018.01917	2018
Genetics	Development of Real-Time PCR Assay to Specifically Detect 22 Bifidobacterium Species and Subspecies Using Comparative Genomics.	Kim HB, Kim E, Yang SM, Lee S, Kim MJ, Kim HY.	Front Microbiol	10.3389/fmicb.2020.02087	2020
	Comparison of Real-Time PCR and Droplet Digital PCR for the Quantitative Detection of Lactiplantibacillus plantarum subsp. plantarum	Choi CH, Kim E, Yang SM, Kim DS, Suh SM, Lee GY, Kim HY.	Foods	10.3390/foods11091331	2022
Genetics	Differentiation of Lacticaseibacillus zeae Using Pan-Genome Analysis and Real-Time PCR Method Targeting a Unique Gene.	Kim E, Yang SM, Kim HY.	Foods	10.3390/foods10092112	2021
Phylogeny	Identification and Monitoring of Lactobacillus delbrueckii Subspecies Using Pangenomic-Based Novel Genetic Markers.	Kim E, Cho EJ, Yang SM, Kim HY.	J Microbiol Biotechnol	10.4014/jmb.2009.09034	2021
Pathogenicity	Effectiveness of two probiotics in preventing necrotising enterocolitis in a cohort of very-low-birth-weight premature new-borns.	Uberos J, Campos-Martinez A, Fernandez-Marin E, Millan IC, Lopez AR, Blanca-Jover E	Benef Microbes	10.3920/BM2021.0088	2021
Metabolism	Bifidobacterium bifidum ATCC 15696 and Bifidobacterium breve 24b Metabolic Interaction Based on 2'-O-Fucosyl-Lactose Studied in Steady-State Cultures in a Freter-Style Chemostat.	Centanni M, Ferguson SA, Sims IM, Biswas A, Tannock GW	Appl Environ Microbiol	10.1128/AEM.02783-18	2019
Metabolism	Sharing of human milk oligosaccharides degradants within bifidobacterial communities in faecal cultures supplemented with Bifidobacterium bifidum.	Gotoh A, Katoh T, Sakanaka M, Ling Y, Yamada C, Asakuma S, Urashima T, Tomabechi Y, Katayama-Ikegami A, Kurihara S, Yamamoto K, Harata G, He F, Hirose J, Kitaoka M, Okuda S, Katayama T	Sci Rep	10.1038/s41598-018-32080-3	2018
Metabolism	Bifidobacterium bifidum Extracellular Sialidase Enhances Adhesion to the Mucosal Surface and Supports Carbohydrate Assimilation.	Nishiyama K, Yamamoto Y, Sugiyama M, Takaki T, Urashima T, Fukiya S, Yokota A, Okada N, Mukai T	mBio	10.1128/mBio.00928-17	2017
Metabolism	Identification and characterization of a sulfoglycosidase from Bifidobacterium bifidum implicated in mucin glycan utilization.	Katoh T, Maeshibu T, Kikkawa KI, Gotoh A, Tomabechi Y, Nakamura M, Liao WH, Yamaguchi M, Ashida H, Yamamoto K, Katayama T	Biosci Biotechnol Biochem	10.1080/09168451.2017.1361810	2017
Phylogeny	Routine Use of Probiotics in Preterm Infants: Longitudinal Impact on the Microbiome and Metabolome.	Abdulkadir B, Nelson A, Skeath T, Marrs EC, Perry JD, Cummings SP, Embleton ND, Berrington JE, Stewart CJ	Neonatology	10.1159/000442936	2016
Metabolism	Probiotic bifidobacteria protect mice from lethal infection with Shiga toxin-producing Escherichia coli O157:H7.	Asahara T, Shimizu K, Nomoto K, Hamabata T, Ozawa A, Takeda Y	Infect Immun	10.1128/IAI.72.4.2240-2247.2004	2004
Metabolism	Andean yacon root (Smallanthus sonchifolius Poepp. Endl) fructooligosaccharides as a potential novel source of prebiotics.	Pedreschi R, Campos D, Noratto G, Chirinos R, Cisneros-Zevallos L	J Agric Food Chem	10.1021/jf0344744	2003
Pathogenicity	Effect of bifidogenic factors on growth characteristics of bifidobacteria in infant formulas.	Dubey UK, Mistry VV	J Dairy Sci	10.3168/jds.S0022-0302(96)76469-X	1996
Pathogenicity	Growth characteristics of bifidobacteria in infant formulas.	Dubey UK, Mistry VV	J Dairy Sci	10.3168/jds.S0022-0302(96)76468-8	1996
Metabolism	Growth and viability of Bifidobacterium bifidum in cheddar cheese.	Dinakar P, Mistry VV	J Dairy Sci	10.3168/jds.S0022-0302(94)77225-8	1994

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 )
#37007	Collection of Institut Pasteur ; Curators of the CIP; CIP 64.65
#65639	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 45219
#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;
#68379	Automatically annotated from API Coryne .
#68380	Automatically annotated from API rID32A .
#68381	Automatically annotated from API rID32STR .
#68382	Automatically annotated from API zym .
#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 )

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Bifidobacterium bifidum (CIP 64.65, ATCC 15696, NCDO 2203)

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