Bifidobacterium catenulatum subsp. catenulatum (DSM 16992, ATCC 27539, CECT 7362)

Name: Bifidobacterium catenulatum subsp. catenulatum (DSM 16992, ATCC 27539, CECT 7362)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1697

Type strain

Strain Designation B669

Culture col. no. DSM 16992 ATCC 27539 CECT 7362 CIP 104175 DSM 20103 13 more

NCBI tax ID(s) 1686 2981616

Special Collections DSMZ CCUG JCM KCTC CIP

History DSMZ <- CIP <- ATCC <- V. Scardovi; B669 JCM <-- ATCC 27539 <-- V. Scardovi B669. CIP <- 1994, ATCC <- V. Scardovi: strain B669

Links

Bifidobacterium catenulatum subsp. catenulatum B669 is an anaerobe bacterium that was isolated from human feces.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 1246

LMG 11043,ATCC 27539,CCUG 18366,DSM 20103,JCM 1194,LMG 10504,NCFB 2246,CIP 104175,CCRC 14667,NCIMB 702246,NCDO2246,KCTC 3221,KCTC 3278,AS 1.2197,CCM 4989,CECT 5780,HAMBI 560,BCRC 14667,NCAIM B.02017,DSM 16992,CGMCC 1.2197,VTT E-011764,CECT 7362

@ref 20215

Last LPSN update 2026-05-29 08:25:19

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Bifidobacterium

Species Bifidobacterium catenulatum subsp. catenulatum

Full scientific name Bifidobacterium catenulatum subsp. catenulatum (Scardovi and Crociani 1974) Nouioui et al. 2018

BacDive ID	Other strains from **Bifidobacterium catenulatum subsp. catenulatum** (1)	Type strain
1698	B. catenulatum subsp. catenulatum F44, DSM 20224, JCM 7130, CGMCC 1.3014, JCM ...

Morphology

Cell morphology

@ref	Motility	Confidence
125439		91.152
125438		90.5

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6595	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
34555	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)
117216	CIP Medium 20	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6595	positive	growth	37
34555	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
6595	anaerobe
125439	facultative anaerobe	94.052

Spore formation

@ref	Spore formation	Confidence
125439		99.408
125438		92.033

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	+	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68380	16634 ChEBI	raffinose	+	fermentation	from API rID32A
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

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-arabinosidase	+	3.2.1.55	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

Fatty acid profile

Metadata FA analysis

@ref

46811

Fatty acid	Percentage	ECL
C16:0	32.8	16
C18:1 ω9c DMA	17.2	18.226
C18:1 ω9c	13.8	17.769
C14:0	7.2	14
C18:0	6.1	18
C13:0 3OH/C15:1 i I/H	4.9	14.469
C18:2 ω6,9c/C18:0 ANTE	4.6	17.724
Unidentified	3.8
C16:1 ω9c	2.7	15.774
C12:0	2.2	12
Unidentified	2.1
C13:1 at 12-13	1.4	12.931
Unidentified	1.2

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
6595	-	-	-	-	+	+	+	-	-	-	+	+	+	-	-	-	-	-	-	+	+/-	+	+/-	+	+	+	+	+	+	+	+	+	+/-	+/-	-	+	-	-	-	+	+	-	-	-	-	-	-	+	-	-
6595	-	-	-	-	+	+	+	-	-	-	+	-	-	-	-	-	-	-	-	+	-	+	-	+	-	+	+	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
6595	-	-	-	-	+	+	+	-	-	-	+	+	+	-	-	-	-	-	-	+	-	-	-	+	+	+	+	-	+	+	+	-	-	-	-	+	-	-	-	+	+	-	-	-	-	-	-	+	-	-
6595	-	-	-	-	+	+	+	-	-	-	+	+	+	-	-	-	-	-	-	+	-	+/-	-	+	+	+	+	+/-	+	+	+	+	+/-	-	-	+	-	-	-	+	+	-	-	-	-	-	-	+	-	+/-
6595	-	-	-	-	+	-	+	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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
46811	-	-	+	+	-	+	+	+	-	-	+	+	-	+	-	-	-	+	+	+	+	+	-	+	+	+	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Host species	Isolation date
6595	human feces	Homo sapiens
46811	Human intestine,adult	Homo sapiens
67770	Human feces	Homo sapiens
117216	Human, Feces	Homo sapiens	1969

Taxonmaps

69479

Global distribution of 16S sequence LC071794 (>99% sequence identity) for Actinobacteria from Microbeatlas

Aquatic Samples	13261
Soil Samples	5076
Animal Samples	262631
Plant Samples	1911
Total Samples	282879

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6595	1	Risk group (German classification) According to TRBA 466
117216	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM102519v1 assembly for Bifidobacterium catenulatum DSM 16992 = JCM 1194 = LMG 11043	complete	GCA_001025195	566552.18		566552	99.02
67770	ASM17345v1 assembly for Bifidobacterium catenulatum DSM 16992 = JCM 1194 = LMG 11043	contig	GCA_000173455	566552.4	642979312	566552	73.11
67770	Bifcat assembly for Bifidobacterium catenulatum DSM 16992 = JCM 1194 = LMG 11043	contig	GCA_000741565	566552.16	2597490243	566552	49.68
67770	DSM-16992 assembly for Bifidobacterium catenulatum DSM 16992 = JCM 1194 = LMG 11043	contig	GCA_000771025	566552.17	2660237904	566552	44.96

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Bifidobacterium catenulatum 16S ribosomal RNA gene, partial sequence	AF432082	1445	566552
20218	Bifidobacterium catenulatum 16S ribosomal RNA gene, complete sequence	M58732	1478	566552
20218	Bifidobacterium catenulatum (ATCC 27539) 16S ribosomal RNA gene, partial	M84784	642	1686
20218	Bifidobacterium catenulatum ATCC27539 16S-23S intergenic spacer	U09522	492	566552
20218	Bifidobacterium catenulatum gene for 16S rRNA, partial sequence, strain: JCM 1194	AB116294	477	566552
20218	Bifidobacterium catenulatum gene for 16S rRNA, partial sequence, strain: JCM 1194	AB507090	682	566552
20218	Bifidobacterium catenulatum strain JCM 1194 16S ribosomal RNA gene, partial sequence	GQ227710	302	566552
20218	Bifidobacterium catenulatum strain KCTC 3221 16S ribosomal RNA gene, partial sequence	GU361816	1480	566552
20218	Bifidobacterium pseudocatenulatum strain LMG11043 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence	FJ231742	775	28026
67770	Bifidobacterium catenulatum gene for 16S ribosomal RNA, partial sequence	AB437357	1509	1686
67770	Bifidobacterium catenulatum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1194	LC071794	1417	566552

GC content

6595

GC-content (mol%)54.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM102519v1 assembly for Bifidobacterium catenulatum DSM 16992 = JCM 1194 = LMG 11043
BV-BRC: 566552.18

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	94.05	no
125439	gram_stain	BacteriaNetⓘ	positive	52.58	no
125439	motility	BacteriaNetⓘ	no	91.15	no
125439	spore_formation	BacteriaNetⓘ	no	99.41	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bifidobacterium catenulatum DSM 16992 = JCM 1194 = LMG 11043 JCM 1194
NCBI: GCA_001025195.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.99	no
125438	anaerobic	anaerobicⓘ	yes	86.06	yes
125438	aerobic	aerobicⓘ	no	94.18	yes
125438	spore-forming	spore-formingⓘ	no	92.03	no
125438	thermophilic	thermophileⓘ	no	95.50	yes
125438	flagellated	motile2+ⓘ	no	90.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Draft Genome Sequence of Bifidobacterium pseudocatenulatum Bif4, Isolated from Healthy Infant Feces.	Chander AM, Singh S, Sharma S, Chaudhry V, Rajarammohan S, Mantri SS, Bishnoi M, Bhadada SK, Kondepudi KK.	Microbiol Resour Announc	10.1128/mra.00561-20	2020
	Bifidobacterium beta-Glucosidase Activity and Fermentation of Dietary Plant Glucosides Is Species and Strain Specific.	Modrackova N, Vlkova E, Tejnecky V, Schwab C, Neuzil-Bunesova V.	Microorganisms	10.3390/microorganisms8060839	2020
	Genomic Island-Mediated Horizontal Transfer of the Erythromycin Resistance Gene erm(X) among Bifidobacteria.	Li B, Chen D, Lin F, Wu C, Cao L, Chen H, Hu Y, Yin Y.	Appl Environ Microbiol	10.1128/aem.00410-22	2022
	Genetic manipulations of nonmodel gut microbes.	Jin WB, Guo CJ.	Imeta	10.1002/imt2.216	2024
Genetics	Genome-Wide Assessment of Stress-Associated Genes in Bifidobacteria.	Schopping M, Vesth T, Jensen K, Franzen CJ, Zeidan AA.	Appl Environ Microbiol	10.1128/aem.02251-21	2022
	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
	Geminiviruses: a tale of a plasmid becoming a virus.	Krupovic M, Ravantti JJ, Bamford DH.	BMC Evol Biol	10.1186/1471-2148-9-112	2009
Metabolism	Slimy partners: the mucus barrier and gut microbiome in ulcerative colitis.	Fang J, Wang H, Zhou Y, Zhang H, Zhou H, Zhang X.	Exp Mol Med	10.1038/s12276-021-00617-8	2021
Enzymology	Characterization of a novel beta-L-arabinofuranosidase in Bifidobacterium longum: functional elucidation of a DUF1680 protein family member.	Fujita K, Takashi Y, Obuchi E, Kitahara K, Suganuma T.	J Biol Chem	10.1074/jbc.m113.528711	2014
	Genomic Analyses of Bifidobacterium moukalabense Reveal Adaptations to Frugivore/Folivore Feeding Behavior.	Segawa T, Fukuchi S, Bodington D, Tsuchida S, Mbehang Nguema PP, Mori H, Ushida K.	Microorganisms	10.3390/microorganisms7040099	2019
Metabolism	Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome.	Wang M, Osborn LJ, Jain S, Meng X, Weakley A, Yan J, Massey WJ, Varadharajan V, Horak A, Banerjee R, Allende DS, Chan ER, Hajjar AM, Wang Z, Dimas A, Zhao A, Nagashima K, Cheng AG, Higginbottom S, Hazen SL, Brown JM, Fischbach MA.	Cell	10.1016/j.cell.2023.05.037	2023
Enzymology	Genetic diversity of bile salt hydrolases among human intestinal bifidobacteria.	Jarocki P, Targonski Z.	Curr Microbiol	10.1007/s00284-013-0362-1	2013
Genetics	Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species.	Zafar H, Saier MH.	Microb Physiol	10.1159/000518954	2022
Enzymology	A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space.	Michelini S, Balakrishnan B, Parolo S, Matone A, Mullaney JA, Young W, Gasser O, Wall C, Priami C, Lombardo R, Kussmann M.	Microbiome	10.1186/s40168-018-0545-x	2018
	Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium.	Briner AE, Lugli GA, Milani C, Duranti S, Turroni F, Gueimonde M, Margolles A, van Sinderen D, Ventura M, Barrangou R.	PLoS One	10.1371/journal.pone.0133661	2015
	Design, construction, and in vivo augmentation of a complex gut microbiome.	Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA.	Cell	10.1016/j.cell.2022.08.003	2022
Metabolism	Oligosaccharide binding proteins from Bifidobacterium longum subsp. infantis reveal a preference for host glycans.	Garrido D, Kim JH, German JB, Raybould HE, Mills DA.	PLoS One	10.1371/journal.pone.0017315	2011
Metabolism	In silico prediction of horizontal gene transfer events in Lactobacillus bulgaricus and Streptococcus thermophilus reveals protocooperation in yogurt manufacturing.	Liu M, Siezen RJ, Nauta A.	Appl Environ Microbiol	10.1128/aem.02898-08	2009
Genetics	Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera.	Lukjancenko O, Ussery DW, Wassenaar TM.	Microb Ecol	10.1007/s00248-011-9948-y	2012
Metabolism	The influence of milk oligosaccharides on microbiota of infants: opportunities for formulas.	Chichlowski M, German JB, Lebrilla CB, Mills DA.	Annu Rev Food Sci Technol	10.1146/annurev-food-022510-133743	2011
	Bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.	Silverio AL, Saier MH.	J Membr Biol	10.1007/s00232-011-9364-8	2011
	Modulation of Designed Gut Bacterial Communities by Prebiotics and the Impact of Their Metabolites on Intestinal Cells.	Roupar D, Gonzalez A, Martins JT, Goncalves DA, Teixeira JA, Botelho C, Nobre C.	Foods	10.3390/foods12234216	2023
Phylogeny	Identification of species belonging to the Bifidobacterium genus by PCR-RFLP analysis of a hsp60 gene fragment.	Baffoni L, Stenico V, Strahsburger E, Gaggia F, Di Gioia D, Modesto M, Mattarelli P, Biavati B.	BMC Microbiol	10.1186/1471-2180-13-149	2013
Metabolism	Hydrolysis of the rutinose-conjugates flavonoids rutin and hesperidin by the gut microbiota and bifidobacteria.	Amaretti A, Raimondi S, Leonardi A, Quartieri A, Rossi M.	Nutrients	10.3390/nu7042788	2015
	A Single Plasmid of Nisin-Controlled Bovine and Human Lactoferrin Expressing Elevated Antibacterial Activity of Lactoferrin-Resistant Probiotic Strains.	Liu ZS, Lin CF, Lee CP, Hsieh MC, Lu HF, Chen YF, Ku YW, Chen PW.	Antibiotics (Basel)	10.3390/antibiotics10020120	2021
Pathogenicity	In Vitro and In Vivo Activities of DS-2969b, a Novel GyrB Inhibitor, against Clostridium difficile.	Mathur T, Barman TK, Kumar M, Singh D, Kumar R, Khera MK, Yamada M, Inoue SI, Upadhyay DJ, Masuda N.	Antimicrob Agents Chemother	10.1128/aac.02157-17	2018
	Beyond Metabolism: The Complex Interplay Between Dietary Phytoestrogens, Gut Bacteria, and Cells of Nervous and Immune Systems.	Cady N, Peterson SR, Freedman SN, Mangalam AK.	Front Neurol	10.3389/fneur.2020.00150	2020
	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
Pathogenicity	Evaluation of impact of exposure of Sudan azo dyes and their metabolites on human intestinal bacteria.	Pan H, Feng J, He GX, Cerniglia CE, Chen H.	Anaerobe	10.1016/j.anaerobe.2012.05.002	2012
Phylogeny	Real-time PCR analysis of the intestinal microbiotas in peritoneal dialysis patients.	Wang IK, Lai HC, Yu CJ, Liang CC, Chang CT, Kuo HL, Yang YF, Lin CC, Lin HH, Liu YL, Chang YC, Wu YY, Chen CH, Li CY, Chuang FR, Huang CC, Lin CH, Lin HC.	Appl Environ Microbiol	10.1128/aem.05605-11	2012
Metabolism	Diversity, ecology and intestinal function of bifidobacteria.	Bottacini F, Ventura M, van Sinderen D, O'Connell Motherway M.	Microb Cell Fact	10.1186/1475-2859-13-s1-s4	2014
Enzymology	Ruminococcin A, a new lantibiotic produced by a Ruminococcus gnavus strain isolated from human feces.	Dabard J, Bridonneau C, Phillipe C, Anglade P, Molle D, Nardi M, Ladire M, Girardin H, Marcille F, Gomez A, Fons M.	Appl Environ Microbiol	10.1128/aem.67.9.4111-4118.2001	2001
Phylogeny	Bifidobacterium lactis DSM 10140: identification of the atp (atpBEFHAGDC) operon and analysis of its genetic structure, characteristics, and phylogeny.	Ventura M, Canchaya C, van Sinderen D, Fitzgerald GF, Zink R.	Appl Environ Microbiol	10.1128/aem.70.5.3110-3121.2004	2004
Enzymology	Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis.	Satokari RM, Vaughan EE, Akkermans AD, Saarela M, de Vos WM.	Appl Environ Microbiol	10.1128/aem.67.2.504-513.2001	2001
Enzymology	Extracellular dextranase activity produced by human oral strains of the genus Bifidobacterium.	Kaster AG, Brown LR.	Infect Immun	10.1128/iai.42.2.716-720.1983	1983
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	Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes.	Schwiertz A, Le Blay G, Blaut M.	Appl Environ Microbiol	10.1128/aem.66.1.375-382.2000	2000
Cultivation	A new selective medium for Bifidobacterium spp.	Nebra Y, Blanch AR.	Appl Environ Microbiol	10.1128/aem.65.11.5173-5176.1999	1999
Enzymology	Identification, detection, and enumeration of human bifidobacterium species by PCR targeting the transaldolase gene.	Requena T, Burton J, Matsuki T, Munro K, Simon MA, Tanaka R, Watanabe K, Tannock GW.	Appl Environ Microbiol	10.1128/aem.68.5.2420-2427.2002	2002
	Distinct gut microbiota profiles and network properties in older Korean individuals with subjective cognitive decline, mild cognitive impairment, and Alzheimer's disease.	Son SJ, Wu X, Roh HW, Cho YH, Hong S, Nam YJ, Hong CH, Park S.	Alzheimers Res Ther	10.1186/s13195-025-01820-9	2025
	Gut microbiota and urine metabolomics signature in autism spectrum disorder children from Southern China.	Huang Z, Wei A, Yuan H, Huang S, Chen X, Han Y, Li X.	BMC Pediatr	10.1186/s12887-025-05922-z	2025
	Microbiome-metabolome generated bile acids gatekeep infliximab efficacy in Crohn's disease by licensing M1 suppression and Treg dominance.	Liu L, Liang L, Liang H, Wang M, Zhou W, Mai G, Yang C, Chen Y.	J Adv Res	10.1016/j.jare.2025.08.017	2025
	Mendelian randomization analysis revealed a gut microbiota-eye axis in acute anterior uveitis.	Mi Y, Chen L, Liao N, Wan M.	Eye (Lond)	10.1038/s41433-025-03715-3	2025
	Structural analysis of gum arabic side chains from Acacia seyal released by bifidobacterial beta-arabino-oligosaccharide 3-O-beta-l-arabinopyranosyl-alpha-l-arabinofuranosidase	Sasaki Y, Matsuo A, Hashiguchi M, Fujimura K, Koshino H, Tanaka K, Ito Y, Kitahara K, Ishiwata A, Fujita K.	Carbohydrate polymers.		2025
	Structural analysis of gum arabic side chains from Acacia seyal released by bifidobacterial beta-arabino-oligosaccharide 3-O-beta-l-arabinopyranosyl-alpha-l-arabinofuranosidase.	Sasaki Y, Matsuo A, Hashiguchi M, Fujimura K, Koshino H, Tanaka K, Ito Y, Kitahara K, Ishiwata A, Fujita K.	Carbohydr Polym	10.1016/j.carbpol.2024.122965	2025
Metabolism	The causal relationship between gut microbiota and lipid metabolism in heart failure: A 2-sample Mendelian randomization study.	Gan J, Hu N, Jiao J, Li S, Li J, Zhang Z, Xu L, Li C, Li J, Yue G.	Medicine (Baltimore)	10.1097/md.0000000000045087	2025
	Alterations in the gut microbiota in patients with long-term follow-up after pancreaticoduodenectomy and their association with postoperative fatty liver: A pilot study.	Uchida Y, Fujii T, Takahashi H, Nakaoka K, Funasaka K, Ohno E, Hirooka Y, Takahara T, Suda K, Tochio T.	Pancreatology	10.1016/j.pan.2024.10.005	2024
Metabolism	Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents.	Ying L, Yuhao W, Yafang H, Jiao L, Lina D, Qinze S, Chenghai Y, Shaoxiong Z, Yuexi G, Mingwang S, Zelin C, Chuangchuang W, Zihan G, Xin L, Lu M, Lei Z.	BMC Microbiol	10.1186/s12866-025-04094-1	2025
	Association Between Gut Microbiota and Chronic Kidney Disease: A Two-Sample Mendelian Randomization Study in a Chinese Population.	Lin W, Liang Z, Fang J, Liu Y, Lei L, Lin J, Xia B, Zheng Z, Yuan J, Tang C.	Biomedicines	10.3390/biomedicines13061397	2025
	A Metagenomics Approach to Frailty in Patients With Cirrhosis Undergoing a Multifactorial Intervention.	Vega-Abellaneda S, Roman E, Soler Z, Ortiz MA, Rossi G, Biagini L, Sanchez E, Pons-Tarin M, Laghi L, Mengucci C, Kaur N, Poca M, Cuyas B, Serrano-Gomez G, Alvarado E, Manichanh C, Soriano G.	Liver Int	10.1111/liv.70418	2025
	Microbiota dysbiosis associated with type 2 diabetes-like effects caused by chronic exposure to a mixture of chlorinated persistent organic pollutants in zebrafish.	Lee H, Yoon S, Park YH, Lee JS, Rhyu DY, Kim KT.	Environ Pollut	10.1016/j.envpol.2023.122108	2023
	Intermittent MDMA Attenuates Ovariectomy-induced Bone Loss via a Gut Microbiota-Bone Axis.	Wan X, Eguchi A, Murayama R, Mori C, Hashimoto K.	Clin Psychopharmacol Neurosci	10.9758/cpn.25.1309	2025
	Characteristics of the gut microbiota in Bifidobacterium catenulatum LI10 pretreated rats with lower levels of D-galactosamine-induced liver damage.	Zha H, Si G, Wang C, Lv J, Zhang H, Li L.	J Appl Microbiol	10.1111/jam.15562	2022
	Postoperative Gut Microbiota Changes after Colorectal Cancer Surgery: A Comparative Study Based on Resection Sites.	Hattori Y, Fujii T, Tochio T, Kumamoto T, Hiro J, Matsuoka H, Masumori K, Funasaka K, Ohno E, Hirooka Y, Suda K, Otsuka K.	J Anus Rectum Colon	10.23922/jarc.2025-048	2025
	Makgeolli Lees as a Novel Prebiotic Candidate: Effects on Human Gut Microbiota and Metabolites.	Kim JH, Kim HR, Seong H, Han SH, Kim G, Choi Y, Han NS.	J Microbiol Biotechnol	10.4014/jmb.2504.04020	2025
	Gut Microbiota in Monozygotic Twins Discordant for Parkinson's Disease.	Bolliri C, Fontana A, Cereda E, Barichella M, Cilia R, Ferri V, Caronni S, Calandrella D, Morelli L, Pezzoli G.	Ann Neurol	10.1002/ana.26454	2022
Genetics	Draft genomes of 12 Bifidobacterium isolates from human IBD fecal samples.	Souza CE, Jacobson NE, An MA, Droit L, Vega AA, Rosales M, Mihindukulasuriya KA, Pastrana K, Handley SA, Parkes M, Rimmer J, Wang D, Dinsdale EA, A Edwards R, Segall AM.	Microbiol Resour Announc	10.1128/mra.00130-23	2024
Genetics	Gut microbiome and major depressive disorder: insights from two-sample Mendelian randomization.	Zhao Q, Baranova A, Cao H, Zhang F.	BMC Psychiatry	10.1186/s12888-024-05942-6	2024
	Reduced abundance of Fusobacterium signifies cardiovascular benefits of sodium glucose cotransporter 2 inhibitor in type 2 diabetes: a single arm clinical trial.	Yang S, Deng J, Weng X, Ma Z, Lin N, Xiao Y, Zuo R, Hu Y, Zheng C, Zeng X, Lin Q, Hou K.	Front Pharmacol	10.3389/fphar.2025.1600464	2025
	Red Raspberry and Fructo-Oligosaccharide Supplementation, Metabolic Biomarkers, and the Gut Microbiota in Adults with Prediabetes: A Randomized Crossover Clinical Trial.	Zhang X, Zhao A, Sandhu AK, Edirisinghe I, Burton-Freeman BM.	J Nutr	10.1093/jn/nxac037	2022
	Gut microbiota and urine metabolomics signature in autism spectrum disorder children from Southern China	Huang Z, Wei A, Yuan H, Huang S, Chen X, Han Y, Li X.	BMC Pediatr		2025
	Association Between the Mode of Delivery and Infant Gut Microbiota Composition Up to 6 Months of Age: A Systematic Literature Review Considering the Role of Breastfeeding.	Princisval L, Rebelo F, Williams BL, Coimbra AC, Crovesy L, Ferreira AL, Kac G.	Nutr Rev	10.1093/nutrit/nuab008	2021
	Naringenin Promotes Gastrointestinal Motility in Mice by Impacting the SCF/c-Kit Pathway and Gut Microbiota.	Wu L, Niu Y, Ren B, Wang S, Song Y, Wang X, Zhao K, Yue Z, Li Y, Gao J.	Foods	10.3390/foods13162520	2024
	Bone morphogenetic proteins, DNA methylation, and gut microbiota interaction in lumbar disc degeneration: A multi-omics Mendelian randomization study.	Li XY, Wang PY, Wang QJ, Wang DF, Wang SK, Wang Y, Zhu WG, Wang W, Kong C, Lu SB, Chen XL.	JOR Spine	10.1002/jsp2.70027	2024
	Gastrointestinal Tolerance and Gut Microbiota Modulation of Encapsulated and Free Forms of Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis.	Kim G, Seong H, Han SH, Kim HR, Kim SH, Ku HJ, Han HJ, Kim CH, Han NS.	J Microbiol Biotechnol	10.4014/jmb.2506.06028	2025
	B. adolescentis alleviates inflammation and suppresses PGE2 through remodling gut microbiota to attenuate pulmonary fibrosis in aging mice.	Ni J, Wang F, Wu Y, Shen J, Zhou Z, Xu L, Lou Z, Shen Y, Qiu B, Xiang Q, Yin P, Chen Y, Li L.	NPJ Sci Food	10.1038/s41538-025-00613-6	2025
Metabolism	Lactulose ingestion causes an increase in the abundance of gut-resident bifidobacteria in Japanese women: a randomised, double-blind, placebo-controlled crossover trial.	Sakai Y, Hamano H, Ochi H, Abe F, Masuda K, Iino H.	Benef Microbes	10.3920/bm2020.0100	2021
	Remodeling of Gut Microbiome of Pakistani Expats in China After Ramadan Fasting.	Sakandar HA, Zhao F, Kang J, Khan MN, Sun Z.	Food Sci Nutr	10.1002/fsn3.70019	2025
	The Possible Preventative Role of Lactate- and Butyrate-Producing Bacteria in Colorectal Carcinogenesis.	Song CH, Kim N, Nam RH, Choi SI, Jang JY, Kim EH, Choi J, Choi Y, Yoon H, Lee SM, Seok YJ.	Gut Liver	10.5009/gnl230385	2024
	Seeding and feeding: nutrition and birth-associated exposures shape gut microbiome assembly in breastfed infants.	Stinson LF, Norrish I, Mhembere F, Cheema AS, Mullally CA, Payne MS, Geddes DT.	Gut Microbes	10.1080/19490976.2025.2557981	2025
	Bacterial dysbiosis in newly diagnosed treatment naïve pediatric ulcerative colitis in Saudi Arabia.	El Mouzan M, Al Mofarreh M, Alsaleem B, Al Sarkhy A, Alanazi A, Khormi M, Almasoud A, Assiri A.	Saudi J Gastroenterol	10.4103/sjg.sjg_66_24	2025
	Various steaming durations alter digestion, absorption, and fermentation by human gut microbiota outcomes of Polygonatum cyrtonema Hua polysaccharides.	Wu W, Wang Y, Yi P, Su X, Mi Y, Wu L, Tan Q.	Front Nutr	10.3389/fnut.2024.1466781	2024
	Sex Difference in the Effect of Bifidobacterium longum on Repeated Water Avoidance Stress-induced Gut Dysbiosis in Wistar Rats.	Choi SI, Kim N, Nam RH, Jang JY, Kim EH, Ha S, Kang K, Lee W, Shin CM, Lee DH.	J Cancer Prev	10.15430/jcp.23.042	2024
	Complementary Feeding and Infant Gut Microbiota: A Narrative Review.	Noles DL, Matzeller KL, Frank DN, Krebs NF, Tang M.	Nutrients	10.3390/nu17050743	2025
	Gut microbiome is associated with asthma and race in children with food allergy.	Mahdavinia M, Fyolek JP, Jiang J, Thivalapill N, Bilaver LA, Warren C, Fox S, Nimmagadda SR, Newmark PJ, Sharma H, Assa'ad A, Seed PC, Gupta RS.	J Allergy Clin Immunol	10.1016/j.jaci.2023.07.024	2023
	Harnessing Lactobacillus-derived SCFAs for food and health: Pathways, genes, and functional implications.	Nami Y, Shaghaghi Ranjbar M, Modarres Aval M, Haghshenas B.	Curr Res Microb Sci	10.1016/j.crmicr.2025.100496	2025
	Disclosing alpha-lactalbumin impact on the intestinal and vaginal microbiota of women suffering from polycystic ovary syndrome.	Alessandri G, Mancabelli L, Fontana F, Lepore E, Forte G, Burratti M, Ventura M, Turroni F.	Microb Biotechnol	10.1111/1751-7915.14540	2024
Genetics	Diet-Gut Microbiota Relations: Critical Appraisal of Evidence From Studies Using Metagenomics.	Lotankar M, Houttu N, Mokkala K, Laitinen K.	Nutr Rev	10.1093/nutrit/nuae192	2025
Genetics	Metagenomics Investigation on Baby Diaper Area Microbiome and Its Association with Skin pH and Dermatitis in the Diapered Area.	Hu P, Carr AN, Parlov M, Swift D, Tiesman JP, Ramji N, Schoch JJ, Teufel AG.	Microorganisms	10.3390/microorganisms13112632	2025
Pathogenicity	Gut microbiome and clinical and lifestyle host factors associated with recurrent positive RT-PCR for SARS-CoV-2.	Jimenez-Arroyo C, Molinero N, Sabater C, Margolles A, Terron-Camero LC, Andres-Leon E, Ramos M, Del Val M, Moreno-Arribas MV.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1494193	2024
Genetics	Comparative genomic analysis revealed genetic divergence between Bifidobacterium catenulatum subspecies present in infant versus adult guts.	Liu J, Li W, Yao C, Yu J, Zhang H.	BMC Microbiol	10.1186/s12866-022-02573-3	2022
Genetics	Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria.	Arzamasov AA, Rodionov DA, Hibberd MC, Guruge JL, Kent JE, Kazanov MD, Leyn SA, Elane ML, Sejane K, Furst A, Bode L, Barratt MJ, Gordon JI, Osterman AL.	Nat Microbiol	10.1038/s41564-025-02056-x	2025
	An optimized culturomics strategy for isolation of human milk microbiota.	Wang F, Yu L, Ren Y, Zhang Q, He S, Zhao M, He Z, Gao Q, Chen J.	Front Microbiol	10.3389/fmicb.2024.1272062	2024
	Enterotype-stratified gut microbial signatures in MASLD and cirrhosis based on integrated microbiome data.	Yuan H, Zhou J, Wu X, Wang S, Park S.	Front Microbiol	10.3389/fmicb.2025.1568672	2025
Genetics	Dual-approach analysis of gut microbiome in patients with type 1 diabetes and diabetic kidney disease.	Bunka L, Rozenberga M, Silamikelis I, Saksis R, Birzniece L, Megnis K, Fedulovs A, Pahirko L, Zalizko P, Krustins E, Klovins J, Sokolovska J, Elbere I.	Ann Med	10.1080/07853890.2025.2531254	2025
	Interplay of Lymphocytes with the Intestinal Microbiota in Children with Nonalcoholic Fatty Liver Disease.	Liang T, Li D, Zunong J, Li M, Amaerjiang N, Xiao H, Khattab NM, Vermund SH, Hu Y.	Nutrients	10.3390/nu14214641	2022
	Gut microbiota differences in five-year-old children that were born preterm with a history of necrotizing enterocolitis: A pilot trial.	Magnusson A, Jabbari Shiadeh SM, Ardalan M, Swolin-Eide D, Elfvin A.	iScience	10.1016/j.isci.2024.110325	2024
Pathogenicity	The effect of quercetin on genetic expression of the commensal gut microbes Bifidobacterium catenulatum, Enterococcus caccae and Ruminococcus gauvreauii.	Firrman J, Liu L, Zhang L, Arango Argoty G, Wang M, Tomasula P, Kobori M, Pontious S, Xiao W.	Anaerobe	10.1016/j.anaerobe.2016.10.004	2016
	Effect of herbal medicine Bojungikgi-tang on gut microbiome and symptoms in anorexic patients with atopic dermatitis: a randomized controlled trial.	Lee B, Ko MM, Ahn YM, Park HJ, Jung SY, Jung HA, Lee H, Kim PW, Choi Y, Han K, Shin S, Jung J.	Front Pharmacol	10.3389/fphar.2025.1593477	2025
	Combining Bifidobacterium longum subsp. infantis and human milk oligosaccharides synergistically increases short chain fatty acid production ex vivo.	De Bruyn F, James K, Cottenet G, Dominick M, Katja J.	Commun Biol	10.1038/s42003-024-06628-1	2024
	Evaluating the prebiotic effect of oligosaccharides on gut microbiome wellness using in vitro fecal fermentation.	Lee DH, Seong H, Chang D, Gupta VK, Kim J, Cheon S, Kim G, Sung J, Han NS.	NPJ Sci Food	10.1038/s41538-023-00195-1	2023
	Dietary polyunsaturated fatty acids effect on cecal microbiome profile of maturing broiler chicken.	Jadhav VV, Fasina YO, Harrison SH.	Poult Sci	10.1016/j.psj.2025.105167	2025
Genetics	The interactions between host genome and gut microbiome increase the risk of psychiatric disorders: Mendelian randomization and biological annotation.	Xiao L, Liu S, Wu Y, Huang Y, Tao S, Liu Y, Tang Y, Xie M, Ma Q, Yin Y, Dai M, Zhang M, Llamocca E, Gui H, Wang Q.	Brain Behav Immun	10.1016/j.bbi.2023.08.003	2023
	Lymphocyte and neutrophil count combined with intestinal bacteria abundance predict the severity of COVID-19.	Chen L, Yin Z, Zhou D, Li X, Yu C, Luo C, Jin Y, Zhang L, Song J, Rasche L, Einsele H, Tu L, Zhou X, Bai T, Hou X.	Microbiol Spectr	10.1128/spectrum.03027-23	2024
Metabolism	The dynamics of the gut microbiota in prediabetes during a four-year follow-up among European patients-an IMI-DIRECT prospective study.	Lyu L, Fan Y, Vogt JK, Clos-Garcia M, Bonnefond A, Pedersen HK, Dutta A, Koivula R, Sharma S, Allin KH, Brorsson C, Cederberg H, Chabanova E, De Masi F, Dermitzakis E, Elders PJ, Blom MT, Hollander M, Eriksen R, Forgie I, Frost G, Giordano GN, Grallert H, Haid M, Hansen TH, Jablonka B, Kokkola T, Mahajan A, Mari A, McDonald TJ, Musholt PB, Pavo I, Prehn C, Ridderstrale M, Ruetten H, Hart LM', Schwenk JM, Stankevic E, Thomsen HS, Vangipurapu J, Vestergaard H, Vinuela A, Walker M, Hansen T, Linneberg A, Nielsen HB, Brunak S, McCarthy MI, Froguel P, Adamski J, Franks PW, Laakso M, Beulens JWJ, Pearson E, Pedersen O.	Genome Med	10.1186/s13073-025-01508-7	2025
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
	Uptake of fucosylated type I human milk oligosaccharide blocks by Bifidobacterium longum subsp. infantis.	Ejby Hansen M, Sakanaka M, Jensen M, Sakanaka H, Pichler MJ, Maeda S, Franck Hovring J, Nakajima A, Kunstmann S, Nielsen TS, Peters GHJ, Slotboom DJ, Morth JP, Katayama T, Abou Hachem M.	mBio	10.1128/mbio.00368-25	2025
	Photocatalytic production and biological activity of D-arabino-1,4-lactone from D-fructose.	Usuki S, Patil PB, Jiang T, Taki N, Uesaka Y, Togawa H, Latthe SS, Liu S, Yamatoya K, Nakata K.	Sci Rep	10.1038/s41598-024-84921-z	2025
	Transmission and Persistence of Infant Gut-Associated Bifidobacteria.	Hilliard MA, Sela DA.	Microorganisms	10.3390/microorganisms12050879	2024
	Miscanthus×giganteus xylooligosaccharides: Purification and fermentation	Chen MH, Bowman M, Cotta MA, Dien BS, Iten LB, Whitehead TR, Rausch KD, Tumbleson ME, Singh V.	Carbohydrate polymers.		2016
	Miscanthus x giganteus xylooligosaccharides: Purification and fermentation	Chen MH, Bowman M, Cotta MA, Dien BS, Iten LB, Whitehead TR, Raush KD, Tumbleson ME, Singh V.	Carbohydrate polymers.		2016
	Microbial interactions and the homeostasis of the gut microbiome: the role of Bifidobacterium.	Martin AJM, Serebrinsky-Duek K, Riquelme E, Saa PA, Garrido D.	Microbiome Res Rep	10.20517/mrr.2023.10	2023
	Quercetin Increases Growth Performance and Decreases Incidence of Diarrhea and Mechanism of Action in Weaned Piglets.	Mao Y, Yang Q, Liu J, Fu Y, Zhou S, Liu J, Ying L, Li Y.	Oxid Med Cell Longev	10.1155/2024/5632260	2024
	Generation of novel prebiotic oligosaccharide pools from fiber drives biological insight in bacterial glycan metabolism.	Masarweh C, Maldonado-Gomez M, Paviani B, Bhattacharya M, Weng C-Y, Suarez C, Ehlers-Cheang S, Stacy A, Castillo J, Krishnakumar N, Kalanetra KA, Barile D, German JB, Lebrilla CB, Mills DA.	Appl Environ Microbiol	10.1128/aem.02077-24	2025
Enzymology	[THE SPECIES CHARACTERISTIC OF BIFIDOBACTERIA IN INTESTINAL BIOTOPE OF CHILDREN WITH FUNCTIONAL DYSPEPSIA].	Rakova EB, Nemichenko UM, Popkova SM, Serdyuk LV, Dolgikh VV, Ivanova EI, Savelkaeva MV.	Klin Lab Diagn		2015
	A survey into the utilization of probiotics and medicinal plants among individuals afflicted with gastrointestinal disorders in healthcare institutions in Saïda, Algeria.	Tazi LA, Benabdesslem Y, Amara S, Hachem K.	Libyan J Med	10.1080/19932820.2024.2317492	2024
Metabolism	Miscanthus×giganteus xylooligosaccharides: Purification and fermentation.	Chen MH, Bowman MJ, Cotta MA, Dien BS, Iten LB, Whitehead TR, Rausch KD, Tumbleson ME, Singh V.	Carbohydr Polym	10.1016/j.carbpol.2015.12.052	2016
	Antagonistic activities of some Bifidobacterium sp. strains isolated from resident infant gastrointestinal microbiota on Gram-negative enteric pathogens.	Delcaru C, Alexandru I, Podgoreanu P, Cristea VC, Bleotu C, Chifiriuc MC, Bezirtzoglou E, Lazar V.	Anaerobe	10.1016/j.anaerobe.2016.02.010	2016
	Exploring the Potential Probiotic Properties of Bifidobacterium breve DSM 32583-A Novel Strain Isolated from Human Milk.	Kujawska M, Neuhaus K, Huptas C, Jimenez E, Arboleya S, Schaubeck M, Hall LJ.	Probiotics Antimicrob Proteins	10.1007/s12602-024-10346-9	2025
	HMOs Exert Marked Bifidogenic Effects on Children's Gut Microbiota Ex Vivo, Due to Age-Related Bifidobacterium Species Composition.	Bajic D, Wiens F, Wintergerst E, Deyaert S, Baudot A, Van den Abbeele P.	Nutrients	10.3390/nu15071701	2023
	Intestinal Barrier Impairment Induced by Gut Microbiome and Its Metabolites in School-Age Children with Zinc Deficiency.	Chai X, Chen X, Yan T, Zhao Q, Hu B, Jiang Z, Guo W, Zhang Y.	Nutrients	10.3390/nu16091289	2024
	Unveiling the connection between gut microbiome and metabolic health in individuals with chronic spinal cord injury.	Li J, Barnes S, Lefkowitz E, Yarar-Fisher C.	Physiol Genomics	10.1152/physiolgenomics.00107.2023	2024
	Intestinal microbiota and allergic diseases: A systematic review.	Melli LC, do Carmo-Rodrigues MS, Araujo-Filho HB, Sole D, de Morais MB.	Allergol Immunopathol (Madr)	10.1016/j.aller.2015.01.013	2016
	2-Fucosyllactose Metabolism by Bifidobacteria Promotes Lactobacilli Growth in Co-Culture.	Nogacka AM, Cuesta I, Gueimonde M, de Los Reyes-Gavilan CG.	Microorganisms	10.3390/microorganisms11112659	2023
Pathogenicity	Therapeutic and Preventive Effect of Orally Administered Prebiotics on Atopic Dermatitis in a Mouse Model.	Kang M, Jung JH, Kim JY, Hong SH, Her Y.	Allergy Asthma Immunol Res	10.4168/aair.2023.15.3.303	2023
	Comparative prebiotic potential of galacto- and fructo-oligosaccharides, native inulin, and acacia gum in Kenyan infant gut microbiota during iron supplementation.	Momo Cabrera P, Rachmuhl C, Derrien M, Bourdet-Sicard R, Lacroix C, Geirnaert A.	ISME Commun	10.1093/ismeco/ycae033	2024
Genetics	Gene-trait matching among Bifidobacterium dentium strains reveals various glycan metabolism loci including a strain-specific fucosyllactose utilization cluster.	Catalano Gonzaga O, McKenna S, O'Neill I, Cotter PD, McAuliffe FM, Coffey A, van Sinderen D, Bottacini F.	Front Microbiol	10.3389/fmicb.2025.1584694	2025
	Galacto-oligosaccharide preconditioning improves metabolic activity and engraftment of Limosilactobacillus reuteri and stimulates osteoblastogenesis ex vivo.	De Bruyn F, Bonnet N, Baruchet M, Sabatier M, Breton I, Bourqui B, Jankovic I, Horcajada MN, Prioult G.	Sci Rep	10.1038/s41598-024-54887-z	2024
	Analysis of Temporal Changes in Growth and Gene Expression for Commensal Gut Microbes in Response to the Polyphenol Naringenin.	Firrman J, Liu L, Argoty GA, Zhang L, Tomasula P, Wang M, Pontious S, Kobori M, Xiao W.	Microbiol Insights	10.1177/1178636118775100	2018
	Construction of a Bioluminescent Labelling Plasmid Vector for Bifidobacteria.	Moon GS, Narbad A.	Korean J Food Sci Anim Resour	10.5851/kosfa.2018.e17	2018
Pathogenicity	Co-Culture with Bifidobacterium catenulatum Improves the Growth, Gut Colonization, and Butyrate Production of Faecalibacterium prausnitzii: In Vitro and In Vivo Studies.	Kim H, Jeong Y, Kang S, You HJ, Ji GE.	Microorganisms	10.3390/microorganisms8050788	2020
	Distinct Gut Microbiota in Patients with Asymptomatic Hyperuricemia: A Potential Protector against Gout Development.	Kim HW, Yoon EJ, Jeong SH, Park MC.	Yonsei Med J	10.3349/ymj.2022.63.3.241	2022
	Characterisation of Indian gut microbiome for B-vitamin production and its comparison with Chinese cohort.	Chandel N, Somvanshi PR, Thakur V.	Br J Nutr	10.1017/s0007114523002179	2024
	Tea Consumption and Gut Microbiome in Older Chinese Adults.	Wang L, Shu XO, Cai H, Yang Y, Xu W, Wu J, Cai Q, Zheng W, Yu D.	J Nutr	10.1016/j.tjnut.2022.12.002	2023
Phylogeny	Distinct gut microbiomes in Thai patients with colorectal polyps.	Intarajak T, Udomchaiprasertkul W, Khoiri AN, Sutheeworapong S, Kusonmano K, Kittichotirat W, Thammarongtham C, Cheevadhanarak S.	World J Gastroenterol	10.3748/wjg.v30.i27.3336	2024
	Exploring the Potential of Oral Microbiome Biomarkers for Colorectal Cancer Diagnosis and Prognosis: A Systematic Review.	Negrut RL, Cote A, Maghiar AM.	Microorganisms	10.3390/microorganisms11061586	2023
	Effect of fructooligosaccharides and galactooligosaccharides on the folate production of some folate-producing bacteria in media cultures or milk	Padalino M, Perez-Conesa D, Lopez-Nicolas R, Frontela-Saseta C, Ros-Berruezo G.	Int Dairy J	10.1016/j.idairyj.2012.06.006	2012
	The novel immunobiotic Clostridium butyricum S-45-5 displays broad-spectrum antiviral activity in vitro and in vivo by inducing immune modulation.	Chathuranga K, Shin Y, Uddin MB, Paek J, Chathuranga WAG, Seong Y, Bai L, Kim H, Shin JH, Chang YH, Lee JS.	Front Immunol	10.3389/fimmu.2023.1242183	2023
	In-depth characterization of a selection of gut commensal bacteria reveals their functional capacities to metabolize dietary carbohydrates with prebiotic potential.	Bedu-Ferrari C, Biscarrat P, Pepke F, Vati S, Chaudemanche C, Castelli F, Chollet C, Rue O, Hennequet-Antier C, Langella P, Cherbuy C.	mSystems	10.1128/msystems.01401-23	2024
	Sugar Composition of Thai Desserts and Their Impact on the Gut Microbiome in Healthy Volunteers: A Randomized Controlled Trial.	Senaprom S, Namjud N, Ondee T, Bumrungpert A, Pongpirul K.	Nutrients	10.3390/nu16223933	2024
Enzymology	Ethnic diversity of gut microbiota: species characterization of Bacteroides fragilis group and genus Bifidobacterium in healthy Belgian adults, and comparison with data from Japanese subjects.	Ishikawa E, Matsuki T, Kubota H, Makino H, Sakai T, Oishi K, Kushiro A, Fujimoto J, Watanabe K, Watanuki M, Tanaka R.	J Biosci Bioeng	10.1016/j.jbiosc.2013.02.010	2013
Metabolism	Impacts of Cigarette Smoking Status on Metabolomic and Gut Microbiota Profile in Male Patients With Coronary Artery Disease: A Multi-Omics Study.	Hu X, Fan Y, Li H, Zhou R, Zhao X, Sun Y, Zhang S.	Front Cardiovasc Med	10.3389/fcvm.2021.766739	2021
	Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses.	Iwase SC, Osawe S, Happel A-U, Gray CM, Holmes SP, Blackburn JM, Abimiku A, Jaspan HB.	Microbiol Spectr	10.1128/spectrum.03190-23	2024
Pathogenicity	The inhibitory effect of polyphenols on human gut microbiota.	Duda-Chodak A.	J Physiol Pharmacol		2012
	Phenolic Compounds Present in Yerba Mate Potentially Increase Human Health: A Critical Review.	de Vasconcellos AC, Frazzon J, Zapata Norena CP.	Plant Foods Hum Nutr	10.1007/s11130-022-01008-8	2022
	The role of Bifidobacterium in longevity and the future of probiotics.	Ku S, Haque MA, Jang MJ, Ahn J, Choe D, Jeon JI, Park MS.	Food Sci Biotechnol	10.1007/s10068-024-01631-y	2024
Metabolism	Effective bifidogenic growth factors cyclo-Val-Leu and cyclo-Val-Ile produced by Bacillus subtilis C-3102 in the human colonic microbiota model.	Hatanaka M, Morita H, Aoyagi Y, Sasaki K, Sasaki D, Kondo A, Nakamura T.	Sci Rep	10.1038/s41598-020-64374-w	2020
Phylogeny	Molecular monitoring of the development of intestinal microbiota in Japanese infants.	Tsuji H, Oozeer R, Matsuda K, Matsuki T, Ohta T, Nomoto K, Tanaka R, Kawashima M, Kawashima K, Nagata S, Yamashiro Y.	Benef Microbes	10.3920/bm2011.0038	2012
	Effects of Gut Microbiome Modulation on Reducing Adverse Health Outcomes among Elderly and Diabetes Patients during the COVID-19 Pandemic: A Randomised, Double-Blind, Placebo-Controlled Trial (IMPACT Study).	Wong MCS, Zhang L, Ching JYL, Mak JWY, Huang J, Wang S, Mok CKP, Wong A, Chiu OL, Fung YT, Cheong PK, Tun HM, Ng SC, Chan FKL.	Nutrients	10.3390/nu15081982	2023
	Gut microbiome pattern in adolescents with functional gastrointestinal disease.	Nafarin AR, Hegar B, Sjakti HA, Vandenplas Y.	Int J Pediatr Adolesc Med	10.1016/j.ijpam.2019.01.005	2019
	Oral Candida administration in a Clostridium difficile mouse model worsens disease severity but is attenuated by Bifidobacterium.	Panpetch W, Somboonna N, Palasuk M, Hiengrach P, Finkelman M, Tumwasorn S, Leelahavanichkul A.	PLoS One	10.1371/journal.pone.0210798	2019
	2'-Fucosyllactose Increases the Abundance of Blautia in the Presence of Extracellular Fucosidase-Possessing Bacteria.	Horigome A, Hashikura N, Yoshida K, Xiao JZ, Odamaki T.	Front Microbiol	10.3389/fmicb.2022.913624	2022
	Short term supplementation with cranberry extract modulates gut microbiota in human and displays a bifidogenic effect.	Lessard-Lord J, Roussel C, Lupien-Meilleur J, Genereux P, Richard V, Guay V, Roy D, Desjardins Y.	NPJ Biofilms Microbiomes	10.1038/s41522-024-00493-w	2024
	The Effect of Human Milk Oligosaccharides and Bifidobacterium longum subspecies infantis Bi-26 on Simulated Infant Gut Microbiome and Metabolites.	Salli K, Hirvonen J, Anglenius H, Hibberd AA, Ahonen I, Saarinen MT, Maukonen J, Ouwehand AC.	Microorganisms	10.3390/microorganisms11061553	2023
Phylogeny	Gut Microbiota Signature of Obese Adults Across Different Classifications.	Hu J, Guo P, Mao R, Ren Z, Wen J, Yang Q, Yan T, Yu J, Zhang T, Liu Y.	Diabetes Metab Syndr Obes	10.2147/dmso.s387523	2022
	Studies of the Impact of the Bifidobacterium Species on Inducible Nitric Oxide Synthase Expression and Nitric Oxide Production in Murine Macrophages of the BMDM Cell Line.	Zablocka A, Jakubczyk D, Leszczynska K, Pacyga-Prus K, Macala J, Gorska S.	Probiotics Antimicrob Proteins	10.1007/s12602-023-10093-3	2024
Genetics	The mutL Gene as a Genome-Wide Taxonomic Marker for High Resolution Discrimination of Lactiplantibacillus plantarum and Its Closely Related Taxa.	Huang CH, Chen CC, Lin YC, Chen CH, Lee AY, Liou JS, Gu CT, Huang L.	Microorganisms	10.3390/microorganisms9081570	2021
Genetics	Gut microbial composition and functionality of school-age Mexican population with metabolic syndrome and type-2 diabetes mellitus using shotgun metagenomic sequencing.	Carrizales-Sanchez AK, Tamez-Rivera O, Garcia-Gamboa R, Garcia-Cayuela T, Rodriguez-Gutierrez NA, Elizondo-Montemayor L, Garcia-Rivas G, Pacheco A, Hernandez-Brenes C, Senes-Guerrero C.	Front Pediatr	10.3389/fped.2023.1193832	2023
	The gut microbial diversity of colon cancer patients and the clinical significance.	He T, Cheng X, Xing C.	Bioengineered	10.1080/21655979.2021.1972077	2021
	Resistome and microbial profiling of pediatric patient's gut infected with multidrug-resistant diarrhoeagenic Enterobacteriaceae using next-generation sequencing; the first study from Pakistan.	Afridi OK, Ali J, Chang JH.	Libyan J Med	10.1080/19932820.2021.1915615	2021
Phylogeny	A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer.	Yuan D, Tao Y, Wang H, Wang J, Cao Y, Cao W, Pan S, Yu Z.	Invest New Drugs	10.1007/s10637-022-01263-1	2022
	Celiac disease gut microbiome studies in the third millennium: reviewing the findings and gaps of available literature.	Luz VCC, Pereira SG.	Front Med Technol	10.3389/fmedt.2024.1413637	2024
	Prebiotic Properties of Non-Fructosylated alpha-Galactooligosaccharides from PEA (Pisum sativum L.) Using Infant Fecal Slurries.	Marin-Manzano MDC, Hernandez-Hernandez O, Diez-Municio M, Delgado-Andrade C, Moreno FJ, Clemente A.	Foods	10.3390/foods9070921	2020
	Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits.	Yersin S, Garneau JR, Schneeberger PHH, Osman KA, Cercamondi CI, Muhummed AM, Tschopp R, Zinsstag J, Vonaesch P.	Sci Rep	10.1038/s41598-023-47748-8	2023
	Acquiring bifidobacteria species from formula-fed and breast-fed newborns: identifying, quantifying and creating an antibiogram.	Kammara R, Nellikka A.	Access Microbiol	10.1099/acmi.0.000590.v3	2023
Pathogenicity	Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10 attenuate D-galactosamine-induced liver injury by modifying the gut microbiota.	Fang D, Shi D, Lv L, Gu S, Wu W, Chen Y, Guo J, Li A, Hu X, Guo F, Ye J, Li Y, Li L.	Sci Rep	10.1038/s41598-017-09395-8	2017
	Bioactive Components in Fruit Interact with Gut Microbes.	Jin Y, Chen L, Yu Y, Hussain M, Zhong H.	Biology (Basel)	10.3390/biology12101333	2023
	Fecal Bacterial Community and Metagenome Function in Asians with Type 2 Diabetes, According to Enterotypes.	Wu X, Park S.	Biomedicines	10.3390/biomedicines10112998	2022
Enzymology	Dissimilarity in the occurrence of Bifidobacteriaceae in vaginal and perianal microbiota in women with bacterial vaginosis.	Swidsinski A, Dorffel Y, Loening-Baucke V, Mendling W, Schilling J, Patterson JL, Verstraelen H.	Anaerobe	10.1016/j.anaerobe.2010.06.011	2010
	Bifidobacterium breve PRL2020: Antibiotic-Resistant Profile and Genomic Detection of Antibiotic Resistance Determinants.	Di Pierro F, Campedelli I, De Marta P, Fracchetti F, Del Casale A, Cavecchia I, Matera M, Cazzaniga M, Bertuccioli A, Guasti L, Zerbinati N.	Microorganisms	10.3390/microorganisms11071649	2023
Pathogenicity	Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes.	Moser B, Moore D, Khadka B, Lyons C, Foxall T, Andam CP, Parker CJ, Ochin C, Garelnabi M, Sevigny J, Thomas WK, Bigornia S, Dao MC.	Front Nutr	10.3389/fnut.2022.1059163	2022
	Carbohydrate Staple Food Modulates Gut Microbiota of Mongolians in China.	Li J, Hou Q, Zhang J, Xu H, Sun Z, Menghe B, Zhang H.	Front Microbiol	10.3389/fmicb.2017.00484	2017
	The Role of Dysbiotic Oral Microbiota in Cardiometabolic Diseases: A Narrative Review.	Le S, Cecchin-Albertoni C, Thomas C, Kemoun P, Minty M, Blasco-Baque V.	Diagnostics (Basel)	10.3390/diagnostics13203184	2023
	Predominant genera of fecal microbiota in children with atopic dermatitis are not altered by intake of probiotic bacteria Lactobacillus acidophilus NCFM and Bifidobacterium animalis subsp. lactis Bi-07.	Larsen N, Vogensen FK, Gobel R, Michaelsen KF, Abu Al-Soud W, Abu Al-Soud W, Sorensen SJ, Hansen LH, Jakobsen M.	FEMS Microbiol Ecol	10.1111/j.1574-6941.2010.01024.x	2011
Phylogeny	Differentiation of Bifidobacterium species using partial RNA polymerase {beta}-subunit (rpoB) gene sequences.	Kim BJ, Kim HY, Yun YJ, Kim BJ, Kook YH.	Int J Syst Evol Microbiol	10.1099/ijs.0.020339-0	2010
Enzymology	Specificity and sensitivity evaluation of novel and existing Bacteroidales and Bifidobacteria-specific PCR assays on feces and sewage samples and their application for microbial source tracking in Ireland.	Dorai-Raj S, O' Grady J, Colleran E.	Water Res	10.1016/j.watres.2009.08.050	2009
	Early-Life Development of the Bifidobacterial Community in the Infant Gut.	Saturio S, Nogacka AM, Suarez M, Fernandez N, Mantecon L, Mancabelli L, Milani C, Ventura M, de Los Reyes-Gavilan CG, Solis G, Arboleya S, Gueimonde M.	Int J Mol Sci	10.3390/ijms22073382	2021
Enzymology	Human milk and mucosa-associated disaccharides impact on cultured infant fecal microbiota.	Rubio-Del-Campo A, Alcantara C, Collado MC, Rodriguez-Diaz J, Yebra MJ.	Sci Rep	10.1038/s41598-020-68718-4	2020
	Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country.	Dwiyanto J, Hussain MH, Reidpath D, Ong KS, Qasim A, Lee SWH, Lee SM, Foo SC, Chong CW, Rahman S.	Sci Rep	10.1038/s41598-021-82311-3	2021
	Microbiota profile in new-onset pediatric Crohn's disease: data from a non-Western population.	El Mouzan MI, Winter HS, Assiri AA, Korolev KS, Al Sarkhy AA, Dowd SE, Al Mofarreh MA, Menon R.	Gut Pathog	10.1186/s13099-018-0276-3	2018
Enzymology	Screening for plasmids among human bifidobacteria species: sequencing and analysis of pBC1 from Bifidobacterium catenulatum L48.	Alvarez-Martin P, Florez AB, Mayo B.	Plasmid	10.1016/j.plasmid.2006.07.004	2007
	Host-microbial co-metabolites modulated by human milk oligosaccharides relate to reduced risk of respiratory tract infections.	Martin FP, Tytgat HLP, Krogh Pedersen H, Moine D, Eklund AC, Berger B, Sprenger N.	Front Nutr	10.3389/fnut.2022.935711	2022
	Protective role of supplement with foreign Bifidobacterium and Lactobacillus in experimental hepatic ischemia-reperfusion injury.	Xing HC, Li LJ, Xu KJ, Shen T, Chen YB, Sheng JF, Chen Y, Fu SZ, Chen CL, Wang JG, Yan D, Dai FW, Zheng SS.	J Gastroenterol Hepatol	10.1111/j.1440-1746.2006.04306.x	2006
Phylogeny	Molecularly assessed shifts of Bifidobacterium ssp. and less diverse microbial communities are characteristic of 5-year-old allergic children.	Stsepetova J, Sepp E, Julge K, Vaughan E, Mikelsaar M, de Vos WM.	FEMS Immunol Med Microbiol	10.1111/j.1574-695x.2007.00306.x	2007
Biotechnology	In vitro evaluation of the probiotic properties of human intestinal Bifidobacterium species and selection of new probiotic candidates.	Delgado S, O'Sullivan E, Fitzgerald G, Mayo B.	J Appl Microbiol	10.1111/j.1365-2672.2007.03642.x	2008
	Breast milk: a source of bifidobacteria for infant gut development and maturation?	Gueimonde M, Laitinen K, Salminen S, Isolauri E.	Neonatology	10.1159/000100088	2007
	Feed Insects as a Reservoir of Granadaene-Producing Lactococci.	Neuzil-Bunesova V, Ramirez Garcia A, Modrackova N, Makovska M, Sabolova M, Sproer C, Bunk B, Blom J, Schwab C.	Front Microbiol	10.3389/fmicb.2022.848490	2022
	Transcriptome analysis of Lactobacillus rhamnosus GG strain treated with prebiotic - bovine lactoferrin under a cold environment.	Liu ZS, Lin CF, Chen PW.	J Food Drug Anal	10.38212/2224-6614.3369	2021
Pathogenicity	Induction of acid resistance in Bifidobacterium: a mechanism for improving desirable traits of potentially probiotic strains.	Collado MC, Sanz Y.	J Appl Microbiol	10.1111/j.1365-2672.2007.03342.x	2007
Metabolism	Selection of phytate-degrading human bifidobacteria and application in whole wheat dough fermentation.	Palacios MC, Haros M, Rosell CM, Sanz Y.	Food Microbiol	10.1016/j.fm.2007.06.001	2008
Phylogeny	Quantitative assessment of faecal bifidobacterial populations by real-time PCR using lanthanide probes.	Gueimonde M, Debor L, Tolkko S, Jokisalo E, Salminen S.	J Appl Microbiol	10.1111/j.1365-2672.2006.03145.x	2007
	Model Selection Reveals the Butyrate-Producing Gut Bacterium Coprococcus eutactus as Predictor for Language Development in 3-Year-Old Rural Ugandan Children.	Kort R, Schlosser J, Vazquez AR, Atukunda P, Muhoozi GKM, Wacoo AP, Sybesma WFH, Westerberg AC, Iversen PO, Schoen ED.	Front Microbiol	10.3389/fmicb.2021.681485	2021
Pathogenicity	Apigenin Impacts the Growth of the Gut Microbiota and Alters the Gene Expression of Enterococcus.	Wang M, Firrman J, Zhang L, Arango-Argoty G, Tomasula P, Liu L, Xiao W, Yam K.	Molecules	10.3390/molecules22081292	2017
	Comparative Metagenomics Reveals Microbial Communities and Their Associated Functions in Two Types of Fuzhuan Brick Tea.	Wang X, Du G, Chen H, Zeng X, Liu B, Guo C, Sheng Q, Yuan Y, Yue T.	Front Microbiol	10.3389/fmicb.2021.705681	2021
	Longitudinal Survey of Fecal Microbiota in Healthy Dogs Administered a Commercial Probiotic.	Ciaravolo S, Martinez-Lopez LM, Allcock RJN, Woodward AP, Mansfield C.	Front Vet Sci	10.3389/fvets.2021.664318	2021
	Iron Supplementation at the Crossroads of Nutrition and Gut Microbiota: The State of the Art.	Puga AM, Samaniego-Vaesken ML, Montero-Bravo A, Ruperto M, Partearroyo T, Varela-Moreiras G.	Nutrients	10.3390/nu14091926	2022
	Adhesion properties and competitive pathogen exclusion ability of bifidobacteria with acquired acid resistance.	Collado MC, Gueimonde M, Sanz Y, Salminen S.	J Food Prot	10.4315/0362-028x-69.7.1675	2006
Phylogeny	Differences in the composition of intestinal Bifidobacterium species and the development of allergic diseases in infants in rural Japan.	Suzuki S, Shimojo N, Tajiri Y, Kumemura M, Kohno Y.	Clin Exp Allergy	10.1111/j.1365-2222.2007.02676.x	2007
Genetics	Gut Microbial SNPs Induced by High-Fiber Diet Dominate Nutrition Metabolism and Environmental Adaption of Faecalibacterium prausnitzii in Obese Children.	Li H, Zhao L, Zhang M.	Front Microbiol	10.3389/fmicb.2021.683714	2021
	Impact of Gut Microbiota on Host Aggression: Potential Applications for Therapeutic Interventions Early in Development.	Mikami K, Watanabe N, Tochio T, Kimoto K, Akama F, Yamamoto K.	Microorganisms	10.3390/microorganisms11041008	2023
	Hesperidin Bioavailability Is Increased by the Presence of 2S-Diastereoisomer and Micronization-A Randomized, Crossover and Double-Blind Clinical Trial.	Crescenti A, Caimari A, Alcaide-Hidalgo JM, Marine-Casado R, Valls RM, Companys J, Salamanca P, Calderon-Perez L, Pla-Paga L, Pedret A, Delpino-Rius A, Herrero P, Samarra I, Arola L, Sola R, Del Bas JM.	Nutrients	10.3390/nu14122481	2022
	Multi-Omic Analyses Reveal Bifidogenic Effect and Metabolomic Shifts in Healthy Human Cohort Supplemented With a Prebiotic Dietary Fiber Blend.	Kang JW, Tang X, Walton CJ, Brown MJ, Brewer RA, Maddela RL, Zheng JJ, Agus JK, Zivkovic AM.	Front Nutr	10.3389/fnut.2022.908534	2022
	Changes in Phenolic Compounds and Antioxidant Activity of Fruit Musts and Fruit Wines during Simulated Digestion.	Tarko T, Duda-Chodak A, Soszka A.	Molecules	10.3390/molecules25235574	2020
	Colonization of Supplemented Bifidobacterium breve M-16V in Low Birth Weight Infants and Its Effects on Their Gut Microbiota Weeks Post-administration.	Horigome A, Hisata K, Odamaki T, Iwabuchi N, Xiao JZ, Shimizu T.	Front Microbiol	10.3389/fmicb.2021.610080	2021
	The Young Age and Plant-Based Diet Hypothesis for Low SARS-CoV-2 Infection and COVID-19 Pandemic in Sub-Saharan Africa.	Losso JN, Losso MN, Toc M, Inungu JN, Finley JW.	Plant Foods Hum Nutr	10.1007/s11130-021-00907-6	2021
	Effect of maternal consumption of lactobacillus GG on transfer and establishment of fecal bifidobacterial microbiota in neonates.	Gueimonde M, Sakata S, Kalliomaki M, Isolauri E, Benno Y, Salminen S.	J Pediatr Gastroenterol Nutr	10.1097/01.mpg.0000189346.25172.fd	2006
	Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach.	Feehily C, O'Neill IJ, Walsh CJ, Moore RL, Killeen SL, Geraghty AA, Lawton EM, Byrne D, Sanchez-Gallardo R, Nori SRC, Nielsen IB, Wortmann E, Matthews E, O'Flaherty R, Rudd PM, Groeger D, Shanahan F, Saldova R, McAuliffe FM, Van Sinderen D, Cotter PD.	Nat Commun	10.1038/s41467-023-38694-0	2023
	Production, Storage Stability, and Susceptibility Testing of Reuterin and Its Impact on the Murine Fecal Microbiome and Volatile Organic Compound Profile.	Castellani C, Obermuller B, Kienesberger B, Singer G, Peterbauer C, Grabherr R, Mayrhofer S, Klymiuk I, Horvath A, Stadlbauer V, Russmayer H, Miekisch W, Fuchs P, Till H, Heinl S.	Front Microbiol	10.3389/fmicb.2021.699858	2021
	Interplay between weight loss and gut microbiota composition in overweight adolescents.	Santacruz A, Marcos A, Warnberg J, Marti A, Martin-Matillas M, Campoy C, Moreno LA, Veiga O, Redondo-Figuero C, Garagorri JM, Azcona C, Delgado M, Garcia-Fuentes M, Collado MC, Sanz Y, EVASYON Study Group.	Obesity (Silver Spring)	10.1038/oby.2009.112	2009
	Alteration of the Gut Microbiome in Chronic Kidney Disease Patients and Its Association With Serum Free Immunoglobulin Light Chains.	Liu F, Xu X, Chao L, Chen K, Shao A, Sun D, Hong Y, Hu R, Jiang P, Zhang N, Xiao Y, Yan F, Feng N.	Front Immunol	10.3389/fimmu.2021.609700	2021
	Strain-level screening of human gut microbes identifies Blautia producta as a new anti-hyperlipidemic probiotic.	Xu W, Yu J, Yang Y, Li Z, Zhang Y, Zhang F, Wang Q, Xie Y, Zhao B, Wu C.	Gut Microbes	10.1080/19490976.2023.2228045	2023
	The genus bifidobacterium: From genomics to functionality of an important component of the mammalian gut microbiota running title: Bifidobacterial adaptation to and interaction with the host.	Alessandri G, van Sinderen D, Ventura M.	Comput Struct Biotechnol J	10.1016/j.csbj.2021.03.006	2021
Enzymology	Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR.	Malinen E, Rinttila T, Kajander K, Matto J, Kassinen A, Krogius L, Saarela M, Korpela R, Palva A.	Am J Gastroenterol	10.1111/j.1572-0241.2005.40312.x	2005
Phylogeny	Lactobacillus paracasei DTA81, a cholesterol-lowering strain having immunomodulatory activity, reveals gut microbiota regulation capability in BALB/c mice receiving high-fat diet.	Tarrah A, Dos Santos Cruz BC, Sousa Dias R, da Silva Duarte V, Pakroo S, Licursi de Oliveira L, Gouveia Peluzio MC, Corich V, Giacomini A, Oliveira de Paula S.	J Appl Microbiol	10.1111/jam.15058	2021
Pathogenicity	Effect of natural polyphenols in Chinese herbal medicine on obesity and diabetes: Interactions among gut microbiota, metabolism, and immunity.	Chen K, Gao Z, Ding Q, Tang C, Zhang H, Zhai T, Xie W, Jin Z, Zhao L, Liu W.	Front Nutr	10.3389/fnut.2022.962720	2022
	In vitro Selection of Probiotics for Microbiota Modulation in Normal-Weight and Severely Obese Individuals: Focus on Gas Production and Interaction With Intestinal Epithelial Cells.	Nogacka AM, de Los Reyes-Gavilan CG, Arboleya S, Ruas-Madiedo P, Martinez-Faedo C, Suarez A, He F, Harata G, Endo A, Salazar N, Gueimonde M.	Front Microbiol	10.3389/fmicb.2021.630572	2021
	Galacto-Oligosaccharide RP-G28 Improves Multiple Clinical Outcomes in Lactose-Intolerant Patients.	Chey W, Sandborn W, Ritter AJ, Foyt H, Azcarate-Peril MA, Savaiano DA.	Nutrients	10.3390/nu12041058	2020
Genetics	Species-Level Analysis of the Human Gut Microbiome Shows Antibiotic Resistance Genes Associated With Colorectal Cancer.	Liu C, Li Z, Ding J, Zhen H, Fang M, Nie C.	Front Microbiol	10.3389/fmicb.2021.765291	2021
	Genus- and species-specific PCR primers for the detection and identification of bifidobacteria.	Matsuki T, Watanabe K, Tanaka R.	Curr Issues Intest Microbiol		2003
	Heat-inactivated Bifidobacterium adolescentis ameliorates colon senescence through Paneth-like-cell-mediated stem cell activation.	Qi Y, He J, Zhang Y, Ge Q, Wang Q, Chen L, Xu J, Wang L, Chen X, Jia D, Lin Y, Xu C, Zhang Y, Hou T, Si J, Chen S, Wang L.	Nat Commun	10.1038/s41467-023-41827-0	2023
Enzymology	Extension of the viral ecology in humans using viral profile hidden Markov models.	Bzhalava Z, Hultin E, Dillner J.	PLoS One	10.1371/journal.pone.0190938	2018
Genetics	Milk glycan metabolism by intestinal bifidobacteria: insights from comparative genomics.	Arzamasov AA, Osterman AL.	Crit Rev Biochem Mol Biol	10.1080/10409238.2023.2182272	2022
Enzymology	Long-term colonization exceeding six years from early infancy of Bifidobacterium longum subsp. longum in human gut.	Oki K, Akiyama T, Matsuda K, Gawad A, Makino H, Ishikawa E, Oishi K, Kushiro A, Fujimoto J.	BMC Microbiol	10.1186/s12866-018-1358-6	2018
	Disrupted intestinal microbiota and intestinal inflammation in children with cystic fibrosis and its restoration with Lactobacillus GG: a randomised clinical trial.	Bruzzese E, Callegari ML, Raia V, Viscovo S, Scotto R, Ferrari S, Morelli L, Buccigrossi V, Lo Vecchio A, Ruberto E, Guarino A.	PLoS One	10.1371/journal.pone.0087796	2014
	Effects of 8 Weeks of 2S-Hesperidin Supplementation on Performance in Amateur Cyclists.	Martinez-Noguera FJ, Marin-Pagan C, Carlos-Vivas J, Alcaraz PE.	Nutrients	10.3390/nu12123911	2020
	Combination of poly-gamma-glutamic acid and galactooligosaccharide improves intestinal microbiota, defecation status, and relaxed mood in humans: a randomized, double-blind, parallel-group comparison trial.	Umeda K, Ikeda A, Uchida R, Sasahara I, Mine T, Murakami H, Kameyama K.	Biosci Microbiota Food Health	10.12938/bmfh.2021-084	2023
	Microbial colonization programs are structured by breastfeeding and guide healthy respiratory development.	Shenhav L, Fehr K, Reyna ME, Petersen C, Dai DLY, Dai R, Breton V, Rossi L, Smieja M, Simons E, Silverman MA, Levy M, Bode L, Field CJ, Marshall JS, Moraes TJ, Mandhane PJ, Turvey SE, Subbarao P, Surette MG, Azad MB.	Cell	10.1016/j.cell.2024.07.022	2024
Metabolism	Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients.	Kerckhoffs AP, Samsom M, van der Rest ME, de Vogel J, Knol J, Ben-Amor K, Akkermans LM.	World J Gastroenterol	10.3748/wjg.15.2887	2009
	The relationship between gut microbiome and human diseases: mechanisms, predisposing factors and potential intervention.	Shabani M, Ghoshehy A, Mottaghi AM, Chegini Z, Kerami A, Shariati A, Taati Moghadam M.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1516010	2025
Phylogeny	Fecal Microbiotas of Indonesian and New Zealand Children Differ in Complexity and Bifidobacterial Taxa during the First Year of Life.	Lawley B, Otal A, Moloney-Geany K, Diana A, Houghton L, Heath AM, Taylor RW, Tannock GW.	Appl Environ Microbiol	10.1128/aem.01105-19	2019
	Molecular microbial analysis of Bifidobacterium isolates from different environments by the species-specific amplified ribosomal DNA restriction analysis (ARDRA).	Ventura M, Elli M, Reniero R, Zink R.	FEMS Microbiol Ecol	10.1111/j.1574-6941.2001.tb00831.x	2001
	Mother-to-infant transmission of intestinal bifidobacterial strains has an impact on the early development of vaginally delivered infant's microbiota.	Makino H, Kushiro A, Ishikawa E, Kubota H, Gawad A, Sakai T, Oishi K, Martin R, Ben-Amor K, Knol J, Tanaka R.	PLoS One	10.1371/journal.pone.0078331	2013
	Variation of Carbohydrate-Active Enzyme Patterns in the Gut Microbiota of Italian Healthy Subjects and Type 2 Diabetes Patients.	Soverini M, Turroni S, Biagi E, Quercia S, Brigidi P, Candela M, Rampelli S.	Front Microbiol	10.3389/fmicb.2017.02079	2017
Metabolism	Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers.	Baxter NT, Schmidt AW, Venkataraman A, Kim KS, Waldron C, Schmidt TM.	mBio	10.1128/mbio.02566-18	2019
	Assessing the antimicrobial activities of Ocins.	Choyam S, Lokesh D, Kempaiah BB, Kammara R.	Front Microbiol	10.3389/fmicb.2015.01034	2015
	Paediatricians play a key role in preventing early harmful events that could permanently influence the development of the gut microbiota in childhood.	Goulet O, Hojsak I, Kolacek S, Pop TL, Cokugras FC, Zuccotti G, Pettoello-Mantovani M, Fabiano V.	Acta Paediatr	10.1111/apa.14900	2019
	Building Robust Assemblages of Bacteria in the Human Gut in Early Life.	Tannock GW.	Appl Environ Microbiol	10.1128/aem.01449-21	2021
Genetics	Association of symptoms with gastrointestinal microbiota in irritable bowel syndrome.	Malinen E, Krogius-Kurikka L, Lyra A, Nikkila J, Jaaskelainen A, Rinttila T, Vilpponen-Salmela T, von Wright AJ, Palva A.	World J Gastroenterol	10.3748/wjg.v16.i36.4532	2010
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
	Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity.	Wilson BC, Vatanen T, Jayasinghe TN, Leong KSW, Derraik JGB, Albert BB, Chiavaroli V, Svirskis DM, Beck KL, Conlon CA, Jiang Y, Schierding W, Holland DJ, Cutfield WS, O'Sullivan JM.	Microbiome	10.1186/s40168-021-01060-7	2021
	Mapping the early life gut microbiome in neonates with critical congenital heart disease: multiomics insights and implications for host metabolic and immunological health.	Huang Y, Lu W, Zeng M, Hu X, Su Z, Liu Y, Liu Z, Yuan J, Li L, Zhang X, Huang L, Hu W, Wang X, Li S, Zhang H.	Microbiome	10.1186/s40168-022-01437-2	2022
	In Vitro Evaluation of Different Prebiotics on the Modulation of Gut Microbiota Composition and Function in Morbid Obese and Normal-Weight Subjects.	Nogacka AM, Salazar N, Arboleya S, Ruas-Madiedo P, Mancabelli L, Suarez A, Martinez-Faedo C, Ventura M, Tochio T, Hirano K, Endo A, G de Los Reyes-Gavilan C, Gueimonde M.	Int J Mol Sci	10.3390/ijms21030906	2020
	Gut microbiome meta-analysis reveals dysbiosis is independent of body mass index in predicting risk of obesity-associated CRC.	Greathouse KL, White JR, Padgett RN, Perrotta BG, Jenkins GD, Chia N, Chen J.	BMJ Open Gastroenterol	10.1136/bmjgast-2018-000247	2019
Genetics	Bacterial community structure alterations within the colorectal cancer gut microbiome.	Loftus M, Hassouneh SA, Yooseph S.	BMC Microbiol	10.1186/s12866-021-02153-x	2021
Pathogenicity	Prebiotic UG1601 mitigates constipation-related events in association with gut microbiota: A randomized placebo-controlled intervention study.	Chu JR, Kang SY, Kim SE, Lee SJ, Lee YC, Sung MK.	World J Gastroenterol	10.3748/wjg.v25.i40.6129	2019
	The genome of Bifidobacterium pseudocatenulatum IPLA 36007, a human intestinal strain with isoflavone-activation activity.	Alegria A, Delgado S, Guadamuro L, Florez AB, Felis GE, Torriani S, Mayo B.	Gut Pathog	10.1186/1757-4749-6-31	2014
	Digoxigenin-labeled deoxyribonucleic acid probes for the enumeration of bifidobacteria in fecal samples.	Kaneko T, Kurihara H.	J Dairy Sci	10.3168/jds.s0022-0302(97)76054-5	1997
Genetics	The Impact of Migration on the Gut Metagenome of South Asian Canadians.	Copeland JK, Chao G, Vanderhout S, Acton E, Wang PW, Benchimol EI, El Sohami A, Croitoru K, Gommerman JL, Guttman DS, GEMINI Research Team.	Gut Microbes	10.1080/19490976.2021.1902705	2021
	Improved cloning vectors for bifidobacteria, based on the Bifidobacterium catenulatum pBC1 replicon.	Alvarez-Martin P, Belen Florez A, Margolles A, del Solar G, Mayo B.	Appl Environ Microbiol	10.1128/aem.00074-08	2008
	Cytokine-specific autoantibodies shape the gut microbiome in autoimmune polyendocrine syndrome type 1.	Petersen AO, Jokinen M, Plichta DR, Liebisch G, Gronwald W, Dettmer K, Oefner PJ, Vlamakis H, Chung DC, Ranki A, Xavier RJ.	J Allergy Clin Immunol	10.1016/j.jaci.2021.03.025	2021
Phylogeny	Exploration of the genomic diversity and core genome of the Bifidobacterium adolescentis phylogenetic group by means of a polyphasic approach.	Duranti S, Turroni F, Milani C, Foroni E, Bottacini F, Dal Bello F, Ferrarini A, Delledonne M, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.02467-12	2013
	Litter Commensal Bacteria Can Limit the Horizontal Gene Transfer of Antimicrobial Resistance to Salmonella in Chickens.	Oladeinde A, Abdo Z, Zwirzitz B, Woyda R, Lakin SM, Press MO, Cox NA, Thomas JC, Looft T, Rothrock MJ, Zock G, Plumblee Lawrence J, Cudnik D, Ritz C, Aggrey SE, Liachko I, Grove JR, Wiersma C.	Appl Environ Microbiol	10.1128/aem.02517-21	2022
Pathogenicity	Oral Microbiota: A Major Player in the Diagnosis of Systemic Diseases.	Thomas C, Minty M, Vinel A, Canceill T, Loubieres P, Burcelin R, Kaddech M, Blasco-Baque V, Laurencin-Dalicieux S.	Diagnostics (Basel)	10.3390/diagnostics11081376	2021
Phylogeny	Diarrhoea-predominant irritable bowel syndrome distinguishable by 16S rRNA gene phylotype quantification.	Lyra A, Rinttila T, Nikkila J, Krogius-Kurikka L, Kajander K, Malinen E, Matto J, Makela L, Palva A.	World J Gastroenterol	10.3748/wjg.15.5936	2009
Metabolism	Autoinducer-2 plays a crucial role in gut colonization and probiotic functionality of Bifidobacterium breve UCC2003.	Christiaen SE, O'Connell Motherway M, Bottacini F, Lanigan N, Casey PG, Huys G, Nelis HJ, van Sinderen D, Coenye T.	PLoS One	10.1371/journal.pone.0098111	2014
Pathogenicity	Mechanisms by which sialylated milk oligosaccharides impact bone biology in a gnotobiotic mouse model of infant undernutrition.	Cowardin CA, Ahern PP, Kung VL, Hibberd MC, Cheng J, Guruge JL, Sundaresan V, Head RD, Barile D, Mills DA, Barratt MJ, Huq S, Ahmed T, Gordon JI.	Proc Natl Acad Sci U S A	10.1073/pnas.1821770116	2019
	Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis.	Duranti S, Milani C, Lugli GA, Mancabelli L, Turroni F, Ferrario C, Mangifesta M, Viappiani A, Sanchez B, Margolles A, van Sinderen D, Ventura M.	Sci Rep	10.1038/srep23971	2016
Enzymology	Fecal excretion of Bifidobacterium infantis 35624 and changes in fecal microbiota after eight weeks of oral supplementation with encapsulated probiotic.	Charbonneau D, Gibb RD, Quigley EM.	Gut Microbes	10.4161/gmic.24196	2013
Genetics	The comparative genomics of Bifidobacterium callitrichos reflects dietary carbohydrate utilization within the common marmoset gut.	Albert K, Rani A, Sela DA.	Microb Genom	10.1099/mgen.0.000183	2018
Metabolism	Ability of bifidobacteria to metabolize chitin-glucan and its impact on the gut microbiota.	Alessandri G, Milani C, Duranti S, Mancabelli L, Ranjanoro T, Modica S, Carnevali L, Statello R, Bottacini F, Turroni F, Ossiprandi MC, Sgoifo A, van Sinderen D, Ventura M.	Sci Rep	10.1038/s41598-019-42257-z	2019
	Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples.	Tarallo S, Ferrero G, Gallo G, Francavilla A, Clerico G, Realis Luc A, Manghi P, Thomas AM, Vineis P, Segata N, Pardini B, Naccarati A, Cordero F.	mSystems	10.1128/msystems.00289-19	2019
	Settlers of our inner surface - factors shaping the gut microbiota from birth to toddlerhood.	Laursen MF, Bahl MI, Licht TR.	FEMS Microbiol Rev	10.1093/femsre/fuab001	2021
	Anaerobes and bacterial vaginosis in pregnancy: virulence factors contributing to vaginal colonisation.	Africa CW, Nel J, Stemmet M.	Int J Environ Res Public Health	10.3390/ijerph110706979	2014
	A Multi-omics Approach to Unraveling the Microbiome-Mediated Effects of Arabinoxylan Oligosaccharides in Overweight Humans.	Benitez-Paez A, Kjolbaek L, Gomez Del Pulgar EM, Brahe LK, Astrup A, Matysik S, Schott HF, Krautbauer S, Liebisch G, Boberska J, Claus S, Rampelli S, Brigidi P, Larsen LH, Sanz Y.	mSystems	10.1128/msystems.00209-19	2019
Pathogenicity	Effects of probiotics and antibiotics on the intestinal homeostasis in a computer controlled model of the large intestine.	Rehman A, Heinsen FA, Koenen ME, Venema K, Knecht H, Hellmig S, Schreiber S, Ott SJ.	BMC Microbiol	10.1186/1471-2180-12-47	2012
Enzymology	Identification and quantitation of mucosal and faecal desulfovibrios using real time polymerase chain reaction.	Fite A, Macfarlane GT, Cummings JH, Hopkins MJ, Kong SC, Furrie E, Macfarlane S.	Gut	10.1136/gut.2003.031245	2004
Phylogeny	Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities.	Lewis ZT, Bokulich NA, Kalanetra KM, Ruiz-Moyano S, Underwood MA, Mills DA.	Anaerobe	10.1016/j.anaerobe.2012.12.005	2013
Genetics	mbImpute: an accurate and robust imputation method for microbiome data.	Jiang R, Li WV, Li JJ.	Genome Biol	10.1186/s13059-021-02400-4	2021
	Effect of a multispecies probiotic supplement on quantity of irritable bowel syndrome-related intestinal microbial phylotypes.	Lyra A, Krogius-Kurikka L, Nikkila J, Malinen E, Kajander K, Kurikka K, Korpela R, Palva A.	BMC Gastroenterol	10.1186/1471-230x-10-110	2010
	Polyphenols as Drivers of a Homeostatic Gut Microecology and Immuno-Metabolic Traits of Akkermansia muciniphila: From Mouse to Man.	Rodriguez-Daza MC, de Vos WM.	Int J Mol Sci	10.3390/ijms24010045	2022
	Interactions between the lipidome and genetic and environmental factors in autism.	Yap CX, Henders AK, Alvares GA, Giles C, Huynh K, Nguyen A, Wallace L, McLaren T, Yang Y, Hernandez LM, Gandal MJ, Hansell NK, Cleary D, Grove R, Hafekost C, Harun A, Holdsworth H, Jellett R, Khan F, Lawson LP, Leslie J, Levis Frenk M, Masi A, Mathew NE, Muniandy M, Nothard M, Miller JL, Nunn L, Strike LT, Cadby G, Moses EK, Busselton Health Study Investigators, de Zubicaray GI, Thompson PM, McMahon KL, Wright MJ, Visscher PM, Dawson PA, Dissanayake C, Eapen V, Heussler HS, Whitehouse AJO, Meikle PJ, Wray NR, Gratten J.	Nat Med	10.1038/s41591-023-02271-1	2023
Pathogenicity	Inhibitory activity spectrum of reuterin produced by Lactobacillus reuteri against intestinal bacteria.	Cleusix V, Lacroix C, Vollenweider S, Duboux M, Le Blay G.	BMC Microbiol	10.1186/1471-2180-7-101	2007
	Fecal microbiota composition of breast-fed infants is correlated with human milk oligosaccharides consumed.	Wang M, Li M, Wu S, Lebrilla CB, Chapkin RS, Ivanov I, Donovan SM.	J Pediatr Gastroenterol Nutr	10.1097/mpg.0000000000000752	2015
Metabolism	Varied Pathways of Infant Gut-Associated Bifidobacterium to Assimilate Human Milk Oligosaccharides: Prevalence of the Gene Set and Its Correlation with Bifidobacteria-Rich Microbiota Formation.	Sakanaka M, Gotoh A, Yoshida K, Odamaki T, Koguchi H, Xiao JZ, Kitaoka M, Katayama T.	Nutrients	10.3390/nu12010071	2019
Metabolism	Biochemical Engineering Approaches for Increasing Viability and Functionality of Probiotic Bacteria.	Nguyen HT, Truong DH, Kouhounde S, Ly S, Razafindralambo H, Delvigne F.	Int J Mol Sci	10.3390/ijms17060867	2016
Pathogenicity	Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria.	Jian X, Zhu Y, Ouyang J, Wang Y, Lei Q, Xia J, Guan Y, Zhang J, Guo J, He Y, Wang J, Li J, Lin J, Su M, Li G, Wu M, Qiu L, Xiang J, Xie L, Jia W, Zhou W, Zhou W.	Microbiome	10.1186/s40168-020-00854-5	2020
	Overgrowth of the indigenous gut microbiome and irritable bowel syndrome.	Bye W, Ishaq N, Bolin TD, Duncombe VM, Riordan SM.	World J Gastroenterol	10.3748/wjg.v20.i10.2449	2014
	Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota.	Martin R, Makino H, Cetinyurek Yavuz A, Ben-Amor K, Roelofs M, Ishikawa E, Kubota H, Swinkels S, Sakai T, Oishi K, Kushiro A, Knol J.	PLoS One	10.1371/journal.pone.0158498	2016
Phylogeny	Identification of a new P335 subgroup through molecular analysis of lactococcal phages Q33 and BM13.	Mahony J, Martel B, Tremblay DM, Neve H, Heller KJ, Moineau S, van Sinderen D.	Appl Environ Microbiol	10.1128/aem.00832-13	2013
Metabolism	Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals.	Azcarate-Peril MA, Ritter AJ, Savaiano D, Monteagudo-Mera A, Anderson C, Magness ST, Klaenhammer TR.	Proc Natl Acad Sci U S A	10.1073/pnas.1606722113	2017
	Discovery of a conjugative megaplasmid in Bifidobacterium breve.	Bottacini F, O'Connell Motherway M, Casey E, McDonnell B, Mahony J, Ventura M, van Sinderen D.	Appl Environ Microbiol	10.1128/aem.02871-14	2015
	Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol.	Milani C, Hevia A, Foroni E, Duranti S, Turroni F, Lugli GA, Sanchez B, Martin R, Gueimonde M, van Sinderen D, Margolles A, Ventura M.	PLoS One	10.1371/journal.pone.0068739	2013
Enzymology	Quantitative real-time PCR assays to identify and quantify fecal Bifidobacterium species in infants receiving a prebiotic infant formula.	Haarman M, Knol J.	Appl Environ Microbiol	10.1128/aem.71.5.2318-2324.2005	2005
	Core gene set as the basis of multilocus sequence analysis of the subclass Actinobacteridae.	Adekambi T, Butler RW, Hanrahan F, Delcher AL, Drancourt M, Shinnick TM.	PLoS One	10.1371/journal.pone.0014792	2011
Metabolism	Bifidobacterium bifidum lacto-N-biosidase, a critical enzyme for the degradation of human milk oligosaccharides with a type 1 structure.	Wada J, Ando T, Kiyohara M, Ashida H, Kitaoka M, Yamaguchi M, Kumagai H, Katayama T, Yamamoto K.	Appl Environ Microbiol	10.1128/aem.00149-08	2008
Enzymology	Establishment of intestinal microbiota during early life: a longitudinal, explorative study of a large cohort of Danish infants.	Bergstrom A, Skov TH, Bahl MI, Roager HM, Christensen LB, Ejlerskov KT, Molgaard C, Michaelsen KF, Licht TR.	Appl Environ Microbiol	10.1128/aem.00342-14	2014
	Population dynamics of Bifidobacterium species in human feces during raffinose administration monitored by fluorescence in situ hybridization-flow cytometry.	Dinoto A, Marques TM, Sakamoto K, Fukiya S, Watanabe J, Ito S, Yokota A.	Appl Environ Microbiol	10.1128/aem.01777-06	2006
Metabolism	Variation in consumption of human milk oligosaccharides by infant gut-associated strains of Bifidobacterium breve.	Ruiz-Moyano S, Totten SM, Garrido DA, Smilowitz JT, German JB, Lebrilla CB, Mills DA.	Appl Environ Microbiol	10.1128/aem.01843-13	2013
Metabolism	Comparison of compositions and metabolic activities of fecal microbiotas in young adults and in antibiotic-treated and non-antibiotic-treated elderly subjects.	Woodmansey EJ, McMurdo ME, Macfarlane GT, Macfarlane S.	Appl Environ Microbiol	10.1128/aem.70.10.6113-6122.2004	2004
Metabolism	Cross-feeding by Bifidobacterium breve UCC2003 during co-cultivation with Bifidobacterium bifidum PRL2010 in a mucin-based medium.	Egan M, Motherway MO, Kilcoyne M, Kane M, Joshi L, Ventura M, van Sinderen D.	BMC Microbiol	10.1186/s12866-014-0282-7	2014
	Probiotic Supplementation During the Perinatal and Infant Period: Effects on Gut Dysbiosis and Disease.	Navarro-Tapia E, Sebastiani G, Sailer S, Toledano LA, Serra-Delgado M, Garcia-Algar O, Andreu-Fernandez V.	Nutrients	10.3390/nu12082243	2020
Metabolism	Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.	Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N.	Nat Med	10.1038/s41591-019-0405-7	2019
Genetics	Gut Bacteria Missing in Severe Acute Malnutrition, Can We Identify Potential Probiotics by Culturomics?	Tidjani Alou M, Million M, Traore SI, Mouelhi D, Khelaifia S, Bachar D, Caputo A, Delerce J, Brah S, Alhousseini D, Sokhna C, Robert C, Diallo BA, Diallo A, Parola P, Golden M, Lagier JC, Raoult D.	Front Microbiol	10.3389/fmicb.2017.00899	2017
Metabolism	Bile-inducible efflux transporter from Bifidobacterium longum NCC2705, conferring bile resistance.	Gueimonde M, Garrigues C, van Sinderen D, de los Reyes-Gavilan CG, Margolles A.	Appl Environ Microbiol	10.1128/aem.00172-09	2009
Phylogeny	Quantitative PCR with 16S rRNA-gene-targeted species-specific primers for analysis of human intestinal bifidobacteria.	Matsuki T, Watanabe K, Fujimoto J, Kado Y, Takada T, Matsumoto K, Tanaka R.	Appl Environ Microbiol	10.1128/aem.70.1.167-173.2004	2004
	Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04.	Barrangou R, Briczinski EP, Traeger LL, Loquasto JR, Richards M, Horvath P, Coute-Monvoisin AC, Leyer G, Rendulic S, Steele JL, Broadbent JR, Oberg T, Dudley EG, Schuster S, Romero DA, Roberts RF.	J Bacteriol	10.1128/jb.00155-09	2009
Phylogeny	Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota.	Bartosch S, Fite A, Macfarlane GT, McMurdo ME.	Appl Environ Microbiol	10.1128/aem.70.6.3575-3581.2004	2004
Metabolism	A two-component regulatory system controls autoregulated serpin expression in Bifidobacterium breve UCC2003.	Alvarez-Martin P, O'Connell Motherway M, Turroni F, Foroni E, Ventura M, van Sinderen D.	Appl Environ Microbiol	10.1128/aem.01776-12	2012
	Probiotics in the treatment and prevention of allergy in children.	Savilahti E, Kukkonen K, Kuitunen M.	World Allergy Organ J	10.1097/wox.0b013e3181a45ee5	2009
Phylogeny	Exploring the diversity of the bifidobacterial population in the human intestinal tract.	Turroni F, Foroni E, Pizzetti P, Giubellini V, Ribbera A, Merusi P, Cagnasso P, Bizzarri B, de'Angelis GL, Shanahan F, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.02216-08	2009
Metabolism	Characterization of the serpin-encoding gene of Bifidobacterium breve 210B.	Turroni F, Foroni E, O'Connell Motherway M, Bottacini F, Giubellini V, Zomer A, Ferrarini A, Delledonne M, Zhang Z, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.02938-09	2010
	Nondigestible oligosaccharides enhance bacterial colonization resistance against Clostridium difficile in vitro.	Hopkins MJ, Macfarlane GT.	Appl Environ Microbiol	10.1128/aem.69.4.1920-1927.2003	2003
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Metabolism	Complete genome sequence of the type strain Piscinibacterium candidicorallinum LMG 29480.	Deb D, Moe WM.	Microbiol Resour Announc	10.1128/mra.00139-25	2025
	Encapsulating potential and functional properties of exopolysaccharide from Limosilactobacillus reuteri KCTC 14626BP isolated from human breast milk.	Vijayalakshmi S, Kim JR, Chelliah R, Barathikannan K, Tyagi A, Aloo SO, Chen X, Yan P, Shan L, Oh DH.	Int J Biol Macromol	10.1016/j.ijbiomac.2023.127330	2023
	Harmony unveiled: Intricate the interplay of dietary factor, gut microbiota, and colorectal cancer-A narrative review.	Endale HT, Tesfaye W, Hassen FS, Asrat WB, Temesgen EY, Shibabaw YY, Asefa T.	SAGE Open Med	10.1177/20503121241274724	2024
	Evaluation of probiotic potential, safety assessment and whole genome sequencing of Lactiplantibacillus plantarum strain MOVIN isolated from toddy sample.	Vijayaganapathi A, Mohanasrinivasan V.	Front Microbiol	10.3389/fmicb.2025.1625659	2025
	Bioactive Potential of Wild Plants from Gardunha Mountain: Phytochemical Characterization and Biological Activities.	Coimbra A, Gallardo E, Luis A, Gaspar PD, Ferreira S, Duarte AP.	Molecules	10.3390/molecules30193876	2025
Metabolism	Lactate- and acetate-based cross-feeding interactions between selected strains of lactobacilli, bifidobacteria and colon bacteria in the presence of inulin-type fructans.	Moens F, Verce M, De Vuyst L.	Int J Food Microbiol	10.1016/j.ijfoodmicro.2016.10.019	2017
	Postharvest Quality of Citrus medica L. (cv Liscia-Diamante) Fruit Stored at Different Temperatures: Volatile Profile and Antimicrobial Activity of Essential Oils.	Quintieri L, Palumbo M, Ricci I, Pace B, Caputo L, Adduci A, Luparelli A, Cefola M, Siano F, Cozzolino R.	Foods	10.3390/foods13111596	2024
Metabolism	Structure-dependent stimulation of gut bacteria by arabinoxylo-oligosaccharides (AXOS): a review.	Leschonski KP, Mortensen MS, Hansen LBS, Krogh KBRM, Kabel MA, Laursen MF.	Gut Microbes	10.1080/19490976.2024.2430419	2024
Enzymology	Monoculture parameters successfully predict coculture growth kinetics of Bacteroides thetaiotaomicron and two Bifidobacterium strains.	Van Wey AS, Cookson AL, Roy NC, McNabb WC, Soboleva TK, Shorten PR.	Int J Food Microbiol	10.1016/j.ijfoodmicro.2014.09.006	2014
	Effect of Fungal and Fungal-Bacterial Tempe-Type Fermentation on the Bioactive Potential of Grass Pea Seeds and Flaxseed Oil Cake Mix.	Stodolak B, Grabacka M, Starzynska-Janiszewska A, Dulinski R.	Int J Food Sci	10.1155/2024/5596798	2024
Metabolism	Development of an ion-exchange chromatography method for monitoring the degradation of prebiotic arabinoxylan-oligosaccharides in a complex fermentation medium.	Riviere A, Eeltink S, Pierlot C, Balzarini T, Moens F, Selak M, De Vuyst L.	Anal Chem	10.1021/ac400187f	2013
	Influence of microbial cell morphology and composition on radio frequency heating of simple media at different frequencies.	Espitia J, Verheyen D, Kozak DS, Van Impe JFM.	Sci Rep	10.1038/s41598-023-35705-4	2023
	Identification of Potential Citrate Metabolism Pathways in Carnobacterium maltaromaticum.	Li H, Ramia NE, Borges F, Revol-Junelles AM, Vogensen FK, Leisner JJ.	Microorganisms	10.3390/microorganisms9102169	2021
	Anti-Inflammatory and Antimicrobial Activities of Portuguese Prunus avium L. (Sweet Cherry) By-Products Extracts.	Nunes AR, Flores-Felix JD, Goncalves AC, Falcao A, Alves G, Silva LR.	Nutrients	10.3390/nu14214576	2022
	Screening of the Potential Bioactivities of Pennyroyal (Mentha pulegium L.) Essential Oil.	Luis A, Domingues F.	Antibiotics (Basel)	10.3390/antibiotics10101266	2021
Metabolism	Conjugated linoleic and linolenic acid production kinetics by bifidobacteria differ among strains.	Gorissen L, De Vuyst L, Raes K, De Smet S, Leroy F.	Int J Food Microbiol	10.1016/j.ijfoodmicro.2012.02.012	2012
Pathogenicity	Lactiplantibacillus plantarum DSM20174 Attenuates the Progression of Non-Alcoholic Fatty Liver Disease by Modulating Gut Microbiota, Improving Metabolic Risk Factors, and Attenuating Adipose Inflammation.	Riezu-Boj JI, Barajas M, Perez-Sanchez T, Pajares MJ, Arana M, Milagro FI, Urtasun R.	Nutrients	10.3390/nu14245212	2022
	Production and Characterization of k-Carrageenan Films Incorporating Cymbopogon winterianus Essential Oil as New Food Packaging Materials.	Santos C, Ramos A, Luis A, Amaral ME.	Foods	10.3390/foods12112169	2023
	Optimization of Whey Protein-Based Films Incorporating Foeniculum vulgare Mill. Essential Oil.	Pedro S, Pereira L, Domingues F, Ramos A, Luis A.	J Funct Biomater	10.3390/jfb14030121	2023
	First Chemical Profile Analysis of Acacia Pods.	Pedro SI, Fernandes TA, Luis A, Antunes AMM, Goncalves JC, Gominho J, Gallardo E, Anjos O.	Plants (Basel)	10.3390/plants12193486	2023
Phylogeny	Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics.	Lugli GA, Milani C, Turroni F, Duranti S, Ferrario C, Viappiani A, Mancabelli L, Mangifesta M, Taminiau B, Delcenserie V, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.02004-14	2014
	Lactiplantibacillus plantarum monolayer enhanced bactericidal action of carvacrol: biofilm inhibition of viable foodborne pathogens and spoilage microorganisms.	Poscente V, Di Gregorio L, Costanzo M, Nobili C, Bernini R, Garavaglia L, Bevivino A.	Front Microbiol	10.3389/fmicb.2023.1296608	2023
	Prevalence of Antibiotic Resistance Genes among Human Gut-Derived Bifidobacteria.	Duranti S, Lugli GA, Mancabelli L, Turroni F, Milani C, Mangifesta M, Ferrario C, Anzalone R, Viappiani A, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.02894-16	2017
Genetics	Probiogenomic In-Silico Analysis and Safety Assessment of Lactiplantibacillus plantarum DJF10 Strain Isolated from Korean Raw Milk.	Kandasamy S, Yoo J, Yun J, Lee KH, Kang HB, Kim JE, Oh MH, Ham JS.	Int J Mol Sci	10.3390/ijms232214494	2022
	Emerging Evidence on the Effects of Dietary Factors on the Gut Microbiome in Colorectal Cancer.	Appunni S, Rubens M, Ramamoorthy V, Tonse R, Saxena A, McGranaghan P, Kaiser A, Kotecha R.	Front Nutr	10.3389/fnut.2021.718389	2021
	Bacterial microcompartments and energy metabolism drive gut colonization by Bilophila wadsworthia	Sayavedra L, Yasir M, Goldson A, Brion A, Le Gall G, Moreno-Gonzalez M, Altera A, Paxhia M, Warren M, Savva G, Turner A, Beraza N, Narbad A.	Nat Commun		2025
	Pullulan-Apple Fiber Biocomposite Films: Optical, Mechanical, Barrier, Antioxidant and Antibacterial Properties.	Luis A, Ramos A, Domingues F.	Polymers (Basel)	10.3390/polym13060870	2021
Metabolism	Surface-bound proteins of Lactobacillus plantarum 423 that contribute to adhesion of Caco-2 cells and their role in competitive exclusion and displacement of Clostridium sporogenes and Enterococcus faecalis.	Ramiah K, van Reenen CA, Dicks LM.	Res Microbiol	10.1016/j.resmic.2008.06.002	2008
	Quantification of folic acid in human feces after administration of Bifidobacterium probiotic strains.	Strozzi GP, Mogna L.	J Clin Gastroenterol	10.1097/mcg.0b013e31818087d8	2008
Genetics	Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family.	Lugli GA, Milani C, Turroni F, Duranti S, Mancabelli L, Mangifesta M, Ferrario C, Modesto M, Mattarelli P, Jiri K, van Sinderen D, Ventura M.	BMC Genomics	10.1186/s12864-017-3955-4	2017
	A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome.	Zhang D, Zhang J, Kalimuthu S, Liu J, Song ZM, He BB, Cai P, Zhong Z, Feng C, Neelakantan P, Li YX.	Microbiome	10.1186/s40168-023-01540-y	2023
Genetics	Mobilome and Resistome Reconstruction from Genomes Belonging to Members of the Bifidobacterium Genus.	Mancino W, Lugli GA, Sinderen DV, Ventura M, Turroni F.	Microorganisms	10.3390/microorganisms7120638	2019
	Antimicrobial Biomasses from Lactic Acid Fermentation of Black Soldier Fly Prepupae and Related By-Products.	Hadj Saadoun J, Luparelli AV, Caligiani A, Macavei LI, Maistrello L, Neviani E, Galaverna G, Sforza S, Lazzi C.	Microorganisms	10.3390/microorganisms8111785	2020
Enzymology	Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family.	Kashima T, Okumura K, Ishiwata A, Kaieda M, Terada T, Arakawa T, Yamada C, Shimizu K, Tanaka K, Kitaoka M, Ito Y, Fujita K, Fushinobu S.	J Biol Chem	10.1016/j.jbc.2021.101324	2021
Pathogenicity	Exploring the Ecology of Bifidobacteria and Their Genetic Adaptation to the Mammalian Gut.	Duranti S, Longhi G, Ventura M, van Sinderen D, Turroni F.	Microorganisms	10.3390/microorganisms9010008	2020
	Design and Characterization of Bioactive Bilayer Films: Release Kinetics of Isopropyl Palmitate.	Luis A, Gallardo E, Ramos A, Domingues F.	Antibiotics (Basel)	10.3390/antibiotics9080443	2020
	Genetic and phenotypic assessment of the antimicrobial activity of three potential probiotic lactobacilli against human enteropathogenic bacteria.	Kiousi DE, Efstathiou C, Tzampazlis V, Plessas S, Panopoulou M, Koffa M, Galanis A.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1127256	2023
	Ayahuasca Beverages: Phytochemical Analysis and Biological Properties.	Goncalves J, Luis A, Gradillas A, Garcia A, Restolho J, Fernandez N, Domingues F, Gallardo E, Duarte AP.	Antibiotics (Basel)	10.3390/antibiotics9110731	2020
	Pullulan Films Containing Rockrose Essential Oil for Potential Food Packaging Applications.	Luis A, Ramos A, Domingues F.	Antibiotics (Basel)	10.3390/antibiotics9100681	2020
	Production of Hydrophobic Zein-Based Films Bioinspired by The Lotus Leaf Surface: Characterization and Bioactive Properties.	Luis A, Domingues F, Ramos A.	Microorganisms	10.3390/microorganisms7080267	2019
	Persistence and Effect of a Multistrain Starter Culture on Antioxidant and Rheological Properties of Novel Wheat Sourdoughs and Bread.	Sidari R, Martorana A, Zappia C, Mincione A, Giuffre AM.	Foods	10.3390/foods9091258	2020
Metabolism	Fungal GH25 muramidases: New family members with applications in animal nutrition and a crystal structure at 0.78Å resolution.	Moroz OV, Blagova E, Taylor E, Turkenburg JP, Skov LK, Gippert GP, Schnorr KM, Ming L, Ye L, Klausen M, Cohn MT, Schmidt EGW, Nymand-Grarup S, Davies GJ, Wilson KS.	PLoS One	10.1371/journal.pone.0248190	2021
	DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq.	Krych L, Castro-Mejia JL, Forero-Junco LM, Moesby DN, Mikkelsen MB, Rasmussen MA, Sykulski M, Nielsen DS.	Commun Biol	10.1038/s42003-019-0617-x	2019
Enzymology	Viability and enzymatic activity of bifidobacteria in milk.	Hughes DB, Hoover DG.	J Dairy Sci	10.3168/jds.s0022-0302(95)76634-6	1995
	Characterization of Fusobacterium nucleatum ATCC 23726 adhesins involved in strain-specific attachment to Porphyromonas gingivalis	Park J, Shokeen B, Haake S, Lux R.	International journal of oral science	10.1038/ijos.2016.27	2016
	Lactobacillus reuteri Reduces the Severity of Experimental Autoimmune Encephalomyelitis in Mice by Modulating Gut Microbiota.	He B, Hoang TK, Tian X, Taylor CM, Blanchard E, Luo M, Bhattacharjee MB, Freeborn J, Park S, Couturier J, Lindsey JW, Tran DQ, Rhoads JM, Liu Y.	Front Immunol	10.3389/fimmu.2019.00385	2019
	Chemical Profiling and Evaluation of Antioxidant and Anti-Microbial Properties of Selected Commercial Essential Oils: A Comparative Study.	Luis A, Duarte AP, Pereira L, Domingues F.	Medicines (Basel)	10.3390/medicines4020036	2017
	Antimicrobial, antibiofilm and cytotoxic activities of Hakea sericea Schrader extracts.	Luis A, Breitenfeld L, Ferreira S, Duarte AP, Domingues F.	Pharmacogn Mag	10.4103/0973-1296.127331	2014
	Therapeutic Effect of Bifidobacterium Administration on Experimental Autoimmune Myasthenia Gravis in Lewis Rats.	Rinaldi E, Consonni A, Cordiglieri C, Sacco G, Crasa C, Fontana A, Morelli L, Elli M, Mantegazza R, Baggi F.	Front Immunol	10.3389/fimmu.2019.02949	2019
	Evaluation of antimicrobial-antibiofilm activity of a hydrogen peroxide decontaminating system used in dental unit water lines.	Orru G, Del Nero S, Tuveri E, Laura Ciusa M, Pilia F, Erriu M, Orru G, Liciardi M, Piras V, Denotti G.	Open Dent J	10.2174/1874210601004010140	2010
Metabolism	Synthesis of Fructooligosaccharides by IslA4, a truncated inulosucrase from Leuconostoc citreum.	Pena-Cardena A, Rodriguez-Alegria ME, Olvera C, Munguia AL.	BMC Biotechnol	10.1186/s12896-015-0116-1	2015
	Administration of bifidobacterium and lactobacillus strains modulates experimental myasthenia gravis and experimental encephalomyelitis in Lewis rats.	Consonni A, Cordiglieri C, Rinaldi E, Marolda R, Ravanelli I, Guidesi E, Elli M, Mantegazza R, Baggi F.	Oncotarget	10.18632/oncotarget.25170	2018
Phylogeny	Nucleic acid hybridization studies on Microbacterium, Curtobacterium, Agromyces and related taxa.	Dopfer H, Stackebrandt E, Fiedler F.	J Gen Microbiol	10.1099/00221287-128-8-1697	1982
Genetics	Diverse Microbial Composition of Sourdoughs From Different Origins.	Comasio A, Verce M, Van Kerrebroeck S, De Vuyst L.	Front Microbiol	10.3389/fmicb.2020.01212	2020
	Stumps of Eucalyptus globulus as a source of antioxidant and antimicrobial polyphenols.	Luis A, Neiva D, Pereira H, Gominho J, Domingues F, Duarte AP.	Molecules	10.3390/molecules191016428	2014
Metabolism	In vitro kinetic analysis of fermentation of prebiotic inulin-type fructans by Bifidobacterium species reveals four different phenotypes.	Falony G, Lazidou K, Verschaeren A, Weckx S, Maes D, De Vuyst L.	Appl Environ Microbiol	10.1128/aem.01488-08	2009
	Inhibitory impact of bifidobacteria on the transfer of beta-lactam resistance among Enterobacteriaceae in the gnotobiotic mouse digestive tract.	Moubareck C, Lecso M, Pinloche E, Butel MJ, Doucet-Populaire F.	Appl Environ Microbiol	10.1128/aem.02001-06	2007
	Lactobacillus equigenerosi strain Le1 invades equine epithelial cells.	Botha M, Botes M, Loos B, Smith C, Dicks LM.	Appl Environ Microbiol	10.1128/aem.00552-12	2012
Metabolism	Coculture fermentations of Bifidobacterium species and Bacteroides thetaiotaomicron reveal a mechanistic insight into the prebiotic effect of inulin-type fructans.	Falony G, Calmeyn T, Leroy F, De Vuyst L.	Appl Environ Microbiol	10.1128/aem.02649-08	2009
Metabolism	Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth.	Lopez-Siles M, Khan TM, Duncan SH, Harmsen HJ, Garcia-Gil LJ, Flint HJ.	Appl Environ Microbiol	10.1128/aem.06858-11	2012
	Usefulness of real time PCR for the differentiation and quantification of 652 and JP2 Actinobacillus actinomycetemcomitans genotypes in dental plaque and saliva.	Orru G, Marini MF, Ciusa ML, Isola D, Cotti M, Baldoni M, Piras V, Pisano E, Montaldo C.	BMC Infect Dis	10.1186/1471-2334-6-98	2006
	Long-term survival and virulence of Mycobacterium leprae in amoebal cysts.	Wheat WH, Casali AL, Thomas V, Spencer JS, Lahiri R, Williams DL, McDonnell GE, Gonzalez-Juarrero M, Brennan PJ, Jackson M.	PLoS Negl Trop Dis	10.1371/journal.pntd.0003405	2014
Metabolism	Kinetic analysis of bifidobacterial metabolism reveals a minor role for succinic acid in the regeneration of NAD+ through its growth-associated production.	Van der Meulen R, Adriany T, Verbrugghe K, De Vuyst L.	Appl Environ Microbiol	10.1128/aem.00146-06	2006
Metabolism	Reconstructing the mosaic glycolytic pathway of the anaerobic eukaryote Monocercomonoides.	Liapounova NA, Hampl V, Gordon PM, Sensen CW, Gedamu L, Dacks JB.	Eukaryot Cell	10.1128/ec.00258-06	2006
Phylogeny	Phylogenetic analysis of anaerobic psychrophilic enrichment cultures obtained from a greenland glacier ice core.	Sheridan PP, Miteva VI, Brenchley JE.	Appl Environ Microbiol	10.1128/aem.69.4.2153-2160.2003	2003
	Bifidobacterium mechanisms of immune modulation and tolerance.	Gavzy SJ, Kensiski A, Lee ZL, Mongodin EF, Ma B, Bromberg JS.	Gut Microbes	10.1080/19490976.2023.2291164	2023
	Substrate recognition mode of a glycoside hydrolase family 42 beta-galactosidase from Bifidobacterium longum subspecies infantis (BiBga42A) revealed by crystallographic and mutational analyses.	Gotoh A, Hidaka M, Sakurama H, Nishimoto M, Kitaoka M, Sakanaka M, Fushinobu S, Katayama T.	Microbiome Res Rep	10.20517/mrr.2023.14	2023
Genetics	Identification of conserved genomic signatures specific to Bifidobacterium species colonising the human gut.	Arjun OK, Prakash T.	3 Biotech	10.1007/s13205-023-03492-4	2023
	Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach.	Fontana F, Alessandri G, Tarracchini C, Bianchi MG, Rizzo SM, Mancabelli L, Lugli GA, Argentini C, Vergna LM, Anzalone R, Longhi G, Viappiani A, Taurino G, Chiu M, Turroni F, Bussolati O, van Sinderen D, Milani C, Ventura M.	Environ Microbiol	10.1111/1462-2920.16205	2022
Phylogeny	Phylogenetic Analysis of the Bifidobacterium Genus Using Glycolysis Enzyme Sequences.	Brandt K, Barrangou R.	Front Microbiol	10.3389/fmicb.2016.00657	2016
	Gene structure and transcriptional organization of the dnaK operon of Bifidobacterium breve UCC 2003 and application of the operon in bifidobacterial tracing.	Ventura M, Zink R, Fitzgerald GF, van Sinderen D.	Appl Environ Microbiol	10.1128/aem.71.1.487-500.2005	2005
	Characterization of the groEL and groES loci in Bifidobacterium breve UCC 2003: genetic, transcriptional, and phylogenetic analyses.	Ventura M, Canchaya C, Zink R, Fitzgerald GF, van Sinderen D.	Appl Environ Microbiol	10.1128/aem.70.10.6197-6209.2004	2004
Genetics	Complete genome sequence of Bifidobacterium catenulatum JCM 1194(T) isolated from human feces.	Morita H, Toh H, Oshima K, Nakano A, Yamashita N, Iioka E, Arakawa K, Suda W, Honda K, Hattori M	J Biotechnol	10.1016/j.jbiotec.2015.06.415	2015
Metabolism	The potential of bifidobacteria as a source of natural folate.	D'Aimmo MR, Mattarelli P, Biavati B, Carlsson NG, Andlid T	J Appl Microbiol	10.1111/j.1365-2672.2012.05261.x	2012
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
Phylogeny	Bifidobacteria in two-toed sloths (Choloepus didactylus): phylogenetic characterization of the novel taxon Bifidobacterium choloepi sp. nov.	Modesto M, Satti M, Watanabe K, Huang CH, Liou JS, Tamura T, Saito S, Mori K, Huang L, Sandri C, Spiezio C, Sgorbati B, Scarafile D, Camma C, Ancora M, Patavino C, Arita M, Mattarelli P.	Int J Syst Evol Microbiol	10.1099/ijsem.0.004506	2020
Phylogeny	Lactobacillus zhachilii sp. nov., a lactic acid bacterium isolated from Zha-Chili.	Zhang Z, Hou Q, Wang Y, Li W, Zhao H, Sun Z, Guo Z.	Int J Syst Evol Microbiol	10.1099/ijsem.0.003362	2019
Phylogeny	Bifidobacterium faecale sp. nov., isolated from human faeces.	Choi JH, Lee KM, Lee MK, Cha CJ, Kim GB.	Int J Syst Evol Microbiol	10.1099/ijs.0.063479-0	2014
Phylogeny	Kaistella koreensis gen. nov., sp. nov., a novel member of the Chryseobacterium-Bergeyella-Riemerella branch.	Kim MK, Im WT, Shin YK, Lim JH, Kim SH, Lee BC, Park MY, Lee KY, Lee ST.	Int J Syst Evol Microbiol	10.1099/ijs.0.02998-0	2004
Phylogeny	Bifidobacterium moukalabense sp. nov., isolated from the faeces of wild west lowland gorilla (Gorilla gorilla gorilla).	Tsuchida S, Takahashi S, Nguema PPM, Fujita S, Kitahara M, Yamagiwa J, Ngomanda A, Ohkuma M, Ushida K	Int J Syst Evol Microbiol	10.1099/ijs.0.055186-0	2013
Phylogeny	Bifidobacterium kashiwanohense sp. nov., isolated from healthy infant faeces.	Morita H, Nakano A, Onoda H, Toh H, Oshima K, Takami H, Murakami M, Fukuda S, Takizawa T, Kuwahara T, Ohno H, Tanabe S, Hattori M	Int J Syst Evol Microbiol	10.1099/ijs.0.024521-0	2010

References

#6595	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16992
#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 )
#34555	; Curators of the CIP;
#46811	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 18366
#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;
#68371	Automatically annotated from API 50CH acid .
#68380	Automatically annotated from API rID32A .
#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 .
#117216	Collection of Institut Pasteur ; Curators of the CIP; CIP 104175
#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 catenulatum subsp. catenulatum (DSM 16992, ATCC 27539, CECT 7362)

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