Bifidobacterium scardovii (DSM 13734, CCUG 13008 A, ATCC BAA-773)

Name: Bifidobacterium scardovii (DSM 13734, CCUG 13008 A, ATCC BAA-773)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1734

Type strain

Culture col. no. DSM 13734 CCUG 13008 A ATCC BAA-773 JCM 12489 CCM 7209 1 more

NCBI tax ID(s) 1150461 158787

Special Collections DSMZ CCUG JCM KCTC

History <- CCUG <- Blood Dept., PHL, Göteborg; SBL 0071/83 CCUG 13008 A <-- Blood Dept., PHL, Göteborg SBL 0071/83.

Links

Bifidobacterium scardovii DSM 13734 is an anaerobe bacterium that was isolated from human blood.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 51923

CCUG 13008 A,CCUG 13008,LMG 21589,DSM 13734,ATCC BAA-773,CCM 7209,JCM 12489,KCTC 5118,KCTC 5152

@ref 20215

Last LPSN update 2026-02-09 11:18:10

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Bifidobacterium

Species Bifidobacterium scardovii

Full scientific name Bifidobacterium scardovii Hoyles et al. 2002

BacDive ID	Other strains from **Bifidobacterium scardovii** (6)	Type strain
145751	B. scardovii CCUG 29475
149098	B. scardovii CCUG 36852
150378	B. scardovii CCUG 39775
151567	B. scardovii CCUG 44350
154841	B. scardovii CCUG 55376
173604	B. scardovii CIMB 04-8881, CRBIP17.33

Morphology

Cell morphology

@ref	Motility	Confidence
125438		91.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5133	BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)		Medium recipe at MediaDive	Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
5133	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

5133

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		97.9

Murein

@ref	Murein short key	Type
5133	A11.20	A3alpha L-Lys-L-Ser-L-Ala₂

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	+	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
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	15824 ChEBI	D-fructose	+	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	17634 ChEBI	D-glucose	+	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
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	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	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	+	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	15443 ChEBI	inulin	-	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
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	17716 ChEBI	lactose	+	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	+	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	+	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	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
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	+	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	vitamin B1 metabolism	100	13 of 13
66794	ppGpp biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	starch degradation	100	10 of 10
66794	acetoin degradation	100	3 of 3
66794	peptidoglycan biosynthesis	93.33	14 of 15
66794	pentose phosphate pathway	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	palmitate biosynthesis	86.36	19 of 22
66794	photosynthesis	85.71	12 of 14
66794	glycogen metabolism	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	NAD metabolism	77.78	14 of 18
66794	valine metabolism	77.78	7 of 9
66794	sulfopterin metabolism	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	phenylalanine metabolism	69.23	9 of 13
66794	oxidative phosphorylation	67.03	61 of 91
66794	serine metabolism	66.67	6 of 9
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	purine metabolism	65.96	62 of 94
66794	degradation of pentoses	64.29	18 of 28
66794	d-xylose degradation	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	methionine metabolism	61.54	16 of 26
66794	glutamate and glutamine metabolism	60.71	17 of 28
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	glycolysis	58.82	10 of 17
66794	pyrimidine metabolism	57.78	26 of 45
66794	propanol degradation	57.14	4 of 7
66794	degradation of hexoses	55.56	10 of 18
66794	d-mannose degradation	55.56	5 of 9
66794	tryptophan metabolism	55.26	21 of 38
66794	histidine metabolism	55.17	16 of 29
66794	metabolism of disaccharids	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	tetrahydrofolate metabolism	50	7 of 14
66794	ethanol fermentation	50	1 of 2
66794	coenzyme A metabolism	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	citric acid cycle	50	7 of 14
66794	glutathione metabolism	50	7 of 14
66794	cysteine metabolism	50	9 of 18
66794	alanine metabolism	48.28	14 of 29
66794	arginine metabolism	45.83	11 of 24
66794	proline metabolism	45.45	5 of 11
66794	lipid metabolism	45.16	14 of 31
66794	degradation of sugar acids	44	11 of 25
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	lysine metabolism	42.86	18 of 42
66794	tyrosine metabolism	42.86	6 of 14
66794	glycine metabolism	40	4 of 10
66794	flavin biosynthesis	40	6 of 15
66794	vitamin K metabolism	40	2 of 5
66794	non-pathway related	39.47	15 of 38
66794	isoprenoid biosynthesis	38.46	10 of 26
66794	urea cycle	38.46	5 of 13
66794	vitamin B6 metabolism	36.36	4 of 11
66794	ascorbate metabolism	36.36	8 of 22
66794	IAA biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	lipid A biosynthesis	33.33	3 of 9
66794	sulfoquinovose degradation	33.33	1 of 3
66794	polyamine pathway	30.43	7 of 23
66794	propionate fermentation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	CMP-KDO biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	sulfate reduction	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9
66794	4-hydroxymandelate degradation	22.22	2 of 9

Fatty acid profile

Metadata FA analysis

@ref

45872

Fatty acid	Percentage	ECL
C16:0	29.4	16
C14:0	24.8	14
C19:0 CYCLO ω9c	9.2	18.87
C18:1 ω9c	8.4	17.769
C18:2 ω6,9c/C18:0 ANTE	6.7	17.724
C10:0	4.2	10
C12:0	3.8	12
C16:1 ω9c	3.6	15.774
C18:1 ω9c DMA	3.4	18.226
C18:0	2.2	18
C13:0 3OH/C15:1 i I/H	2	14.469
Unidentified	0.9	19.329
Unidentified	0.8	18.187
C17:1 ω9c	0.6	16.773

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
5133	-	-	-	-	+	+	+	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	-	+	+	+	+	+	+	+	+	+	+	-	+	+	+	-	-	+	+	+	-	-	-	-	-	+	-	+/-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Fluids	#Blood

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
5133	human blood			Sweden	SWE	Europe
45872	Human blood,50-yr-old woman	1982-11-22	Göteborg	Sweden	SWE	Europe
67770	Human blood			Sweden	SWE	Europe

Taxonmaps

69479

Global distribution of 16S sequence LC383820 (>99% sequence identity) for Bifidobacterium scardovii subclade from Microbeatlas

Aquatic Samples	130
Soil Samples	172
Animal Samples	16622
Plant Samples	37
Total Samples	16961

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
5133	yes, in single cases	1	Risk group (German 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	ASM104263v1 assembly for Bifidobacterium scardovii JCM 12489 = DSM 13734	complete	GCA_001042635	1150461.5		1150461	97.48
67770	Bifsca assembly for Bifidobacterium scardovii LMG 21589	contig	GCA_000741405	158787.3	2597490265	158787	71.08
67770	ASM100506v1 assembly for Bifidobacterium scardovii JCM 12489 = DSM 13734	contig	GCA_001005065	1150461.4	2651869654	1150461	66.76
67770	DSM-13734 assembly for Bifidobacterium scardovii JCM 12489 = DSM 13734	contig	GCA_000770985	1150461.3	2700989372	1150461	50.34

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Bifidobacterium scardovii partial 16S rRNA gene, strain CCUG 13008	AJ307005	1380	1150461
20218	Bifidobacterium scardovii gene for 16S rRNA, partial sequence, strain: JCM 12489	AB507155	642	1150461
67770	Bifidobacterium scardovii gene for 16S ribosomal RNA, partial sequence	AB437363	1506	158787
67770	Bifidobacterium scardovii JCM 12489 = DSM 13734 gene for 16S ribosomal RNA, partial sequence	LC383820	1472	1150461

GC content

@ref	GC-content (mol%)	Method
67770	60.1	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bifidobacterium scardovii JCM 12489 = DSM 13734
PATRIC: 1150461.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	89.70	no
125439	gram_stain	BacteriaNetⓘ	negative	76.80	no
125439	motility	BacteriaNetⓘ	yes	75.40	no
125439	spore_formation	BacteriaNetⓘ	no	97.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bifidobacterium scardovii JCM 12489 = DSM 13734 JCM 12489
NCBI: GCA_001042635.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.04	no
125438	anaerobic	anaerobicⓘ	yes	69.83	yes
125438	aerobic	aerobicⓘ	no	84.17	no
125438	spore-forming	spore-formingⓘ	no	89.51	no
125438	thermophilic	thermophileⓘ	no	92.50	yes
125438	flagellated	motile2+ⓘ	no	91.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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	Identification and characterization of a 20beta-HSDH from the anaerobic gut bacterium Butyricicoccus desmolans ATCC 43058.	Devendran S, Mendez-Garcia C, Ridlon JM.	J Lipid Res	10.1194/jlr.m074914	2017
Enzymology	Microbial Hydroxysteroid Dehydrogenases: From Alpha to Omega.	Doden HL, Ridlon JM.	Microorganisms	10.3390/microorganisms9030469	2021
	Dysbiosis involving methionine and PPAR-gamma pathways is associated with early onset atopic dermatitis and food allergy.	Senavonge A, Nakphaichit M, Vongsangnak W, Roytrakul S, Patumcharoenpol P, Kingkaw A, Wongoutong C, Weerapakorn W, Pornputtapong N, La-Ongkham O, Poovorawan Y, Wanlapakorn N, Kittipongpattana P, Nitisinprasert S, Chatchatee P, Suratannon N.	Asian Pac J Allergy Immunol	10.12932/ap-131223-1749	2025
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
	"Breast abscess in a male patient due to Finegoldia magna and Bifidobacterium scardovii: An unusual entity".	Sunil Krishna M, Shenoy PA, Priyanka KS, Vishwanath S.	Anaerobe	10.1016/j.anaerobe.2022.102536	2022
Genetics	Unraveling gut microbiome alterations and metabolic signatures in hereditary transthyretin amyloidosis.	Li H, Wang Z, He S, Zhao X, Wu Q, Sun Y, Fan Y, Hu X, Tian Z, Zhang S.	Microbiol Spectr	10.1128/spectrum.02302-24	2025
Genetics	Complete genome of Vibrio japonicus strain JCM 31412^T and assessment of the Nereis clade of the genus Vibrio.	Shlafstein MD, Emsley SA, Loughran RM, O'Hanlon SM, Ushijima B, Videau P, Saw JH.	Antonie Van Leeuwenhoek	10.1007/s10482-022-01784-y	2023
	In-depth Microbiological Characterization of Urine From Subjects With Type 2 Diabetes.	Calvigioni M, Biancalana E, Mazzantini D, Celandroni F, Rossi C, Mengozzi A, Ghelardi E, Solini A.	J Clin Endocrinol Metab	10.1210/clinem/dgae389	2024
Genetics	Complete genome sequences of Bifidobacterium faecale strain JCM19861^T, isolated from human feces.	Okuhama S, Takahashi H, Nakayama Y, Ogata Y, Suda W.	Microbiol Resour Announc	10.1128/mra.00784-23	2024
Genetics	Complete genome sequences of Ruminococcus torques strains JCM 36208 and JCM 36209, isolated from the feces of a healthy Japanese male.	Hisatomi A, Tourlousse DM, Hamajima M, Ohkuma M, Sekiguchi Y, Sakamoto M.	Microbiol Resour Announc	10.1128/mra.00632-23	2023
	Optimisation of Laccase Activity From Bacillus atrophaeus Using Response Surface Methodology: A Proof-Of-Concept Dye Decolourisation Study.	Kocak K, Altin Yavuz A, Berberler S, Filik Iscen C.	Environ Microbiol Rep	10.1111/1758-2229.70138	2025
	[Bifidobacterium scardovii isolated from 2 consecutive urine samples].	Guevara Nunez D, De Paulis AN, Bertona E, Gutierrez MA, Vay CA, Suarez JP, Predari SC.	Rev Argent Microbiol	10.1016/j.ram.2017.04.004	2017
	Characterization of the ruminal microbiota in sheep and goats fed different levels of tannin-rich Sericea lespedeza hay.	Min BR, Wang W, Pitta DW, Indugu N, Patra AK, Wang HH, Abrahamsen F, Hilaire M, Puchala R.	J Anim Sci	10.1093/jas/skae198	2024
Metabolism	Analysis of polyamine biosynthetic- and transport ability of human indigenous Bifidobacterium.	Sugiyama Y, Nara M, Sakanaka M, Kitakata A, Okuda S, Kurihara S.	Biosci Biotechnol Biochem	10.1080/09168451.2018.1475211	2018
	Community metabolic modeling of host-microbiota interactions through multi-objective optimization.	Lambert A, Budinich M, Mahe M, Chaffron S, Eveillard D.	iScience	10.1016/j.isci.2024.110092	2024
	Health benefits, antimicrobial activities, and potential applications of probiotics: A review.	Sepehr A, Miri ST, Aghamohammad S, Rahimirad N, Milani M, Pourshafie MR, Rohani M.	Medicine (Baltimore)	10.1097/md.0000000000032412	2024
Pathogenicity	Antimicrobial susceptibility of clinical isolates of Actinomyces and related genera reveals an unusual clindamycin resistance among Actinomyces urogenitalis strains.	Barberis C, Budia M, Palombarani S, Rodriguez CH, Ramirez MS, Arias B, Bonofiglio L, Famiglietti A, Mollerach M, Almuzara M, Vay C.	J Glob Antimicrob Resist	10.1016/j.jgar.2016.11.007	2017
Enzymology	Characterization of a thermostable protease from Bacillus subtilis BSP strain.	Majeed T, Lee CC, Orts WJ, Tabassum R, Shah TA, Jardan YAB, Dawoud TM, Bourhia M.	BMC Biotechnol	10.1186/s12896-024-00870-5	2024
	Endometrial microbiota profile in in-vitro fertilization (IVF) patients by culturomics-based analysis.	Cariati F, Carotenuto C, Bagnulo F, Pacella D, Marrone V, Paolillo R, Catania MR, Di Girolamo R, Conforti A, Strina I, Alviggi C.	Front Endocrinol (Lausanne)	10.3389/fendo.2023.1204729	2023
	Isolation and Characterization of Two New Deoxynivalenol-Degrading Strains, Bacillus sp. HN117 and Bacillus sp. N22.	Li B, Duan J, Ren J, Francis F, Li G.	Toxins (Basel)	10.3390/toxins14110781	2022
Pathogenicity	Saponin treatment for eukaryotic DNA depletion alters the microbial DNA profiles by reducing the abundance of Gram-negative bacteria in metagenomics analyses	Longhi G, Argentini C, Fontana F, Tarracchini C, Mancabelli L, Lugli G, Alessandri G, Lahner E, Pivetta G, Turroni F, Ventura M, Milani C.	Microbiome Res Rep		2023
Genetics	dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation.	Huang L, Zhang H, Wu P, Entwistle S, Li X, Yohe T, Yi H, Yang Z, Yin Y.	Nucleic Acids Res	10.1093/nar/gkx894	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
	Cross-feeding interactions between human gut commensals belonging to the Bacteroides and Bifidobacterium genera when grown on dietary glycans.	Fernandez-Julia P, Commane DM, van Sinderen D, Munoz-Munoz J.	Microbiome Res Rep	10.20517/mrr.2021.05	2022
Phylogeny	Recurrent urinary infection with Bifidobacterium scardovii.	Barberis CM, Cittadini RM, Almuzara MN, Feinsilberg A, Famiglietti AM, Ramirez MS, Vay CA.	J Clin Microbiol	10.1128/jcm.06027-11	2012
	Draft Genome Sequences of Methanoculleus horonobensis Strain JCM 15517, Methanoculleus thermophilus Strain DSM 2373, and Methanofollis ethanolicus Strain JCM 15103, Hydrogenotrophic Methanogens Belonging to the Family Methanomicrobiaceae.	Narihiro T, Kusada H, Yoneda Y, Tamaki H.	Genome Announc	10.1128/genomea.00199-16	2016
	Clinical Significance of Composition and Functional Diversity of the Vaginal Microbiome in Recurrent Vaginitis.	Kim MJ, Lee S, Kwon MY, Kim M.	Front Microbiol	10.3389/fmicb.2022.851670	2022
	Improved antioxidant capacity of three Brassica vegetables by two-step controlled fermentation using isolated autochthone strains of the genus Leuconostoc spp. and Lactiplantibacillus spp.	Parada RB, Marguet E, Campos C, Vallejo M.	Food Chem (Oxf)	10.1016/j.fochms.2023.100163	2023
Genetics	FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling.	Xie Z, Manichanh C.	Comput Struct Biotechnol J	10.1016/j.csbj.2022.07.010	2022
	Gut Microbiome of Patients With Breast Cancer in Vietnam.	Nguyen SM, Tran HTT, Long J, Shrubsole MJ, Cai H, Yang Y, Nguyen LM, Nguyen GH, Nguyen CV, Ta TV, Wu J, Cai Q, Zheng W, Tran TV, Shu XO.	JCO Glob Oncol	10.1200/go.23.00234	2024
	Intracellular granule formation in response to oxidative stress in Bifidobacterium.	Qian Y, Borowski WJ, Calhoon WD.	Int J Food Microbiol	10.1016/j.ijfoodmicro.2010.11.026	2011
	The Effect of Herbal Feed Additives in the Diet of Dairy Goats on Intestinal Lactic Acid Bacteria (LAB) Count.	Foksowicz-Flaczyk J, Wojtowski JA, Dankow R, Mikolajczak P, Pikul J, Gryszczynska A, Lowicki Z, Zajaczek K, Stanislawski D.	Animals (Basel)	10.3390/ani12030255	2022
	Non-oral bifidobacteria and the aciduric microbiota of the denture plaque biofilm.	Mantzourani M, Gilbert SC, Fenlon M, Beighton D.	Mol Oral Microbiol	10.1111/j.2041-1014.2009.00565.x	2010
	Transmission and dynamics of mother-infant gut viruses during pregnancy and early life.	Garmaeva S, Sinha T, Gulyaeva A, Kuzub N, Spreckels JE, Andreu-Sanchez S, Gacesa R, Vich Vila A, Brushett S, Kruk M, Lifelines NEXT cohort study, Dekens J, Sikkema J, Kuipers F, Shkoporov AN, Hill C, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A.	Nat Commun	10.1038/s41467-024-45257-4	2024
Phylogeny	A Combined Analysis of Gut and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Study.	Los-Rycharska E, Golebiewski M, Sikora M, Grzybowski T, Gorzkiewicz M, Popielarz M, Gawryjolek J, Krogulska A.	Nutrients	10.3390/nu13051682	2021
	Comparative study of composition, antioxidant and antimicrobial activity of two adult edible insects from Tenebrionidae family.	Flores DR, Casados LE, Velasco SF, Ramirez AC, Velazquez G.	BMC Chem	10.1186/s13065-020-00707-0	2020
Phylogeny	Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1-V2 and V3-V4 primer sets.	Kameoka S, Motooka D, Watanabe S, Kubo R, Jung N, Midorikawa Y, Shinozaki NO, Sawai Y, Takeda AK, Nakamura S.	BMC Genomics	10.1186/s12864-021-07746-4	2021
Phylogeny	Oral microbiome and obesity in a large study of low-income and African-American populations.	Yang Y, Cai Q, Zheng W, Steinwandel M, Blot WJ, Shu XO, Long J.	J Oral Microbiol	10.1080/20002297.2019.1650597	2019
Enzymology	Bifidobacterium--friend or foe? A case of urinary tract infection with Bifidobacterium species.	Pathak P, Trilligan C, Rapose A.	BMJ Case Rep	10.1136/bcr-2014-205122	2014
	Draft Genome Sequences of Cyclodextrin-Producing Alkaliphilic Bacillus Strains JCM 19045, JCM 19046, and JCM 19047.	Kudo T, Sakamoto K, Akinaga M, Kawauchi A, Nakahara T, Zhang X, Yamada A, Oshima K, Suda W, Kuwahara H, Nakamura N, Nogi Y, Kitamura K, Yuki M, Iida T, Moriya S, Inoue T, Hongoh Y, Hattori M, Ohkuma M.	Genome Announc	10.1128/genomea.00211-14	2014
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
	Prenatal versus Postnatal Initial Colonization of Healthy Neonates' Colon Ecosystem by the Enterobacterium Escherichia coli.	Al-Balawi M, Morsy FM.	Microbiol Spectr	10.1128/spectrum.00379-21	2021
	Enterococcus faecalis Is a Better Competitor Than Other Lactic Acid Bacteria in the Initial Colonization of Colon of Healthy Newborn Babies at First Week of Their Life.	Al-Balawi M, Morsy FM.	Front Microbiol	10.3389/fmicb.2020.02017	2020
	Amplicon-based sequencing and co-occurence network analysis reveals notable differences of microbial community structure in healthy and dandruff scalps.	Wang L, Yu T, Zhu Y, Luo Y, Dong F, Lin X, Zhao W, He Z, Hu S, Dong Z.	BMC Genomics	10.1186/s12864-022-08534-4	2022
	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
	Association between ustekinumab therapy and changes in specific anti-microbial response, serum biomarkers, and microbiota composition in patients with IBD: A pilot study.	Rob F, Schierova D, Stehlikova Z, Kreisinger J, Roubalova R, Coufal S, Mihula M, Jackova Z, Kverka M, Thon T, Kostovcikova K, Bajer L, Drastich P, Hercogova JT, Novakova M, Kolar M, Vasatko M, Lukas M, Tlaskalova-Hogenova H, Jiraskova Zakostelska Z.	PLoS One	10.1371/journal.pone.0277576	2022
	Fecal Microbiome Changes and Specific Anti-Bacterial Response in Patients with IBD during Anti-TNF Therapy.	Schierova D, Roubalova R, Kolar M, Stehlikova Z, Rob F, Jackova Z, Coufal S, Thon T, Mihula M, Modrak M, Kverka M, Bajer L, Kostovcikova K, Drastich P, Hercogova J, Novakova M, Vasatko M, Lukas M, Tlaskalova-Hogenova H, Jiraskova Zakostelska Z.	Cells	10.3390/cells10113188	2021
	In vitro activity of nifuratel on vaginal bacteria: could it be a good candidate for the treatment of bacterial vaginosis?	Togni G, Battini V, Bulgheroni A, Mailland F, Caserini M, Mendling W.	Antimicrob Agents Chemother	10.1128/aac.01623-10	2011
Enzymology	Two Cases of Urinary Tract Infection Caused by Propionimicrobium lymphophilum.	Williams GD.	J Clin Microbiol	10.1128/jcm.00438-15	2015
	Multilamellar and Multivesicular Outer Membrane Vesicles Produced by a Buttiauxella agrestis tolB Mutant.	Takaki K, Tahara YO, Nakamichi N, Hasegawa Y, Shintani M, Ohkuma M, Miyata M, Futamata H, Tashiro Y.	Appl Environ Microbiol	10.1128/aem.01131-20	2020
	In Vitro Evaluation of Probiotic Properties of Lactic Acid Bacteria Isolated from Some Traditionally Fermented Ethiopian Food Products.	Mulaw G, Sisay Tessema T, Muleta D, Tesfaye A.	Int J Microbiol	10.1155/2019/7179514	2019
Metabolism	Potential application values of a marine red yeast, Rhodosporidiums sphaerocarpum YLY01, in aquaculture and tail water treatment assessed by the removal of ammonia nitrogen, the inhibition to Vibrio spp., and nutrient composition.	Yun L, Wang W, Li Y, Xie M, Chen T, Hu C, Luo P, Li D.	PLoS One	10.1371/journal.pone.0246841	2021
Metabolism	Urethral Catheter Biofilms Reveal Plasticity in Bacterial Composition and Metabolism and Withstand Host Immune Defenses in Hypoxic Environment.	Yu Y, Singh H, Tsitrin T, Bekele S, Lin YH, Sikorski P, Moncera KJ, Torralba MG, Morrow L, Wolcott R, Nelson KE, Pieper R.	Front Med (Lausanne)	10.3389/fmed.2021.667462	2021
	A completeness-independent method for pre-selection of closely related genomes for species delineation in prokaryotes.	Zhou Y, Zheng J, Wu Y, Zhang W, Jin J.	BMC Genomics	10.1186/s12864-020-6597-x	2020
Enzymology	Lectin-like activity of Lactobacillus acidophilus strain JCM 1026.	Mukai T, Arihara K, Itoh H.	FEMS Microbiol Lett	10.1016/0378-1097(92)90134-a	1992
Enzymology	Site and clinical significance of Alloscardovia omnicolens and Bifidobacterium species isolated in the clinical laboratory.	Mahlen SD, Clarridge JE.	J Clin Microbiol	10.1128/jcm.00555-09	2009
Genetics	Taxonogenomic description of four new Clostridium species isolated from human gut: 'Clostridium amazonitimonense', 'Clostridium merdae', 'Clostridium massilidielmoense' and 'Clostridium nigeriense'.	Alou MT, Ndongo S, Fregere L, Labas N, Andrieu C, Richez M, Couderc C, Baudoin JP, Abrahao J, Brah S, Diallo A, Sokhna C, Cassir N, La Scola B, Cadoret F, Raoult D.	New Microbes New Infect	10.1016/j.nmni.2017.11.003	2018
Genetics	Genomics of the Genus Bifidobacterium Reveals Species-Specific Adaptation to the Glycan-Rich Gut Environment.	Milani C, Turroni F, Duranti S, Lugli GA, Mancabelli L, Ferrario C, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.03500-15	2016
Metabolism	Structural and biochemical characterization of 20beta-hydroxysteroid dehydrogenase from Bifidobacterium adolescentis strain L2-32.	Doden HL, Pollet RM, Mythen SM, Wawrzak Z, Devendran S, Cann I, Koropatkin NM, Ridlon JM.	J Biol Chem	10.1074/jbc.ra119.009390	2019
Metabolism	Methanogenic food web in the gut contents of methane-emitting earthworm Eudrilus eugeniae from Brazil.	Schulz K, Hunger S, Brown GG, Tsai SM, Cerri CC, Conrad R, Drake HL.	ISME J	10.1038/ismej.2014.262	2015
Metabolism	Bifidobacterium dentium Fortifies the Intestinal Mucus Layer via Autophagy and Calcium Signaling Pathways.	Engevik MA, Luk B, Chang-Graham AL, Hall A, Herrmann B, Ruan W, Endres BT, Shi Z, Garey KW, Hyser JM, Versalovic J.	mBio	10.1128/mbio.01087-19	2019
Phylogeny	Genomic encyclopedia of type strains of the genus Bifidobacterium.	Milani C, Lugli GA, Duranti S, Turroni F, Bottacini F, Mangifesta M, Sanchez B, Viappiani A, Mancabelli L, Taminiau B, Delcenserie V, Barrangou R, Margolles A, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.02308-14	2014
	ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples.	Gonzalez E, Pitre FE, Brereton NJB.	Environ Microbiol	10.1111/1462-2920.14632	2019
	Isolation of Mycobacterium avium subspecies paratuberculosis reactive CD4 T cells from intestinal biopsies of Crohn's disease patients.	Olsen I, Tollefsen S, Aagaard C, Reitan LJ, Bannantine JP, Andersen P, Sollid LM, Lundin KE.	PLoS One	10.1371/journal.pone.0005641	2009
Metabolism	Characterization of the collagen-binding S-layer protein CbsA of Lactobacillus crispatus.	Sillanpaa J, Martinez B, Antikainen J, Toba T, Kalkkinen N, Tankka S, Lounatmaa K, Keranen J, Hook M, Westerlund-Wikstrom B, Pouwels PH, Korhonen TK.	J Bacteriol	10.1128/jb.182.22.6440-6450.2000	2000
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
Genetics	Complete Genome Sequence of Bifidobacterium scardovii Strain JCM 12489T, Isolated from Human Blood.	Toh H, Oshima K, Nakano A, Yamashita N, Iioka E, Kurokawa R, Morita H, Hattori M	Genome Announc	10.1128/genomeA.00285-15	2015
	Clostridium culturomicium sp. nov. and Clostridium jeddahitimonense sp. nov., novel members of the Clostridium genus isolated from the stool of an obese Saudi Arabian.	Kieu HT, Garrigou N, Fadlane A, Brechard L, Armstrong N, Decloquement P, Yasir M, Azhar EI, Al-Masaudi SB, Lagier JC, Tidjani Alou M, Raoult D.	Curr Microbiol	10.1007/s00284-021-02616-4	2021
Genetics	Parabacteroides pekinense sp. nov.: a new bacterium isolated from the stool of a healthy man living in China.	Li Z, Zhou X, Xu W, Chen R, Zhao B, Wu C.	New Microbes New Infect	10.1016/j.nmni.2022.100973	2022
	Philodulcilactobacillus myokoensis gen. nov., sp. nov., a fructophilic, acidophilic, and agar-phobic lactic acid bacterium isolated from fermented vegetable extracts.	Kouya T, Ishiyama Y, Ohashi S, Kumakubo R, Yamazaki T, Otaki T.	PLoS One	10.1371/journal.pone.0286677	2023
Genetics	Noncontiguous finished genome sequences and descriptions of Actinomyces ihuae, Actinomyces bouchesdurhonensis, Actinomyces urinae, Actinomyces marseillensis, Actinomyces mediterranea and Actinomyces oralis sp. nov. identified by culturomics.	Mbogning Fonkou MD, Mailhe M, Ndongo S, Ricaboni D, Morand A, Cornu F, Tidjani Alou M, Bilen M, Andrieu C, Levasseur A, Cadoret F, Raoult D.	New Microbes New Infect	10.1016/j.nmni.2018.06.004	2018
Phylogeny	Bifidobacterium aerophilum sp. nov., Bifidobacterium avesanii sp. nov. and Bifidobacterium ramosum sp. nov.: Three novel taxa from the faeces of cotton-top tamarin (Saguinus oedipus L.).	Michelini S, Modesto M, Filippini G, Spiezio C, Sandri C, Biavati B, Pisi A, Mattarelli P	Syst Appl Microbiol	10.1016/j.syapm.2016.04.005	2016
Phylogeny	Bifidobacterium aesculapii sp. nov., from the faeces of the baby common marmoset (Callithrix jacchus).	Modesto M, Michelini S, Stefanini I, Ferrara A, Tacconi S, Biavati B, Mattarelli P	Int J Syst Evol Microbiol	10.1099/ijs.0.056937-0	2014
Phylogeny	Bifidobacterium scardovii sp. nov., from human sources.	Hoyles L, Inganas E, Falsen E, Drancourt M, Weiss N, McCartney AL, Collins MD	Int J Syst Evol Microbiol	10.1099/00207713-52-3-995	2002

References

#5133	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13734
#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 )
#45872	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 13008 A
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#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 scardovii (DSM 13734, CCUG 13008 A, ATCC BAA-773)

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