Bifidobacterium biavatii (DSM 23969, JCM 17299, AFB23-4)

Name: Bifidobacterium biavatii (DSM 23969, JCM 17299, AFB23-4)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1756

Type strain

Strain Designation AFB23-4

Culture col. no. DSM 23969 JCM 17299 AFB23-4 KCTC 15319

NCBI tax ID(s) 1437608 762212

Special Collections DSMZ JCM KCTC

History <- A. Endo, Dept. Microbiology, Stellenbosch Univ., South Africa; AFB23-4 A. Endo AFB23-4.

Links

Bifidobacterium biavatii AFB23-4 is an anaerobe, mesophilic prokaryote that was isolated from feces of tamarin .

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 379792

DSM 23969,JCM 17299,LMG 27583

@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 biavatii

Full scientific name Bifidobacterium biavatii Endo et al. 2012

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125438		90.5
125439		95.3	positive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17460	BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)		Medium recipe at MediaDive	Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
17460	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

17460

Oxygen toleranceanaerobe

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		Potassium 5-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	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	peptidoglycan biosynthesis	100	15 of 15
66794	ppGpp biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	starch degradation	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
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	acetoin degradation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	vitamin B1 metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	photosynthesis	85.71	12 of 14
66794	pentose phosphate pathway	81.82	9 of 11
66794	cellulose degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	lipoate biosynthesis	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	serine metabolism	77.78	7 of 9
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	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	NAD metabolism	72.22	13 of 18
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	phenylalanine metabolism	69.23	9 of 13
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	glycolysis	64.71	11 of 17
66794	d-xylose degradation	63.64	7 of 11
66794	metabolism of disaccharids	63.64	7 of 11
66794	isoleucine metabolism	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	purine metabolism	61.7	58 of 94
66794	methionine metabolism	61.54	16 of 26
66794	degradation of hexoses	61.11	11 of 18
66794	methylglyoxal degradation	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	pyrimidine metabolism	60	27 of 45
66794	glutathione metabolism	57.14	8 of 14
66794	glutamate and glutamine metabolism	57.14	16 of 28
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	oxidative phosphorylation	57.14	52 of 91
66794	degradation of sugar alcohols	56.25	9 of 16
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	d-mannose degradation	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	leucine metabolism	53.85	7 of 13
66794	urea cycle	53.85	7 of 13
66794	degradation of pentoses	53.57	15 of 28
66794	non-pathway related	52.63	20 of 38
66794	degradation of sugar acids	52	13 of 25
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	citric acid cycle	50	7 of 14
66794	tetrahydrofolate metabolism	50	7 of 14
66794	adipate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	coenzyme A metabolism	50	2 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	butanoate fermentation	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	quinate degradation	50	1 of 2
66794	cysteine metabolism	50	9 of 18
66794	arginine metabolism	45.83	11 of 24
66794	proline metabolism	45.45	5 of 11
66794	vitamin B6 metabolism	45.45	5 of 11
66794	propanol degradation	42.86	3 of 7
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	lipid metabolism	41.94	13 of 31
66794	lysine metabolism	40.48	17 of 42
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	propionate fermentation	40	4 of 10
66794	tryptophan metabolism	39.47	15 of 38
66794	tyrosine metabolism	35.71	5 of 14
66794	cyanate degradation	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	sulfoquinovose degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	octane oxidation	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	polyamine pathway	30.43	7 of 23
66794	myo-inositol biosynthesis	30	3 of 10
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	CMP-KDO biosynthesis	25	1 of 4
66794	sulfate reduction	23.08	3 of 13
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	nitrate assimilation	22.22	2 of 9

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
17460	-	-	-	-	+	-	+	-	-	-	+	+	+	+	-	-	-	-	-	-	+	+	+	+	+	+	+	+	+	+	+	+	-	-	-	+	+	+	-	+	+	-	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Primates
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17460	feces of tamarin (red-handed marmoset)	Cape Town	South Africa	ZAF	Africa
67770	Feces of a red-handed tamarin collected at Cape Town		South Africa	ZAF	Africa

Taxonmaps

69479

Global distribution of 16S sequence LC519989 (>99% sequence identity) for Bifidobacterium biavatii subclade from Microbeatlas

Aquatic Samples	308
Soil Samples	125
Animal Samples	33798
Plant Samples	61
Total Samples	34292

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17460	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
67770	Bifbia assembly for Bifidobacterium biavatii DSM 23969	contig	GCA_000741165	1437608.3	2597490240	1437608	67.14
67770	DSM-23969 assembly for Bifidobacterium biavatii DSM 23969	contig	GCA_000771645	1437608.4	2657245625	1437608	58.06

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17460	Bifidobacterium biavatii gene for 16S rRNA, partial sequence	AB559506	1441		1437608
67770	Bifidobacterium biavatii JCM 17299 gene for 16S rRNA, partial sequence	LC519989	1431		762212

GC content

@ref	GC-content (mol%)	Method
17460	63.1	high performance liquid chromatography (HPLC)
67770	63.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bifidobacterium biavatii DSM 23969
NCBI: GCA_000771645

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	80.40	no
125439	motility	BacteriaNetⓘ	no	74.70	no
125439	gram_stain	BacteriaNetⓘ	positive	95.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	84.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bifidobacterium biavatii DSM 23969
PATRIC: 1437608.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	86.02	no
125438	anaerobic	anaerobicⓘ	yes	74.08	no
125438	spore-forming	spore-formingⓘ	no	87.61	no
125438	aerobic	aerobicⓘ	no	85.16	yes
125438	thermophilic	thermophileⓘ	no	92.50	yes
125438	flagellated	motile2+ⓘ	no	90.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genetic insights into the dark matter of the mammalian gut microbiota through targeted genome reconstruction.	Lugli GA, Alessandri G, Milani C, Viappiani A, Fontana F, Tarracchini C, Mancabelli L, Argentini C, Ruiz L, Margolles A, van Sinderen D, Turroni F, Ventura M.	Environ Microbiol	10.1111/1462-2920.15559	2021
Genetics	Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches.	Lugli GA, Milani C, Duranti S, Alessandri G, Turroni F, Mancabelli L, Tatoni D, Ossiprandi MC, van Sinderen D, Ventura M.	Genome Biol	10.1186/s13059-019-1711-6	2019
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
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
Phylogeny	Phylogenetic Analysis of the Bifidobacterium Genus Using Glycolysis Enzyme Sequences.	Brandt K, Barrangou R.	Front Microbiol	10.3389/fmicb.2016.00657	2016
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
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
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
Phylogeny	Five novel bifidobacterial species isolated from faeces of primates in two Czech zoos: Bifidobacterium erythrocebi sp. nov., Bifidobacterium moraviense sp. nov., Bifidobacterium oedipodis sp. nov., Bifidobacterium olomucense sp. nov. and Bifidobacterium panos sp. nov.	Neuzil-Bunesova V, Lugli GA, Modrackova N, Vlkova E, Bolechova P, Burtscher J, Longhi G, Mancabelli L, Killer J, Domig K, Ventura M	Int J Syst Evol Microbiol	10.1099/ijsem.0.004573	2020
Phylogeny	Characterization of the phylogenetic diversity of five novel species belonging to the genus Bifidobacterium: Bifidobacterium castoris sp. nov., Bifidobacterium callimiconis sp. nov., Bifidobacterium goeldii sp. nov., Bifidobacterium samirii sp. nov. and Bifidobacterium dolichotidis sp. nov.	Duranti S, Lugli GA, Napoli S, Anzalone R, Milani C, Mancabelli L, Alessandri G, Turroni F, Ossiprandi MC, van Sinderen D, Ventura M	Int J Syst Evol Microbiol	10.1099/ijsem.0.003306	2019
Phylogeny	Bifidobacterium reuteri sp. nov., Bifidobacterium callitrichos sp. nov., Bifidobacterium saguini sp. nov., Bifidobacterium stellenboschense sp. nov. and Bifidobacterium biavatii sp. nov. isolated from faeces of common marmoset (Callithrix jacchus) and red-handed tamarin (Saguinus midas).	Endo A, Futagawa-Endo Y, Schumann P, Pukall R, Dicks LM	Syst Appl Microbiol	10.1016/j.syapm.2011.11.006	2012

References

#17460	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23969
#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 )
#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 biavatii (DSM 23969, JCM 17299, AFB23-4)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Pathway annotation

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000741165

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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