Bifidobacterium xylocopae (DSM 104955, LMG 30142, XV2)

Name: Bifidobacterium xylocopae (DSM 104955, LMG 30142, XV2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158514

Type strain

Strain Designation XV2

Culture col. no. DSM 104955 LMG 30142 XV2 JCM 33372

NCBI tax ID(s) 2493119

Special Collections DSMZ JCM

History <- D. Alberoni; University of Bologna, Bologna, ITALY; XV2 <-Teagasc <-Unibo LMG 30142 <-- D. Alberoni; Dept. of Agric. & Food Sci., Univ. of Bologna, Italy; XV2.

Links

Bifidobacterium xylocopae XV2 is a mesophilic prokaryote that was isolated from Isolated from the gut of Xylocopa violacea .

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 404932

LMG 30142,JCM 33372,DSM 104955

@ref 20215

Last LPSN update 2026-02-09 11:38:21

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Bifidobacterium

Species Bifidobacterium xylocopae

Full scientific name Bifidobacterium xylocopae Alberoni et al. 2019

BacDive ID	Other strains from **Bifidobacterium xylocopae** (1)	Type strain
158515	B. xylocopae XV16, DSM 106833, LMG 30564

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	94.1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
65191	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
65191	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	anaerobe	98

Spore formation

@ref	Spore formation	Confidence
125439		96.3

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Arthropoda	#Insecta
#Host Body-Site	#Gastrointestinal tract	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Host species
65191	Isolated from the gut of Xylocopa violacea (Carpenter solitary bee)	(44.526268, 10.994889)	Italy	ITA	Europe
67770	Gut samples of carpenter bees (Xylocopa violacea)		Italy	ITA	Europe	Xylocopa violacea

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM331561v1 assembly for Bifidobacterium xylocopae XV2	contig	GCA_003315615	2041613.3	2865983822	2493119	50.82

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
65191	Bifidobacterium xylocopae strain XV2 16S ribosomal RNA gene, partial sequence	MH043275	1500		2493119

GC content

@ref	GC-content (mol%)	Method
67770	61.3	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 xylocopae XV2
NCBI: GCA_003315615

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.30	no
125439	motility	BacteriaNetⓘ	no	86.60	no
125439	gram_stain	BacteriaNetⓘ	positive	94.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Exploring the biodiversity of Bifidobacterium asteroides among honey bee microbiomes.	Lugli GA, Fontana F, Tarracchini C, Mancabelli L, Milani C, Turroni F, Ventura M.	Environ Microbiol	10.1111/1462-2920.16223	2022
	Symbiosis of Carpenter Bees with Uncharacterized Lactic Acid Bacteria Showing NAD Auxotrophy.	Kawasaki S, Ozawa K, Mori T, Yamamoto A, Ito M, Ohkuma M, Sakamoto M, Matsutani M.	Microbiol Spectr	10.1128/spectrum.00782-23	2023
Metabolism	Unique Microbial Catabolic Pathway for the Human Core N-Glycan Constituent Fucosyl-alpha-1,6-N-Acetylglucosamine-Asparagine.	Becerra JE, Rodriguez-Diaz J, Gozalbo-Rovira R, Palomino-Schatzlein M, Zuniga M, Monedero V, Yebra MJ.	mBio	10.1128/mbio.02804-19	2020
	Bifidobacterium mizhiense sp. nov., isolated from the gut of honeybee (Apis mellifera).	Li TT, Zhang HX, Gu CT.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005390	2022
Phylogeny	Bifidobacterium xylocopae sp. nov. and Bifidobacterium aemilianum sp. nov., from the carpenter bee (Xylocopa violacea) digestive tract.	Alberoni D, Gaggia F, Baffoni L, Modesto MM, Biavati B, Di Gioia D	Syst Appl Microbiol	10.1016/j.syapm.2018.11.005	2018

References

#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#65191	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104955
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 xylocopae (DSM 104955, LMG 30142, XV2)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003315615

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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