Bombilactobacillus mellifer (DSM 26316, CCUG 65819, Bin4)

Name: Bombilactobacillus mellifer (DSM 26316, CCUG 65819, Bin4)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130371

Type strain

Strain Designation Bin4

Culture col. no. DSM 26316 CCUG 65819 Bin4

NCBI tax ID(s) 1218492

Special Collections DSMZ CCUG

History <- T. Olofsson, Dept. Biotechnol., Lund Univ., Sweden; Bin4

Links

Bombilactobacillus mellifer Bin4 is an anaerobe, mesophilic prokaryote that was isolated from honey stomach of honey bee.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406309

DSM 26316,CCUG 65819

@ref 20215

Last LPSN update 2026-02-09 11:31:12

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Lactobacillaceae

Genus Bombilactobacillus

Species Bombilactobacillus mellifer

Full scientific name Bombilactobacillus mellifer (Olofsson et al. 2014) Zheng et al. 2020

Synonyms (1)

Lactobacillus mellifer

BacDive ID	Other strains from **Bombilactobacillus mellifer** (1)	Type strain
130370	B. mellifer Bin4N, DSM 26254, CCUG 63291, JCM 30768 (type strain)

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125438		93
125438		93.193	positive

Colony morphology

63254

Incubation period3 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21907	MRS MEDIUM (DSMZ Medium 11)		Medium recipe at MediaDive	Name: MRS MEDIUM (DSMZ Medium 11; with strain-specific modifications) Composition: Fructose 20.0 g/l Glucose 20.0 g/l Meat extract 10.0 g/l Casein peptone 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
21907	positive	growth	30	mesophilic
63254	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
21907	anaerobe
63254	anaerobe
125439	facultative anaerobe	95.5

Spore formation

@ref	Spore formation	Confidence
125439		98.9

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	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	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	gluconeogenesis	100	8 of 8
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	pentose phosphate pathway	100	11 of 11
66794	ribulose monophosphate pathway	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	acetoin degradation	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	degradation of sugar alcohols	93.75	15 of 16
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	vitamin B12 metabolism	82.35	28 of 34
66794	Entner Doudoroff pathway	80	8 of 10
66794	photosynthesis	78.57	11 of 14
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	ketogluconate metabolism	75	6 of 8
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	vitamin B1 metabolism	69.23	9 of 13
66794	purine metabolism	69.15	65 of 94
66794	NAD metabolism	66.67	12 of 18
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	valine metabolism	66.67	6 of 9
66794	serine metabolism	66.67	6 of 9
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	glycolysis	64.71	11 of 17
66794	phenylalanine metabolism	61.54	8 of 13
66794	cellulose degradation	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	glycogen metabolism	60	3 of 5
66794	pyrimidine metabolism	57.78	26 of 45
66794	methionine metabolism	53.85	14 of 26
66794	oxidative phosphorylation	53.85	49 of 91
66794	degradation of pentoses	53.57	15 of 28
66794	threonine metabolism	50	5 of 10
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	isoleucine metabolism	50	4 of 8
66794	sulfopterin metabolism	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	glutamate and glutamine metabolism	50	14 of 28
66794	ethanol fermentation	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	urea cycle	46.15	6 of 13
66794	proline metabolism	45.45	5 of 11
66794	lysine metabolism	45.24	19 of 42
66794	alanine metabolism	44.83	13 of 29
66794	d-mannose degradation	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	degradation of sugar acids	44	11 of 25
66794	heme metabolism	42.86	6 of 14
66794	propanol degradation	42.86	3 of 7
66794	mevalonate metabolism	42.86	3 of 7
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	non-pathway related	42.11	16 of 38
66794	arginine metabolism	41.67	10 of 24
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	methylglyoxal degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
66794	vitamin B6 metabolism	36.36	4 of 11
66794	metabolism of disaccharids	36.36	4 of 11
66794	tetrahydrofolate metabolism	35.71	5 of 14
66794	citric acid cycle	35.71	5 of 14
66794	lipid metabolism	35.48	11 of 31
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	cysteine metabolism	33.33	6 of 18
66794	IAA biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	leucine metabolism	30.77	4 of 13
66794	propionate fermentation	30	3 of 10
66794	starch degradation	30	3 of 10
66794	tryptophan metabolism	28.95	11 of 38
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	d-xylose degradation	27.27	3 of 11
66794	flavin biosynthesis	26.67	4 of 15
66794	lactate fermentation	25	1 of 4
66794	biotin biosynthesis	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	glycogen biosynthesis	25	1 of 4
66794	histidine metabolism	24.14	7 of 29
66794	sulfate reduction	23.08	3 of 13
66794	ascorbate metabolism	22.73	5 of 22
66794	nitrate assimilation	22.22	2 of 9
66794	lipid A biosynthesis	22.22	2 of 9
66794	glutathione metabolism	21.43	3 of 14
66794	tyrosine metabolism	21.43	3 of 14

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
21907	-	-	-	-	-	-	-	-	-	-	-	+	+/-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
21907	honey stomach of honey bee		Lund	Sweden	SWE	Europe
63254	Honey bee,honey stomach	2006	Helsingborg	Sweden	SWE	Europe

Taxonmaps

69479

Global distribution of 16S sequence EF187245 (>99% sequence identity) for Bombilactobacillus mellifer subclade from Microbeatlas

Aquatic Samples	127
Soil Samples	38
Animal Samples	3619
Plant Samples	155
Total Samples	3939

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21907	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
66792	ASM97079v1 assembly for Bombilactobacillus mellifer Bin4	scaffold	GCA_000970795	2630968413	1218492	72.88

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21907	Lactobacillus mellifer strain Bin4 16S ribosomal RNA gene, partial sequence	EF187245	1409		1218492

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bombilactobacillus mellifer Bin4
NCBI: GCA_000970795

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.90	no
125439	motility	BacteriaNetⓘ	no	71.00	no
125439	gram_stain	BacteriaNetⓘ	negative	73.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	95.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bombilactobacillus mellifer Bin4
NCBI: GCA_000970795.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	93.19	no
125438	anaerobic	anaerobicⓘ	no	61.33	yes
125438	aerobic	aerobicⓘ	no	97.14	yes
125438	spore-forming	spore-formingⓘ	no	87.78	no
125438	thermophilic	thermophileⓘ	no	94.40	no
125438	flagellated	motile2+ⓘ	no	93.00	no

Literature

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 )
#21907	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26316
#63254	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 65819
#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 )
#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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