Bombiscardovia coagulans (DSM 22924, ATCC BAA-1568, BLAPIII-AGV)

Name: Bombiscardovia coagulans (DSM 22924, ATCC BAA-1568, BLAPIII-AGV)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1768

Type strain

Strain Designation BLAPIII-AGV

Culture col. no. DSM 22924 ATCC BAA-1568 BLAPIII-AGV

NCBI tax ID(s) 686666

Special Collections DSMZ

History DSMZ <- J. Killer, Inst. Animal Physiol. and Genetics, Czech Acad. Sci., Prague; BLAPIII-AGV

Links

Bombiscardovia coagulans BLAPIII-AGV is an anaerobe bacterium that was isolated from bumblebee digestive tract.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407803

LMG 28283,ATCC BAA-1568,DSM 22924

@ref 20215

Last LPSN update 2026-05-29 08:25:20

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Bombiscardovia

Species Bombiscardovia coagulans

Full scientific name Bombiscardovia coagulans Killer et al. 2014

Morphology

Cell morphology

@ref	Motility	Confidence
125438		95
125439		92.891

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16621	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)		Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
16621	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
16621	anaerobe
125439	facultative anaerobe	94.556

Spore formation

@ref	Spore formation	Confidence
125439		98.322

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	+	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	+	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

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

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	acetate fermentation	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	chorismate metabolism	88.89	8 of 9
66794	palmitate biosynthesis	86.36	19 of 22
66794	pentose phosphate pathway	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	metabolism of disaccharids	72.73	8 of 11
66794	photosynthesis	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	phenylalanine metabolism	69.23	9 of 13
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	d-xylose degradation	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	ketogluconate metabolism	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	starch degradation	60	6 of 10
66794	glycogen metabolism	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	oxidative phosphorylation	58.24	53 of 91
66794	mevalonate metabolism	57.14	4 of 7
66794	degradation of pentoses	57.14	16 of 28
66794	serine metabolism	55.56	5 of 9
66794	valine metabolism	55.56	5 of 9
66794	NAD metabolism	55.56	10 of 18
66794	pyrimidine metabolism	55.56	25 of 45
66794	methionine metabolism	53.85	14 of 26
66794	glycolysis	52.94	9 of 17
66794	purine metabolism	51.06	48 of 94
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	coenzyme A metabolism	50	2 of 4
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	glycogen biosynthesis	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	adipate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	vitamin B1 metabolism	46.15	6 of 13
66794	non-pathway related	44.74	17 of 38
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	propanol degradation	42.86	3 of 7
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	tetrahydrofolate metabolism	42.86	6 of 14
66794	tyrosine metabolism	42.86	6 of 14
66794	alanine metabolism	41.38	12 of 29
66794	glycine metabolism	40	4 of 10
66794	Entner Doudoroff pathway	40	4 of 10
66794	cellulose degradation	40	2 of 5
66794	glutamate and glutamine metabolism	39.29	11 of 28
66794	lipid metabolism	38.71	12 of 31
66794	C4 and CAM-carbon fixation	37.5	3 of 8
66794	isoprenoid biosynthesis	34.62	9 of 26
66794	lipid A biosynthesis	33.33	3 of 9
66794	degradation of hexoses	33.33	6 of 18
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	flavin biosynthesis	33.33	5 of 15
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	L-lactaldehyde degradation	33.33	1 of 3
66794	leucine metabolism	30.77	4 of 13
66794	threonine metabolism	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	arginine metabolism	29.17	7 of 24
66794	tryptophan metabolism	28.95	11 of 38
66794	cysteine metabolism	27.78	5 of 18
66794	histidine metabolism	27.59	8 of 29
66794	ascorbate metabolism	27.27	6 of 22
66794	vitamin B6 metabolism	27.27	3 of 11
66794	proline metabolism	27.27	3 of 11
66794	lysine metabolism	26.19	11 of 42
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	gluconeogenesis	25	2 of 8
66794	urea cycle	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9
66794	glutathione metabolism	21.43	3 of 14

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
16621	-	-	+	+	-	+	+	+	-	-	-	+	+	-	-	-	-	+	+	-	+	+	-	+	-	-	+	-	+

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
16621	bumblebee digestive tract	Czech Republic	CZE	Europe

Taxonmaps

69479

Global distribution of 16S sequence EU127550 (>99% sequence identity) for Bombiscardovia coagulans subclade from Microbeatlas

Aquatic Samples	8
Soil Samples	7
Animal Samples	311
Plant Samples	1
Total Samples	327

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16621	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	ASM225958v1 assembly for Bombiscardovia coagulans DSM 22924	contig	GCA_002259585	686666.4	2788500098	686666	72.08

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16621	Bombiscardovia coagulans strain BLAPIII-AGV 16S ribosomal RNA gene, partial sequence	EU127550	1420		686666

GC content

@ref	GC-content (mol%)	Method
16621	46.6	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: ASM225958v1 assembly for Bombiscardovia coagulans DSM 22924
BV-BRC: 686666.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	94.56	no
125439	gram_stain	BacteriaNetⓘ	positive	86.07	no
125439	motility	BacteriaNetⓘ	no	92.89	no
125439	spore_formation	BacteriaNetⓘ	no	98.32	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bombiscardovia coagulans strain DSM 22924
PATRIC: 686666.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	80.52	no
125438	anaerobic	anaerobicⓘ	yes	69.29	yes
125438	spore-forming	spore-formingⓘ	no	87.52	no
125438	aerobic	aerobicⓘ	no	93.50	yes
125438	thermophilic	thermophileⓘ	no	95.01	yes
125438	flagellated	motile2+ⓘ	no	95.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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
Phylogeny	Bombiscardovia coagulans gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of bumblebees.	Killer J, Kopecny J, Mrazek J, Havlik J, Koppova I, Benada O, Rada V, Kofronova O	Syst Appl Microbiol	10.1016/j.syapm.2010.08.002	2010

References

#16621	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22924
#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 )
#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 )
#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 .
#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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Bombiscardovia coagulans (DSM 22924, ATCC BAA-1568, BLAPIII-AGV)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002259585

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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