Boudabousia liubingyangii (DSM 104050, CGMCC 4.7370, VUL4_1)

Name: Boudabousia liubingyangii (DSM 104050, CGMCC 4.7370, VUL4_1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140290

Type strain

Strain Designation VUL4_1

Culture col. no. DSM 104050 CGMCC 4.7370 VUL4_1

NCBI tax ID(s) 1921764

Special Collections DSMZ Literature strains

History <- X. Meng, Chinese Center for Disease Control and Prevention, Beijing, China; VUL4_1

Links

Boudabousia liubingyangii VUL4_1 is a facultative anaerobe, mesophilic, Gram-positive prokaryote that forms circular colonies and was isolated from faeces from a wild vulture Gypaetus barbatus.

Gram-positive rod-shaped colony-forming facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 405285

DSM 104050

@ref 20215

Last LPSN update 2025-12-16 10:03:33

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Actinomycetales

Family Actinomycetaceae

Genus Boudabousia

Species Boudabousia liubingyangii

Full scientific name Boudabousia liubingyangii (Meng et al. 2017) Yang et al. 2021

Synonyms (1)

Actinomyces liubingyangii

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
43236	positive	0.8-1.2 µm	0.6-1.0 µm	rod-shaped
125438						94

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43236	<1 mm	greyish white	circular	2 days	sheep-blood agar

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
43236	sheep-blood agar
42897	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
42897	BBL ACTINOMYCES BROTH (DSMZ Medium 1029)	Medium recipe at MediaDive	Name: BBL ACTINOMYCES BROTH (DSMZ Medium 1029) Composition: Infusion Broth 1.425 g/l Potassium Phosphate 0.855 g/l Dextrose 0.285 g/l Yeast extract 0.285 g/l Pancreatic digest of casein 0.228 g/l L-Cysteine HCl 0.057 g/l Starch 0.057 g/l Ammonium Sulfate 0.057 g/l Magnesium sulfate 0.0114 g/l Calcium Chloride 0.00057 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
42897	positive	growth	37	mesophilic
43236	positive	optimum	37	mesophilic

Culture pH

@ref	Ability	Type	PH
43236	positive	optimum	6-7

Physiology and metabolism

Oxygen tolerance

43236

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Type of spore	Spore formation
43236	spore

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43236	NaCl	positive	optimum	1 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43236	17057 ChEBI	cellobiose	-	builds acid from
43236	17108 ChEBI	D-arabinose	-	builds acid from
43236	18333 ChEBI	D-arabitol	-	builds acid from
43236	15824 ChEBI	D-fructose	+	builds acid from
43236	28847 ChEBI	D-fucose	-	builds acid from
43236	12936 ChEBI	D-galactose	+	builds acid from
43236	17634 ChEBI	D-glucose	+	builds acid from
43236	62318 ChEBI	D-lyxose	-	builds acid from
43236	16024 ChEBI	D-mannose	+	builds acid from
43236	16988 ChEBI	D-ribose	-	builds acid from
43236	65327 ChEBI	D-xylose	+	builds acid from
43236	17113 ChEBI	erythritol	-	builds acid from
43236	16813 ChEBI	galactitol	-	builds acid from
43236	5291 ChEBI	gelatin	-	hydrolysis
43236	28066 ChEBI	gentiobiose	-	builds acid from
43236	17754 ChEBI	glycerol	+	builds acid from
43236	28087 ChEBI	glycogen	-	builds acid from
43236	606565 ChEBI	hippurate	+	hydrolysis
43236	15443 ChEBI	inulin	-	builds acid from
43236	30849 ChEBI	L-arabinose	-	builds acid from
43236	18403 ChEBI	L-arabitol	-	builds acid from
43236	18287 ChEBI	L-fucose	-	builds acid from
43236	62345 ChEBI	L-rhamnose	-	builds acid from
43236	17266 ChEBI	L-sorbose	-	builds acid from
43236	65328 ChEBI	L-xylose	-	builds acid from
43236	17716 ChEBI	lactose	+	builds acid from
43236	17306 ChEBI	maltose	+	builds acid from
43236	6731 ChEBI	melezitose	-	builds acid from
43236	28053 ChEBI	melibiose	-	builds acid from
43236	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
43236	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
43236		methyl alpha-D-xylopyranoside	-	builds acid from
43236	320055 ChEBI	methyl beta-D-glucopyranoside	-	builds acid from
43236	506227 ChEBI	N-acetylglucosamine	+	builds acid from
43236		potassium 2-dehydro-D-gluconate	-	builds acid from
43236		potassium 5-dehydro-D-gluconate	+/-	builds acid from
43236	32032 ChEBI	potassium gluconate	-	builds acid from
43236	16634 ChEBI	raffinose	-	builds acid from
43236	15963 ChEBI	ribitol	-	builds acid from
43236	17814 ChEBI	salicin	-	builds acid from
43236	28017 ChEBI	starch	-	builds acid from
43236	17992 ChEBI	sucrose	-	builds acid from
43236	27082 ChEBI	trehalose	-	builds acid from
43236	32528 ChEBI	turanose	-	builds acid from
43236	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43236	15688 ChEBI	acetoin

Enzymes

@ref	Value	Activity	Ec
43236	acid phosphatase	+/-	3.1.3.2
43236	alkaline phosphatase	+	3.1.3.1
43236	alpha-fucosidase	-	3.2.1.51
43236	alpha-galactosidase	-	3.2.1.22
43236	alpha-glucosidase	+	3.2.1.20
43236	alpha-mannosidase	-	3.2.1.24
43236	arginine dihydrolase	-	3.5.3.6
43236	beta-galactosidase	+	3.2.1.23
43236	beta-glucosidase	-	3.2.1.21
43236	beta-glucuronidase	-	3.2.1.31
43236	beta-mannosidase	-	3.2.1.25
43236	catalase	-	1.11.1.6
43236	cystine arylamidase	-	3.4.11.3
43236	glycyl tryptophan arylamidase	+
43236	leucine arylamidase	+	3.4.11.1
43236	lipase (C 14)	-
43236	N-acetyl-beta-glucosaminidase	+	3.2.1.52
43236	naphthol-AS-BI-phosphohydrolase	+
43236	pyrazinamidase	+	3.5.1.B15
43236	pyroglutamic acid arylamidase	-
43236	pyrrolidonyl arylamidase	-	3.4.19.3
43236	tripeptide aminopeptidase	+	3.4.11.4
43236	trypsin	+/-	3.4.21.4
43236	urease	-	3.5.1.5
43236	valine arylamidase	-

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	starch degradation	100	10 of 10
66794	acetate fermentation	100	4 of 4
66794	vitamin K metabolism	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	teichoic acid biosynthesis	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	chorismate metabolism	88.89	8 of 9
66794	palmitate biosynthesis	86.36	19 of 22
66794	peptidoglycan biosynthesis	80	12 of 15
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	glycogen biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	purine metabolism	71.28	67 of 94
66794	pyrimidine metabolism	71.11	32 of 45
66794	glycolysis	70.59	12 of 17
66794	UDP-GlcNAc biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	methionine metabolism	61.54	16 of 26
66794	phenylalanine metabolism	61.54	8 of 13
66794	vitamin B1 metabolism	61.54	8 of 13
66794	NAD metabolism	61.11	11 of 18
66794	glycogen metabolism	60	3 of 5
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	valine metabolism	55.56	5 of 9
66794	oxidative phosphorylation	53.85	49 of 91
66794	ethanol fermentation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	isoleucine metabolism	50	4 of 8
66794	tetrahydrofolate metabolism	50	7 of 14
66794	suberin monomers biosynthesis	50	1 of 2
66794	non-pathway related	47.37	18 of 38
66794	proline metabolism	45.45	5 of 11
66794	alanine metabolism	44.83	13 of 29
66794	tryptophan metabolism	44.74	17 of 38
66794	cysteine metabolism	44.44	8 of 18
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	serine metabolism	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	glutamate and glutamine metabolism	42.86	12 of 28
66794	tyrosine metabolism	42.86	6 of 14
66794	threonine metabolism	40	4 of 10
66794	glycine metabolism	40	4 of 10
66794	coenzyme M biosynthesis	40	4 of 10
66794	Entner Doudoroff pathway	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	pentose phosphate pathway	36.36	4 of 11
66794	metabolism of disaccharids	36.36	4 of 11
66794	citric acid cycle	35.71	5 of 14
66794	lipid metabolism	35.48	11 of 31
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	pantothenate biosynthesis	33.33	2 of 6
66794	L-lactaldehyde degradation	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	degradation of sugar alcohols	31.25	5 of 16
66794	leucine metabolism	30.77	4 of 13
66794	propionate fermentation	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	degradation of pentoses	28.57	8 of 28
66794	lysine metabolism	28.57	12 of 42
66794	histidine metabolism	27.59	8 of 29
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	vitamin B6 metabolism	27.27	3 of 11
66794	flavin biosynthesis	26.67	4 of 15
66794	polyamine pathway	26.09	6 of 23
66794	cyclohexanol degradation	25	1 of 4
66794	arginine metabolism	25	6 of 24
66794	lactate fermentation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	degradation of aromatic, nitrogen containing compounds	25	3 of 12
66794	CMP-KDO biosynthesis	25	1 of 4
66794	urea cycle	23.08	3 of 13
66794	arachidonic acid metabolism	22.22	4 of 18
66794	nitrate assimilation	22.22	2 of 9
66794	allantoin degradation	22.22	2 of 9
66794	heme metabolism	21.43	3 of 14
66794	glutathione metabolism	21.43	3 of 14

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Birds	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)
#Host Body-Site	#Gastrointestinal tract	#Rectum
#Infection	#Patient	#Swab

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
42897	faeces (rectal swab) from a wild vulture Gypaetus barbatus	Gypaetus barbatus	Tibetan autonomous region, Qinghai province	China	CHN	Asia
43236	faecal sample of a wild vulture		The Tibetan autonomous region, Qinghai province, China	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence KY268292 (>99% sequence identity) for Boudabousia from Microbeatlas

Aquatic Samples	18
Soil Samples	17
Animal Samples	3202
Plant Samples	1
Total Samples	3238

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42897	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
66792	ASM190724v1 assembly for Boudabousia liubingyangii VUL4_1	scaffold	GCA_001907245	2788500611	1921764	74.89

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
42897	Boudabousia liubingyangii strain VUL4_1 16S ribosomal RNA gene, partial sequence	KY268292	1455		1921764

GC content

@ref	GC-content (mol%)	Method
43236	54.9	genome sequence analysis
42897	54.9	sequence analysis

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Boudabousia liubingyangii VUL4_1
NCBI: GCA_001907245.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.35	no
125438	anaerobic	anaerobicⓘ	no	77.87	no
125438	aerobic	aerobicⓘ	no	82.55	yes
125438	spore-forming	spore-formingⓘ	no	88.34	yes
125438	thermophilic	thermophileⓘ	no	97.48	yes
125438	flagellated	motile2+ⓘ	no	94.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Actinomyces liubingyangii sp. nov. isolated from the vulture Gypaetus barbatus.	Meng X, Lu S, Lai XH, Wang Y, Wen Y, Jin D, Yang J, Xu J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001884	2017

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 )
#42897	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104050
#43236	Xiangli Meng, Shan Lu, Xin-He Lai, Yiting Wang, Yumeng Wen, Dong Jin, Jing Yang and Jianguo Xu: Actinomyces liubingyangii sp. nov. isolated from the vulture Gypaetus barbatus. IJSEM 67: 1873 - 1879 2017 ( DOI 10.1099/ijsem.0.001884 , PubMed 28629506 )
#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 )
#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 )
#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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Boudabousia liubingyangii (DSM 104050, CGMCC 4.7370, VUL4_1)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001907245

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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