Virgibacillus massiliensis (DSM 28587, CSUR P971, Vm-5)

Name: Virgibacillus massiliensis (DSM 28587, CSUR P971, Vm-5)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132494

Type strain

Strain Designation Vm-5

Culture col. no. DSM 28587 CSUR P971 Vm-5

NCBI tax ID(s) 61016

Special Collections DSMZ Cadoret human gut

Links

Virgibacillus massiliensis Vm-5 is a mesophilic prokaryote that was isolated from human stool, 10-year old healthy Amazonian boy.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406295

DSM 28587

@ref 20215

Last LPSN update 2025-12-16 10:01:31

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Virgibacillus

Species Virgibacillus massiliensis

Full scientific name Virgibacillus massiliensis Khelaifia et al. 2023

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24283	BHI MEDIUM (DSMZ Medium 215)		Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
24283	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.6

Spore formation

@ref	Spore formation	Confidence
125439		90.1
125438		94.902

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	methylglyoxal degradation	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	ribulose monophosphate pathway	100	2 of 2
66794	enterobactin biosynthesis	100	3 of 3
66794	aspartate and asparagine metabolism	100	9 of 9
66794	pentose phosphate pathway	100	11 of 11
66794	kanosamine biosynthesis II	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	lipoate biosynthesis	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	degradation of sugar alcohols	93.75	15 of 16
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	vitamin B1 metabolism	92.31	12 of 13
66794	starch degradation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	alanine metabolism	89.66	26 of 29
66794	valine metabolism	88.89	8 of 9
66794	pyrimidine metabolism	88.89	40 of 45
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	propanol degradation	85.71	6 of 7
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	purine metabolism	81.91	77 of 94
66794	peptidoglycan biosynthesis	80	12 of 15
66794	Entner Doudoroff pathway	80	8 of 10
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	glycine betaine biosynthesis	80	4 of 5
66794	heme metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	degradation of sugar acids	76	19 of 25
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	lysine metabolism	73.81	31 of 42
66794	proline metabolism	72.73	8 of 11
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tryptophan metabolism	68.42	26 of 38
66794	non-pathway related	68.42	26 of 38
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	cyanate degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	histidine metabolism	65.52	19 of 29
66794	methionine metabolism	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	degradation of pentoses	64.29	18 of 28
66794	vitamin B6 metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	sulfate reduction	61.54	8 of 13
66794	urea cycle	61.54	8 of 13
66794	degradation of hexoses	61.11	11 of 18
66794	propionate fermentation	60	6 of 10
66794	gallate degradation	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	arginine metabolism	58.33	14 of 24
66794	oxidative phosphorylation	56.04	51 of 91
66794	cysteine metabolism	55.56	10 of 18
66794	glycine metabolism	50	5 of 10
66794	ascorbate metabolism	50	11 of 22
66794	pantothenate biosynthesis	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	androgen and estrogen metabolism	50	8 of 16
66794	ethanol fermentation	50	1 of 2
66794	glutathione metabolism	50	7 of 14
66794	coenzyme M biosynthesis	50	5 of 10
66794	lipid metabolism	48.39	15 of 31
66794	cholesterol biosynthesis	45.45	5 of 11
66794	metabolism of disaccharids	45.45	5 of 11
66794	allantoin degradation	44.44	4 of 9
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	polyamine pathway	43.48	10 of 23
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	creatinine degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	phenol degradation	40	8 of 20
66794	myo-inositol biosynthesis	40	4 of 10
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	tyrosine metabolism	35.71	5 of 14
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	arachidonic acid metabolism	33.33	6 of 18
66794	octane oxidation	33.33	1 of 3
66794	mevalonate metabolism	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	#Child
#Host	#Human	#Male
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
24283	human stool, 10-year old healthy Amazonian boy	Brazil	BRA	Middle and South America

Taxonmaps

69479

Global distribution of 16S sequence HG931931 (>99% sequence identity) for Virgibacillus from Microbeatlas

Aquatic Samples	2
Soil Samples	3
Animal Samples	6
Plant Samples
Total Samples	11

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	PRJEB5515_assembly_1 assembly for Virgibacillus massiliensis Vm-5	contig	GCA_000723585	1462526.3	2617271113	1462526	76.24
66792	ASM1490547v1 assembly for Virgibacillus massiliensis Vm-5	scaffold	GCA_014905475	1462526.12	8119053442	1462526

Genome browser: GCA_000723585

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24283	Virgibacillus sp. Vm-5 partial 16S rRNA gene, isolate Vm-5	HG931931	1530		1462526

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Virgibacillus massiliensis Vm-5
NCBI: GCA_014905475

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	90.10	no
125439	motility	BacteriaNetⓘ	yes	86.10	no
125439	gram_stain	BacteriaNetⓘ	variable	75.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Virgibacillus massiliensis Vm-5
NCBI: GCA_014905475.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	83.45	no
125438	anaerobic	anaerobicⓘ	no	96.93	no
125438	aerobic	aerobicⓘ	yes	67.60	no
125438	spore-forming	spore-formingⓘ	yes	94.90	no
125438	thermophilic	thermophileⓘ	no	92.90	yes
125438	flagellated	motile2+ⓘ	yes	87.27	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Systematically investigating and identifying bacteriocins in the human gut microbiome.	Zhang D, Zou Y, Shi Y, Zhang J, Liu J, Wu G, Zhang J, Gao Y, Chen M, Li YX.	Cell Genom	10.1016/j.xgen.2025.100983	2025
Metabolism	Distribution of class IId bacteriocin-producing Virgibacillus salexigens in various environments.	Omachi H, Terahara T, Futami K, Kawato S, Imada C, Kamei K, Waku T, Kondo A, Naganuma T, Agustini TW, Kobayashi T	World J Microbiol Biotechnol	10.1007/s11274-021-03085-4	2021
Metabolism	Identification of a New Serine Alkaline Peptidase from the Moderately Halophilic Virgibacillus natechei sp. nov., Strain FarD(T) and its Application as Bioadditive for Peptide Synthesis and Laundry Detergent Formulations.	Mechri S, Bouacem K, Amziane M, Dab A, Nateche F, Jaouadi B	Biomed Res Int	10.1155/2019/6470897	2019
Genetics	Noncontiguous finished genome sequence and description of Virgibacillus massiliensis sp. nov., a moderately halophilic bacterium isolated from human gut.	Khelaifia S, Croce O, Lagier JC, Robert C, Couderc C, Di Pinto F, Davoust B, Djossou F, Raoult D, Fournier PE	New Microbes New Infect	10.1016/j.nmni.2015.09.012	2015

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 )
#24283	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28587
#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 )
#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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Virgibacillus massiliensis (DSM 28587, CSUR P971, Vm-5)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_000723585

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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