Viridibacillus arvi (DSM 16317, LMG 22165, R-16993)

Name: Viridibacillus arvi (DSM 16317, LMG 22165, R-16993)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 570

Type strain

Strain Designation R-16993

Culture col. no. DSM 16317 LMG 22165 R-16993

NCBI tax ID(s) 263475

Special Collections DSMZ Literature strains

History <- J. Heyrman; R-16993 <- A. Felske

Links

Viridibacillus arvi R-16993 is an anaerobe, spore-forming, mesophilic prokaryote that forms irregular colonies and was isolated from soil.

spore-forming Gram-variable motile rod-shaped colony-forming anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 128652

LMG 22165,DSM 16317

@ref 20215

Last LPSN update 2026-02-09 11:17:54

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Viridibacillus

Species Viridibacillus arvi

Full scientific name Viridibacillus arvi (Heyrman et al. 2005) Albert et al. 2007

Synonyms (1)

Bacillus arvi

BacDive ID	Other strains from **Viridibacillus arvi** (1)	Type strain
139886	V. arvi 433-D9, DSM 16704

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
23359	variable	3.0-8.0 µm	0.8-1.0 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
23359	1.0-3.0 mm	cream	irregular	1 day	NA
23358					PCA, TSA and R2A

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6363	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
23359	BFA, NA
23358	PCA, TSA and R2A

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6363	positive	growth	30	mesophilic
23359	positive	growth	20-30
23359	negative	growth	45

Culture pH

@ref	Ability	Type	PH	PH range
23359		growth	5.0
23359	positive	growth	7-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
23359	anaerobe
125439	facultative anaerobe	93.8

Spore formation

@ref	Spore description	Type of spore	Spore formation	Confidence
23359	abundantly,spherical and appear in terminal positions, swelling the sporangia slightly	endospore
125438				90.547

Halophily

@ref	Salt	Growth	Tested relation	Concentration
23359	NaCl	positive	growth	5 %(w/v)
23359	NaCl		growth	7 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23359		casein	+/-	hydrolysis
23358	17057 ChEBI	cellobiose	-	builds acid from
23359	16947 ChEBI	citrate	-	other
23359	15824 ChEBI	D-fructose	+	builds acid from
23358	12936 ChEBI	D-galactose	-	builds acid from
23358	17634 ChEBI	D-glucose	-	builds acid from
23358	16899 ChEBI	D-mannitol	-	builds acid from
23358	16024 ChEBI	D-mannose	-	builds acid from
23358	16988 ChEBI	D-ribose	-	builds acid from
23358	65327 ChEBI	D-xylose	-	builds acid from
23359	4853 ChEBI	esculin	-	hydrolysis
23359	5291 ChEBI	gelatin	-	hydrolysis
23358	17754 ChEBI	glycerol	-	builds acid from
23359	16136 ChEBI	hydrogen sulfide	-	other
23358	30849 ChEBI	L-arabinose	-	builds acid from
23358	17716 ChEBI	lactose	-	builds acid from
23359	506227 ChEBI	N-acetylglucosamine	+/-	builds acid from
23359	17632 ChEBI	nitrate	-	reduction
23359	28017 ChEBI	starch	-	hydrolysis
23358	17992 ChEBI	sucrose	-	builds acid from
23359	27897 ChEBI	tryptophan	-	energy source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
23359	15688 ChEBI	acetoin
23359	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
23359	15688 ChEBI	acetoin	-
23359	35581 ChEBI	indole		-

Enzymes

@ref	Value	Activity	Ec
23359	arginine dihydrolase	-	3.5.3.6
23359	beta-galactosidase	+/-	3.2.1.23
23359	catalase	+	1.11.1.6
23359	cytochrome oxidase	-	1.9.3.1
23359	lysine decarboxylase	-	4.1.1.18
23359	ornithine decarboxylase	-	4.1.1.17
23359	tryptophan deaminase	-	4.1.99.1
23359	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6363	soil	Drentse A research area	Netherlands	NLD	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ627211 (>99% sequence identity) for Viridibacillus arvi from Microbeatlas

Aquatic Samples	689
Soil Samples	2124
Animal Samples	1411
Plant Samples	342
Total Samples	4566

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6363	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	ASM127494v1 assembly for Viridibacillus arvi DSM 16317	scaffold	GCA_001274945	263475.9	2651869790	263475	59.71

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
23359	Bacillus arvi partial 16S rRNA gene, type strain LMG 22165	AJ627211	1505		263475

GC content

@ref	GC-content (mol%)	Method
23359	35.0	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: Viridibacillus arvi DSM 16317
NCBI: GCA_001274945

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	85.30	no
125439	motility	BacteriaNetⓘ	yes	68.90	no
125439	gram_stain	BacteriaNetⓘ	variable	77.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	93.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Viridibacillus arvi DSM 16317
NCBI: GCA_001274945.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	61.77	yes
125438	anaerobic	anaerobicⓘ	no	96.86	no
125438	aerobic	aerobicⓘ	yes	68.33	yes
125438	spore-forming	spore-formingⓘ	yes	90.55	yes
125438	thermophilic	thermophileⓘ	no	94.07	yes
125438	flagellated	motile2+ⓘ	yes	81.72	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Strong Antimicrobial Activity of Silver Nanoparticles Obtained by the Green Synthesis in Viridibacillus sp. Extracts.	Singh P, Mijakovic I.	Front Microbiol	10.3389/fmicb.2022.820048	2022
Metabolism	Characterization of Three Different Unusual S-Layer Proteins from Viridibacillus arvi JG-B58 That Exhibits Two Super-Imposed S-Layer Proteins.	Suhr M, Lederer FL, Gunther TJ, Raff J, Pollmann K.	PLoS One	10.1371/journal.pone.0156785	2016
	Viridibacillus culture derived silver nanoparticles exert potent anticancer action in 2D and 3D models of lung cancer via mitochondrial depolarization-mediated apoptosis.	Joshi AS, Bapat MV, Singh P, Mijakovic I.	Mater Today Bio	10.1016/j.mtbio.2024.100997	2024
Phylogeny	Proposal of Viridibacillus gen. nov. and reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov., Viridibacillus arenosi comb. nov. and Viridibacillus neidei comb. nov.	Albert RA, Archambault J, Lempa M, Hurst B, Richardson C, Gruenloh S, Duran M, Worliczek HL, Huber BE, Rossello-Mora R, Schumann P, Busse HJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65256-0	2007
Phylogeny	Viridibacillus soli sp. nov., isolated from forest soil in Ailaoshan National Nature Reserve.	Xu Y, Zhao JY, Geng Y, Yuan HR, Li LL, Wen ML, Li MG, Tang SK	Arch Microbiol	10.1007/s00203-021-02676-x	2021
Phylogeny	Bacillus arenosi sp. nov., Bacillus arvi sp. nov. and Bacillus humi sp. nov., isolated from soil.	Heyrman J, Rodriguez-Diaz M, Devos J, Felske A, Logan NA, De Vos P	Int J Syst Evol Microbiol	10.1099/ijs.0.63240-0	2005

References

#6363	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16317
#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 )
#23358	Richard A. Albert, Julieta Archambault, Melissa Lempa, Beth Hurst, Christine Richardson, Stephanie Gruenloh, Metin Duran, Hanna Lucia Worliczek, Birgit E. Huber, Ramon Rosselló-Mora, Peter Schumann, Hans-Jürgen Busse: Proposal of Viridibacillus gen. nov. and reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov., Viridibacillus arenosi comb. nov. and Viridibacillus neidei comb. nov.. IJSEM 57: 2729 - 2737 2007 ( DOI 10.1099/ijs.0.65256-0 , PubMed 18048716 )
#23359	Jeroen Heyrman, Marina Rodríguez-Díaz, Joke Devos, Andreas Felske, Niall A. Logan, Paul De Vos: Bacillus arenosi sp. nov., Bacillus arvi sp. nov. and Bacillus humi sp. nov., isolated from soil. IJSEM 55: 111 - 117 2005 ( DOI 10.1099/ijs.0.63240-0 , PubMed 15653863 )
#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) .
#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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Viridibacillus arvi (DSM 16317, LMG 22165, R-16993)

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

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001274945

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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