Name: Viridibacillus arvi R-16993
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 570

Type strain:

Species: Viridibacillus arvi

Strain Designation: R-16993

Culture col. no.: DSM 16317, LMG 22165

Strain history: <- J. Heyrman; R-16993 <- A. Felske

NCBI tax ID(s): 263475 (species)

SI-ID 128652

LMG 22165, DSM 16317

Other strains from Viridibacillus arvi

V. arvi 433-D9, DSM 16704

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Bacillaceae*
	Genus	*Viridibacillus*
	Species	**Viridibacillus arvi**
	Full Scientific Name (LPSN)	Viridibacillus arvi (Heyrman et al. 2005) Albert et al. 2007

Synonym

Bacillus arvi

Information on morphological and physiological properties Morphology

[Ref.: #23359]	Gram stain	variable
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #23359]	Cell length	3.0-8.0 µm

[Ref.: #23359]	Cell width	0.8-1.0 µm

[Ref.: #23359]	Cell shape	rod-shaped

[Ref.: #23359]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %91.173

[Ref.: #23359]	Colony size	1.0-3.0 mm
[Ref.: #23359]	Colony color	cream
[Ref.: #23359]	Colony shape	irregular
[Ref.: #23359]	Incubation period	1 day
[Ref.: #23359]	Cultivation medium used	NA

[Ref.: #23358]	Cultivation medium used	PCA, TSA and R2A

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6363]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #6363]

Culture medium composition

expand / minimize

[Ref.: #23359]

Culture medium

BFA, NA

[Ref.: #23359]

Culture medium growth

[Ref.: #23358]

Culture medium

PCA, TSA and R2A

[Ref.: #23358]

Culture medium growth

	Kind of temperature		Temperature
[Ref.: #6363]		growth	30 °C
[Ref.: #23359]		growth	20-30 °C
[Ref.: #23359]	no	growth	45 °C

[Ref.: #6363]	Temperature range	mesophilic
[Ref.: #23359]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #23359]		no	growth	5.0
[Ref.: #23359]			growth	7-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23359]

Oxygen tolerance

anaerobe

[Ref.: #23359]	Spore description	abundantly,spherical and appear in terminal positions, swelling the sporangia slightly
[Ref.: #23359]	Type of spore	endospore
[Ref.: #23359]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23359]		NaCl		growth	5	%(w/v)
[Ref.: #23359]		NaCl	no	growth	7	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23359]	casein	+/-	hydrolysis
[Ref.: #23358]	cellobiose ChEBI	-	builds acid from
[Ref.: #23359]	citrate ChEBI	-	other
[Ref.: #23359]	D-fructose ChEBI	+	builds acid from
[Ref.: #23358]	D-galactose ChEBI	-	builds acid from
[Ref.: #23358]	D-glucose ChEBI	-	builds acid from
[Ref.: #23358]	D-mannitol ChEBI	-	builds acid from
[Ref.: #23358]	D-mannose ChEBI	-	builds acid from
[Ref.: #23358]	D-ribose ChEBI	-	builds acid from
[Ref.: #23358]	D-xylose ChEBI	-	builds acid from
[Ref.: #23359]	esculin ChEBI	-	hydrolysis
[Ref.: #23359]	gelatin ChEBI	-	hydrolysis
[Ref.: #23358]	glycerol ChEBI	-	builds acid from
[Ref.: #23359]	hydrogen sulfide ChEBI	-	other
[Ref.: #23358]	L-arabinose ChEBI	-	builds acid from
[Ref.: #23358]	lactose ChEBI	-	builds acid from
[Ref.: #23359]	N-acetylglucosamine ChEBI	+/-	builds acid from
[Ref.: #23359]	nitrate ChEBI	-	reduction
[Ref.: #23359]	starch ChEBI	-	hydrolysis
[Ref.: #23358]	sucrose ChEBI	-	builds acid from
[Ref.: #23359]	tryptophan ChEBI	-	energy source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #23359]		acetoin ChEBI	no
[Ref.: #23359]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #23359]		acetoin ChEBI	-
[Ref.: #23359]		indole ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #23359]	arginine dihydrolase	-	3.5.3.6
[Ref.: #23359]	beta-galactosidase	+/-	3.2.1.23
[Ref.: #23359]	catalase	+	1.11.1.6
[Ref.: #23359]	cytochrome oxidase	-	1.9.3.1
[Ref.: #23359]	lysine decarboxylase	-	4.1.1.18
[Ref.: #23359]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #23359]	tryptophan deaminase	-	4.1.99.1
[Ref.: #23359]	urease	+	3.5.1.5

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #6363]	Sample type/isolated from	soil
[Ref.: #6363]	Geographic location (country and/or sea, region)	Drentse A research area
[Ref.: #6363]	Country	Netherlands
[Ref.: #6363]	Country ISO 3 Code	NLD
[Ref.: #6363]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #6363]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #23359]	Bacillus arvi partial 16S rRNA gene, type strain LMG 22165	AJ627211	1505	GenBank	263475 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Viridibacillus arvi DSM 16317	GCA_001274945	scaffold	GenBank	263475 tax ID	*
[Ref.: #66792]	Viridibacillus arvi strain DSM 16317	263475.9	wgs	PATRIC	263475 tax ID	*
[Ref.: #66792]	Viridibacillus arvi DSM 16317	2651869790	draft	JGI IMG/M	263475 tax ID	*

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GC-content

35.0 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Viridibacillus arvi DSM 16317 NCBI: GCA_001274945.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Viridibacillus arvi DSM 16317 NCBI: GCA_001274945.1
[Ref.: #69480]	motile	yes	89.41	yes
[Ref.: #69480]	flagellated	yes	81.785	no
[Ref.: #69480]	gram-positive	yes	75.655	yes
[Ref.: #69480]	anaerobic	no	98.291	no
[Ref.: #69480]	halophile	no	87.103	no
[Ref.: #69480]	spore-forming	yes	95.246	yes
[Ref.: #69480]	thermophile	no	99.867	no
[Ref.: #69480]	glucose-util	yes	90.036	no
[Ref.: #69480]	aerobic	yes	83.577	yes
[Ref.: #69480]	glucose-ferment	no	85.901	no

Availability in culture collections External links

[Ref.: #6363]

Culture collection no.

DSM 16317, LMG 22165

[Ref.: #70247]

SI-ID 128652

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	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	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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#70247

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID128652.1 )

* These data were automatically processed and therefore are not curated

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Viridibacillus arvi DSM 16317

Viridibacillus arvi DSM 16317

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