Name: Virgibacillus phasianinus LM2416
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 158787

Type strain:

Species: Virgibacillus phasianinus

Strain Designation: LM2416

Culture col. no.: KCTC 33927, JCM 32144

Strain history: J.-W. Bae; Dept. of Biol., Kyung Hee Univ., South Korea; LM2416.

NCBI tax ID(s): 2017483 (species)

Special Collections

Section

Virgibacillus phasianinus LM2416 is an aerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from faecal sample of Swinhoe's pheasant.

colony-forming
Gram-positive
motile
rod-shaped
spore-forming
aerobe
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	*Virgibacillus*
	Species	**Virgibacillus phasianinus**
	Full Scientific Name (LPSN)	Virgibacillus phasianinus Tak et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65542]	Gram stain	positive

[Ref.: #65542]	Cell length	1.2-1.9 µm

[Ref.: #65542]	Cell width	0.3-0.4 µm

[Ref.: #65542]	Cell shape	rod-shaped

[Ref.: #65542]	Motility	yes

[Ref.: #65542]	Colony size	0.5-1 mm
[Ref.: #65542]	Colony color	beige
[Ref.: #65542]	Colony shape	circular
[Ref.: #65542]	Incubation period	2 days
[Ref.: #65542]	Cultivation medium used	MA

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65542]

Culture medium

Marine agar (MA)

[Ref.: #65542]

Culture medium growth

		Temperature
[Ref.: #65542]	growth	10-30 °C
[Ref.: #65542]	optimum	30 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #65542]			optimum	6-7
[Ref.: #65542]			growth	6-7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65542]

Oxygen tolerance

aerobe

[Ref.: #69481]

Ability of spore formation

yes Confidence in %100

[Ref.: #65542]

Halophily / tolerance level

moderately halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65542]		NaCl		growth	0-20	%(w/v)
[Ref.: #65542]		NaCl		optimum	10	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65542]	D-arabitol ChEBI	+	builds acid from
[Ref.: #65542]	D-fructose ChEBI	+	builds acid from
[Ref.: #65542]	D-galactose ChEBI	+	builds acid from
[Ref.: #65542]	D-glucose ChEBI	+	builds acid from
[Ref.: #65542]	D-lyxose ChEBI	-	builds acid from
[Ref.: #65542]	D-mannitol ChEBI	+	assimilation
[Ref.: #65542]	D-mannitol ChEBI	+	builds acid from
[Ref.: #65542]	D-mannose ChEBI	+	assimilation
[Ref.: #65542]	D-mannose ChEBI	+	builds acid from
[Ref.: #65542]	D-ribose ChEBI	+	builds acid from
[Ref.: #65542]	D-tagatose ChEBI	+	builds acid from
[Ref.: #65542]	D-xylose ChEBI	-	builds acid from
[Ref.: #65542]	esculin ChEBI	+	builds acid from
[Ref.: #65542]	glycerol ChEBI	+	builds acid from
[Ref.: #65542]	L-fucose ChEBI	+	builds acid from
[Ref.: #65542]	L-sorbose ChEBI	-	builds acid from
[Ref.: #65542]	maltose ChEBI	+	assimilation
[Ref.: #65542]	maltose ChEBI	+	builds acid from
[Ref.: #65542]	melezitose ChEBI	+	builds acid from
[Ref.: #65542]	methyl alpha-D-glucopyranoside ChEBI	+	builds acid from
[Ref.: #65542]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #65542]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #65542]	nitrate ChEBI	+	reduction
[Ref.: #65542]	potassium 5-dehydro-D-gluconate	+	builds acid from
[Ref.: #65542]	potassium gluconate ChEBI	+	assimilation
[Ref.: #65542]	potassium gluconate ChEBI	+	builds acid from
[Ref.: #65542]	sucrose ChEBI	+	builds acid from
[Ref.: #65542]	trehalose ChEBI	+	builds acid from
[Ref.: #65542]	turanose ChEBI	+	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #65542]	acid phosphatase	+	3.1.3.2
[Ref.: #65542]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65542]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #65542]	alpha-glucosidase	+	3.2.1.20
[Ref.: #65542]	beta-galactosidase	+	3.2.1.23
[Ref.: #65542]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65542]	catalase	+	1.11.1.6
[Ref.: #65542]	cytochrome oxidase	-	1.9.3.1
[Ref.: #65542]	esterase (C 4)	+
[Ref.: #65542]	esterase Lipase (C 8)	+
[Ref.: #65542]	leucine arylamidase	+	3.4.11.1
[Ref.: #65542]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #65542]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65542]	protease	+
[Ref.: #65542]	urease	-	3.5.1.5
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	alanine metabolism	86.21	25 of 29
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	cysteine metabolism	77.78	14 of 18
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	lysine metabolism	71.43	30 of 42
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	oxidative phosphorylation	65.93	60 of 91
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	lipid A biosynthesis	55.56	5 of 9
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	vitamin B12 metabolism	38.24	13 of 34
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	35.29	6 of 17
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #65542]	Sample type/isolated from	faecal sample of Swinhoe's pheasant
[Ref.: #65542]	Geographic location (country and/or sea, region)	Seoul Grand Park, Makgye-dong, Gwacheon-si, Gyeonggido
[Ref.: #65542]	Country	Republic of Korea
[Ref.: #65542]	Country ISO 3 Code	KOR
[Ref.: #65542]	Continent	Asia
[Ref.: #65542]	Enrichment culture	MA
[Ref.: #65542]	Enrichment culture temperature	20 ̊C
[Ref.: #65542]	Isolation/enrichment procedure	10000 times diluted sample

[Ref.: #67770]	Sample type/isolated from	Faecal sample of Swinhoe's pheasant in Seoul Grand Park
[Ref.: #67770]	Geographic location (country and/or sea, region)	Makgye-dong, Gwacheon-si, Gyeonggi-do
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host Body Product	#Gastrointestinal tract	#Feces (Stool)
#Host	#Birds	-

What are isolation sources categories?

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.: #65542]	Virgibacillus phasianinus strain LM2416 16S ribosomal RNA gene, partial sequence	KY785406		GenBank ENA

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Virgibacillus phasianinus LM2416	GCA_002216775	complete	GenBank ENA	2017483 tax ID	*

[Ref.: #65542]

GC-content

39.5 mol%

genome sequence analysis

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Virgibacillus phasianinus LM2416 NCBI: GCA_002216775.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Virgibacillus phasianinus LM2416 NCBI: GCA_002216775.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	81.605	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.887	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	75.439	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	81.626	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	92.133	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	60.826	no

Availability in culture collections External links

[Ref.: #65542]

Culture collection no.

KCTC 33927, JCM 32144

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Virgibacillus phasianinus sp. nov., a halophilic bacterium isolated from faeces of a Swinhoe's pheasant, Lophura swinhoii.	Tak EJ, Kim HS, Lee JY, Kang W, Sung H, Kim PS, Hyun DW, Shin NR, Roh JR, Park SD, Shim HE, Bae JW	Int J Syst Evol Microbiol	10.1099/ijsem.0.002650	2018	*

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 )

#65542

Euon Jung Tak, Hyun Sik Kim, June-Young Lee, Woorim Kang, Hojun Sung, Pil Soo Kim, Dong-Wook Hyun, Na-Ri Shin, Jeong Rae Roh, Sun Duk Park, Hyung Eun Shim and Jin-Woo Bae: Virgibacillus phasianinus sp. nov., a halophilic bacterium isolated from faeces of a Swinhoe's pheasant, Lophura swinhoii. IJSEM 68: 1190 - 1196 2018 ( DOI 10.1099/ijsem.0.002650 , PubMed 29465338 )

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

* These data were automatically processed and therefore are not curated

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