Name: Virgibacillus necropolis mccs2660
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1481

Type strain:

Species: Virgibacillus necropolis

Strain Designation: mccs2660

Culture col. no.: DSM 14866, JCM 16509, LMG 19488, KCTC 3820, CIP 108265

Strain history: CIP <- 2010, DSMZ <- LMG: strain mccs2660 <- J. Heyrman, Univ. Ghent, Belgium

NCBI tax ID(s): 163877 (species)

SI-ID 13178

LMG 19488, DSM 14866, KCTC 3820, CIP 108265, JCM 16509

Special Collections

Section

Virgibacillus necropolis mccs2660 is an aerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from mural painting.

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 necropolis**
	Full Scientific Name (LPSN)	Virgibacillus necropolis Heyrman et al. 2003

Information on morphological and physiological properties Morphology

[Ref.: #23062]	Gram stain	positive
[Ref.: #121254]	Gram stain	positive

[Ref.: #23062]	Cell length	2.0-5.0 µm

[Ref.: #23062]	Cell width	0.5-0.7 µm

[Ref.: #23062]	Cell shape	rod-shaped
[Ref.: #121254]	Cell shape	rod-shaped

[Ref.: #23062]	Motility	yes
[Ref.: #121254]	Motility	yes

[Ref.: #23062]	Colony size	0.2-0.5 mm
[Ref.: #23062]	Colony color	cream-coloured
[Ref.: #23062]	Colony shape	circular
[Ref.: #23062]	Incubation period	1 day
[Ref.: #23062]	Cultivation medium used	MA medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5585]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #5585]

Culture medium growth

[Ref.: #5585]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5585]

Culture medium composition

expand / minimize

[Ref.: #23062]

Culture medium

MA medium

[Ref.: #23062]

Culture medium growth

[Ref.: #40485]

Culture medium

Marine agar (MA)

[Ref.: #40485]

Culture medium growth

[Ref.: #40485]

Culture medium composition

expand / minimize

[Ref.: #121254]

Culture medium

CIP Medium 13

[Ref.: #121254]

Culture medium growth

[Ref.: #121254]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #5585]		growth	28 °C
[Ref.: #23062]		growth	10.0-40.0 °C
[Ref.: #23062]		optimum	25.0-35.0 °C
[Ref.: #40485]		growth	30 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #121254]		growth	10-37 °C
[Ref.: #121254]	no	growth	45 °C
[Ref.: #121254]	no	growth	55 °C

	pH	Kind of pH		pH
[Ref.: #121254]			growth	6

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23062]

Oxygen tolerance

aerobe

[Ref.: #23062]	Spore description	ellipsoidal,terminal or subterminal or central,in swollen sporangia
[Ref.: #23062]	Type of spore	endospore
[Ref.: #23062]	Ability of spore formation	yes
[Ref.: #69480]	Ability of spore formation	yes Confidence in %91.14
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100

	Salt	Tested relation		Salt conc.
[Ref.: #23062]	NaCl		optimum	5.0	%
[Ref.: #23062]	NaCl		optimum	10.0	%
[Ref.: #23062]	NaCl	no	growth	0.0	%
[Ref.: #121254]	NaCl		growth	0-2	%
[Ref.: #121254]	NaCl	no	growth	4	%
[Ref.: #121254]	NaCl	no	growth	6	%
[Ref.: #121254]	NaCl	no	growth	8	%
[Ref.: #121254]	NaCl	no	growth	10	%

[Ref.: #23062]	Murein short key	A31
[Ref.: #23062]	Murein types	A1gamma m-Dpm-direct

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23062]	5-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #23062]	amygdalin ChEBI	-	builds acid from
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	casein	+	hydrolysis
[Ref.: #23062]	cellobiose ChEBI	+	carbon source
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #121254]	citrate ChEBI	-	carbon source
[Ref.: #23062]	D-arabinose ChEBI	-	builds acid from
[Ref.: #23062]	D-arabinose ChEBI	-	growth
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	D-fructose ChEBI	-	builds acid from
[Ref.: #23062]	D-fructose ChEBI	-	growth
[Ref.: #68371]	D-fructose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	D-glucose ChEBI	-	builds acid from
[Ref.: #23062]	D-glucose ChEBI	+	carbon source
[Ref.: #68371]	D-glucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	D-mannose ChEBI	-	builds acid from
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	D-tagatose ChEBI	-	builds acid from
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	D-trehalose ChEBI	-	builds acid from
[Ref.: #23062]	D-trehalose ChEBI	+	carbon source
[Ref.: #23062]	D-xylose ChEBI	-	growth
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #121254]	esculin ChEBI	-	hydrolysis
[Ref.: #68371]	esculin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	galactose ChEBI	-	builds acid from
[Ref.: #68371]	gentiobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	glycerol ChEBI	-	builds acid from
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	glycogen ChEBI	-	builds acid from
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	L-fucose ChEBI	-	builds acid from
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	lactose ChEBI	+	carbon source
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	mannitol ChEBI	-	builds acid from
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	melibiose ChEBI	-	builds acid from
[Ref.: #23062]	melibiose ChEBI	+	carbon source
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	myo-inositol ChEBI	-	builds acid from
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	nitrate ChEBI	+	reduction
[Ref.: #121254]	nitrate ChEBI	+	reduction
[Ref.: #121254]	nitrite ChEBI	+	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	raffinose ChEBI	+	carbon source
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	ribose ChEBI	-	builds acid from
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	sucrose ChEBI	+	carbon source
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23062]	tryptophan ChEBI	-	energy source
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #23062]	acetoin ChEBI	no
[Ref.: #23062]	hydrogen sulfide ChEBI	no
[Ref.: #23062]	indole ChEBI	no
[Ref.: #121254]	indole ChEBI	no

	Metabolite	Voges-Proskauer-test	Methylred-test	Indole test
[Ref.: #23062]	acetoin ChEBI	-
[Ref.: #121254]	acetoin ChEBI	-
[Ref.: #121254]	glucose ChEBI		-
[Ref.: #23062]	indole ChEBI			-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #121254]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #121254]	amylase	-
[Ref.: #23062]	arginine dihydrolase	-	3.5.3.6
[Ref.: #23062]	beta-galactosidase	-	3.2.1.23
[Ref.: #121254]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #121254]	caseinase	-	3.4.21.50
[Ref.: #23062]	catalase	+	1.11.1.6
[Ref.: #121254]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #23062]	gelatinase	+
[Ref.: #121254]	gelatinase	-
[Ref.: #121254]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #121254]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #23062]	lysine decarboxylase	-	4.1.1.18
[Ref.: #121254]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #23062]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121254]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121254]	oxidase	-
[Ref.: #121254]	protease	-
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #23062]	tryptophan deaminase	-	4.1.99.1
[Ref.: #121254]	tween esterase	-
[Ref.: #23062]	urease	-	3.5.1.5
[Ref.: #121254]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #121254]	11243	not determinedn.d.	-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	+/-

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #121254]	2678	not determinedn.d.	+	-	-	-	-	-	-	+	-	+	-	-	-	-	+	+	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #121254]	11038	-	+	+	+	-	+	+	-	+	+	+	+	-	-	-	+	+	+	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	propionate fermentation	100	10 of 10
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	pyrimidine metabolism	88.89	40 of 45
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	degradation of sugar alcohols	87.5	14 of 16
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	alanine metabolism	86.21	25 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	urea cycle	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	cysteine metabolism	77.78	14 of 18
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	degradation of sugar acids	76	19 of 25
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	lysine metabolism	73.81	31 of 42
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	oxidative phosphorylation	67.03	61 of 91
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin 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]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	allantoin degradation	55.56	5 of 9
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	vitamin B12 metabolism	47.06	16 of 34
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	41.18	7 of 17
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	ginsenoside metabolism	31.25	5 of 16
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	daunorubicin biosynthesis	22.22	2 of 9
[Ref.: #66794]	nitrate assimilation	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.: #5585]	Sample type/isolated from	mural painting
[Ref.: #5585]	Geographic location (country and/or sea, region)	Seville, Carmona
[Ref.: #5585]	Country	Spain
[Ref.: #5585]	Country ISO 3 Code	ESP
[Ref.: #5585]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Biofilm formation on the mural paintings of the Servilia tomb
[Ref.: #67770]	Geographic location (country and/or sea, region)	necropolis of Carmona
[Ref.: #67770]	Country	Spain
[Ref.: #67770]	Country ISO 3 Code	ESP
[Ref.: #67770]	Continent	Europe

[Ref.: #121254]	Sample type/isolated from	Mural painting
[Ref.: #121254]	Country	Spain
[Ref.: #121254]	Country ISO 3 Code	ESP
[Ref.: #121254]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Built environment	-
#Engineered	#Other	#Painting

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ315056 (>99% sequence identity) for Virgibacillus from Microbeatlas

Aquatic Samples	9
Soil Samples	6
Animal Samples	28
Plant Samples	5
Total Samples	48

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

[Ref.: #5585]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121254]	Biosafety level	1	Risk group (French classification)

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.: #5585]	Virgibacillus necropolis 16S rRNA gene, type strain LMG 19488T	AJ315056	1522	GenBank ENA	163877 tax ID
[Ref.: #20218]	Virgibacillus necropolis genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 505	AB367186	505	GenBank ENA	163877 tax ID	*
[Ref.: #20218]	Virgibacillus necropolis genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 589	AB367187	589	GenBank ENA	163877 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Virgibacillus necropolis LMG 19488	GCA_002224365	complete	GenBank ENA	163877 tax ID	*
[Ref.: #66792]	Virgibacillus necropolis strain LMG 19488	163877.4	complete	PATRIC	163877 tax ID	*

[Ref.: #67770]

GC-content

37.3 mol%

high performance liquid chromatography (HPLC)

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 necropolis LMG 19488 NCBI: GCA_002224365.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Virgibacillus necropolis LMG 19488 NCBI: GCA_002224365.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	80.318	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.442	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	78.346	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	91.14	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	89.283	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	67.244	no

Availability in culture collections External links

[Ref.: #5585]

Culture collection no.

DSM 14866, JCM 16509, LMG 19488, KCTC 3820, CIP 108265

[Ref.: #71127]

SI-ID 13178

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	*
Phylogeny	Virgibacillus alimentarius sp. nov., isolated from a traditional Korean food.	Kim J, Jung MJ, Roh SW, Nam YD, Shin KS, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.028191-0	2011	*
Phylogeny	Virgibacillus byunsanensis sp. nov., isolated from a marine solar saltern.	Yoon JH, Kang SJ, Jung YT, Lee KC, Oh HW, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.009837-0	2009	*
Phylogeny	Virgibacillus salinus sp. nov., a moderately halophilic bacterium from sediment of a saline lake.	Carrasco IJ, Marquez MC, Ventosa A	Int J Syst Evol Microbiol	10.1099/ijs.0.009530-0	2009	*
Phylogeny	Virgibacillus carmonensis sp. nov., Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov., three novel species isolated from deteriorated mural paintings, transfer of the species of the genus salibacillus to Virgibacillus, as Virgibacillus marismortui comb. nov. and Virgibacillus salexigens comb. nov., and emended description of the genus Virgibacillus.	Heyrman J, Logan NA, Busse HJ, Balcaen A, Lebbe L, Rodriguez-Diaz M, Swings J, De Vos P	Int J Syst Evol Microbiol	10.1099/ijs.0.02371-0	2003	*

References

#5585

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14866

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#23062

Jeroen Heyrman,Niall A. Logan,Hans-Jürgen Busse,An Balcaen,Liesbeth Lebbe,Marina Rodriguez-Diaz,Jean Swings,Paul De Vos: Virgibacillus carmonensis sp. nov., Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov., three novel species isolated from deteriorated mural paintings, transfer of the species of the genus Salibacillus to Virgibacillus, as Virgibacillus marismortui comb. nov. and Virgibacillus salexigens comb. nov., and emended description of the genus Virgibacillus. IJSEM 53: 501 - 511 2003 ( DOI 10.1099/ijs.0.02371-0 , PubMed 12710619 )

#40485 ; Curators of the CIP;

#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;

#68371

Automatically annotated from API 50CH acid .

#68382

Automatically annotated from API zym .

#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 )

#71127

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-ID13178.1 )

#121254 Collection of Institut Pasteur ; Curators of the CIP; CIP 108265
* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Virgibacillus necropolis in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Virgibacillus necropolis LMG 19488

Virgibacillus necropolis LMG 19488

Change proposal

Change proposal