Name: Virgibacillus indicus P2-C2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158739

Type strain:

Species: Virgibacillus indicus

Strain Designation: P2-C2

Culture col. no.: CGMCC 1.16138, NBRC 113014

NCBI tax ID(s): 2024554 (species)

Section

Virgibacillus indicus P2-C2 is an aerobe, spore-forming, Gram-variable bacterium that was isolated from marine sediment collected from the Southwest Indian Ridge, a mid-ocean ridge located along the floors, at a depth of 1675.9 m.

Gram-variable
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	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Bacillaceae*
	Genus	*Virgibacillus*
	Species	**Virgibacillus indicus**
	Full Scientific Name (PNU)	Virgibacillus indicus Xu et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65490]	Gram stain	variable
[Ref.: #65490]	Cell length	1.6-2.3 µm
[Ref.: #65490]	Cell width	0.8-1.0 µm
[Ref.: #65490]	Cell shape	rod-shaped
[Ref.: #65490]	Motility	yes
[Ref.: #65490]	Flagellum arrangement	peritrichous

[Ref.: #65490]	Colony size	2-3 mm
[Ref.: #65490]	Colony color	cream
[Ref.: #65490]	Colony shape	circular
[Ref.: #65490]	Cultivation medium used	marine agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65490]

Culture medium

Marine agar (MA)

[Ref.: #65490]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #65490]			growth	4-42 °C
[Ref.: #65490]		no	growth	45 °C

[Ref.: #65490]

Temperature range

thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65490]	Oxygen tolerance	aerobe
[Ref.: #65490]	Oxygen tolerance	anaerobe

[Ref.: #65490]	Type of spore	endospore
[Ref.: #65490]	Ability of spore formation	yes

[Ref.: #65490]	Observation	cells are Gram-stain-variable (young cells stain Gram-stain-positive)
[Ref.: #65490]	Observation	tests for ability to grow on chemical inhibitors are positive for barium chloride, cobalt chloride and zinc chloride, but negative for potassium tellurite and sodium azide
[Ref.: #65490]	Observation	peptidoglycan contains meso-diaminopimelic acid
[Ref.: #65490]	Observation	polar lipid profile contains diphosphatidylglycerol and phosphatidylglycerol
[Ref.: #65490]	Observation	predominant menaquinone is MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65490]	adenine ChEBI	+	assimilation
[Ref.: #65490]	allantoin ChEBI	+	hydrolysis
[Ref.: #65490]	arbutin ChEBI	+	hydrolysis
[Ref.: #65490]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #65490]	casein	+	hydrolysis
[Ref.: #65490]	chitin ChEBI	-	hydrolysis
[Ref.: #65490]	D-fructose ChEBI	+	carbon source
[Ref.: #65490]	D-fructose ChEBI	+	fermentation
[Ref.: #65490]	D-galactose ChEBI	+	fermentation
[Ref.: #65490]	D-glucose ChEBI	+	carbon source
[Ref.: #65490]	D-glucose ChEBI	+	fermentation
[Ref.: #65490]	D-mannitol ChEBI	-	fermentation
[Ref.: #65490]	D-mannose ChEBI	+	carbon source
[Ref.: #65490]	D-mannose ChEBI	+	fermentation
[Ref.: #65490]	D-xylose ChEBI	+	carbon source
[Ref.: #65490]	D-xylose ChEBI	+	fermentation
[Ref.: #65490]	esculin ChEBI	+	hydrolysis
[Ref.: #65490]	gelatin ChEBI	+	hydrolysis
[Ref.: #65490]	glycerol ChEBI	+	carbon source
[Ref.: #65490]	glycerol ChEBI	+	fermentation
[Ref.: #65490]	glycogen ChEBI	-	fermentation
[Ref.: #65490]	guanine ChEBI	-	assimilation
[Ref.: #65490]	hippurate ChEBI	+	hydrolysis
[Ref.: #65490]	hypoxanthine ChEBI	+	assimilation
[Ref.: #65490]	L-arabinose ChEBI	-	fermentation
[Ref.: #65490]	L-arabinose ChEBI	+	carbon source
[Ref.: #65490]	L-rhamnose ChEBI	-	fermentation
[Ref.: #65490]	lactose ChEBI	+	carbon source
[Ref.: #65490]	lactose ChEBI	+	fermentation
[Ref.: #65490]	maltose ChEBI	+	carbon source
[Ref.: #65490]	maltose ChEBI	+	fermentation
[Ref.: #65490]	melibiose ChEBI	-	fermentation
[Ref.: #65490]	myo-inositol ChEBI	-	fermentation
[Ref.: #65490]	N-acetylglucosamine ChEBI	+	fermentation
[Ref.: #65490]	nitrate ChEBI	+	reduction
[Ref.: #65490]	pectin ChEBI	-	hydrolysis
[Ref.: #65490]	starch ChEBI	-	hydrolysis
[Ref.: #65490]	sucrose ChEBI	+	carbon source
[Ref.: #65490]	sucrose ChEBI	+	fermentation
[Ref.: #65490]	trehalose ChEBI	+	carbon source
[Ref.: #65490]	trehalose ChEBI	+	fermentation
[Ref.: #65490]	tween 20 ChEBI	-	hydrolysis
[Ref.: #65490]	tween 40 ChEBI	-	hydrolysis
[Ref.: #65490]	tween 60 ChEBI	-	hydrolysis
[Ref.: #65490]	tween 80 ChEBI	-	hydrolysis
[Ref.: #65490]	tyrosine ChEBI	-	assimilation
[Ref.: #65490]	urea ChEBI	-	hydrolysis
[Ref.: #65490]	xanthine ChEBI	+	assimilation
[Ref.: #65490]	xylan ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #65490]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #65490]	ciprofloxacin ChEBI				yes	5	µg (disc)
[Ref.: #65490]	erythromycin ChEBI				yes	15	µg (disc)
[Ref.: #65490]	lincomycin ChEBI				yes	2	µg (disc)
[Ref.: #65490]	rifampicin ChEBI	yes	5	µg (disc)
[Ref.: #65490]	streptomycin ChEBI				yes	10	µg (disc)
[Ref.: #65490]	tetracycline ChEBI	yes	30	µg (disc)
[Ref.: #65490]	vancomycin ChEBI	yes	30	µg (disc)

	Metabolite production	Metabolite
[Ref.: #65490]		hydrogen sulfide ChEBI

	Enzyme	Enzyme activity	EC number
[Ref.: #65490]	acid phosphatase	+	3.1.3.2
[Ref.: #65490]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65490]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #65490]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65490]	alpha-galactosidase	-	3.2.1.22
[Ref.: #65490]	alpha-glucosidase	+	3.2.1.20
[Ref.: #65490]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65490]	arginine dihydrolase	-	3.5.3.6
[Ref.: #65490]	beta-galactosidase	-	3.2.1.23
[Ref.: #65490]	beta-glucosidase	-	3.2.1.21
[Ref.: #65490]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65490]	catalase	+	1.11.1.6
[Ref.: #65490]	cystine arylamidase	-	3.4.11.3
[Ref.: #65490]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65490]	esterase (C 4)	+
[Ref.: #65490]	esterase Lipase (C 8)	+
[Ref.: #65490]	leucine arylamidase	-	3.4.11.1
[Ref.: #65490]	lipase (C 14)	-
[Ref.: #65490]	lysine decarboxylase	-	4.1.1.18
[Ref.: #65490]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #65490]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65490]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #65490]	phenylalanine deaminase	-	4.3.1.5
[Ref.: #65490]	trypsin	-	3.4.21.4
[Ref.: #65490]	tryptophan deaminase	-	4.1.99.1
[Ref.: #65490]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65490]

Fatty acid	Percentage
C15:0 anteiso	57
C17:0 anteiso	25.2
C16:0 iso	6.9

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	pyrimidine metabolism	80	36 of 45
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	oxidative phosphorylation	61.54	56 of 91
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	lipid metabolism	51.61	16 of 31
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	vitamin B12 metabolism	38.24	13 of 34
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	degradation of sugar acids	32	8 of 25
[Ref.: #66794]	ginsenoside metabolism	31.25	5 of 16
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	4-hydroxymandelate 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.: #65490]	Sample type/isolated from	marine sediment collected from the Southwest Indian Ridge, a mid-ocean ridge located along the floors, at a depth of 1675.9 m
[Ref.: #65490]	Sampling date	June 2016
[Ref.: #65490]	Geographic location (country and/or sea, region)	Southwest Indian Ocean and Southeast Atlantic Ocean
[Ref.: #65490]	Geographic location	-54.5589°/34.9489°
[Ref.: #65490]	Isolation/enrichment procedure	subsurface sediments (collected at 5 cm depth) were collected by a television-grabbing bucket and stored in aliquots at 4°C for the cultivation study
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

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.: #65490]	16S rRNA gene sequence	KY800369		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Virgibacillus indicus P2-C2	GCA_002266285	contig	GenBank	2024554 tax ID	*

[Ref.: #65490]

GC-content

38.3 mol%

sequence analysis

Availability in culture collections External links

[Ref.: #65490]

Culture collection no.

CGMCC 1.16138, NBRC 113014

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Virgibacillus indicus sp. nov. and Virgibacillus profundi sp. nov, two moderately halophilic bacteria isolated from marine sediment by using microfluidic streak plates.	Xu B, Hu B, Wang J, Lan Y, Zhu Y, Dai X, Huang L, Huang Y, Du W	Int J Syst Evol Microbiol	10.1099/ijsem.0.002782	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 )

#65490

Bingxue Xu, Beiyu Hu, Jian Wang, Ying Lan, Yaxin Zhu, Xin Dai, Li Huang, Ying Huang, Wenbin Du: Virgibacillus indicus sp. nov. and Virgibacillus profundi sp. nov, two moderately halophilic bacteria isolated from marine sediment by using microfluidic streak plates. IJSEM 68: 2015 - 2023 2018 ( DOI 10.1099/ijsem.0.002782 , PubMed 29688169 )

#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 )

#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) .

* 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 indicus in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF