Strain identifier

BacDive ID: 158739

Type strain: Yes

Species: Virgibacillus indicus

Strain Designation: P2-C2

NCBI tax ID(s): 2024554 (species)

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General

@ref: 65490

BacDive-ID: 158739

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-variable, motile, rod-shaped

description: 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.

NCBI tax id

  • NCBI tax id: 2024554
  • Matching level: species

doi: 10.13145/bacdive158739.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Virgibacillus
  • species: Virgibacillus indicus
  • full scientific name: Virgibacillus indicus Xu et al. 2018

@ref: 65490

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Bacillaceae

genus: Virgibacillus

species: Virgibacillus indicus

strain designation: P2-C2

type strain: yes

Morphology

cell morphology

  • @ref: 65490
  • gram stain: variable
  • cell length: 1.6-2.3 µm
  • cell width: 0.8-1.0 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: peritrichous

colony morphology

@refcolony sizecolony colorcolony shapemedium used
65490
654902-3 mmcreamcircularmarine agar

Culture and growth conditions

culture medium

  • @ref: 65490
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65490positivegrowth4-42
65490nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65490aerobe
65490anaerobe

spore formation

  • @ref: 65490
  • type of spore: endospore
  • spore formation: yes

observation

@refobservation
65490cells are Gram-stain-variable (young cells stain Gram-stain-positive)
65490tests 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
65490peptidoglycan contains meso-diaminopimelic acid
65490polar lipid profile contains diphosphatidylglycerol and phosphatidylglycerol
65490predominant menaquinone is MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6549016708adenine+assimilation
6549015676allantoin+hydrolysis
6549018305arbutin+hydrolysis
6549085146carboxymethylcellulose-hydrolysis
65490casein+hydrolysis
6549017029chitin-hydrolysis
6549015824D-fructose+carbon source
6549015824D-fructose+fermentation
6549012936D-galactose+fermentation
6549017634D-glucose+carbon source
6549017634D-glucose+fermentation
6549016899D-mannitol-fermentation
6549016024D-mannose+carbon source
6549016024D-mannose+fermentation
6549065327D-xylose+carbon source
6549065327D-xylose+fermentation
654904853esculin+hydrolysis
654905291gelatin+hydrolysis
6549017754glycerol+carbon source
6549017754glycerol+fermentation
6549028087glycogen-fermentation
6549016235guanine-assimilation
65490606565hippurate+hydrolysis
6549017368hypoxanthine+assimilation
6549030849L-arabinose-fermentation
6549030849L-arabinose+carbon source
6549062345L-rhamnose-fermentation
6549017716lactose+carbon source
6549017716lactose+fermentation
6549017306maltose+carbon source
6549017306maltose+fermentation
6549028053melibiose-fermentation
6549017268myo-inositol-fermentation
65490506227N-acetylglucosamine+fermentation
6549017632nitrate+reduction
6549017309pectin-hydrolysis
6549028017starch-hydrolysis
6549017992sucrose+carbon source
6549017992sucrose+fermentation
6549027082trehalose+carbon source
6549027082trehalose+fermentation
6549053424tween 20-hydrolysis
6549053423tween 40-hydrolysis
6549053425tween 60-hydrolysis
6549053426tween 80-hydrolysis
6549018186tyrosine-assimilation
6549016199urea-hydrolysis
6549015318xanthine+assimilation
6549037166xylan-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
6549028077rifampicinyesyes5 µg (disc)
6549017698chloramphenicolyesyes30 µg (disc)
6549027902tetracyclineyesyes30 µg (disc)
6549028001vancomycinyesyes30 µg (disc)
654906472lincomycinyesyes2 µg (disc)
65490100241ciprofloxacinyesyes5 µg (disc)
6549017076streptomycinyesyes10 µg (disc)
6549048923erythromycinyesyes15 µg (disc)

metabolite production

  • @ref: 65490
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
65490cytochrome oxidase+1.9.3.1
65490catalase+1.11.1.6
65490phenylalanine deaminase-4.3.1.5
65490tryptophan deaminase-4.1.99.1
65490arginine dihydrolase-3.5.3.6
65490lysine decarboxylase-4.1.1.18
65490ornithine decarboxylase-4.1.1.17
65490alkaline phosphatase+3.1.3.1
65490alpha-glucosidase+3.2.1.20
65490naphthol-AS-BI-phosphohydrolase+
65490acid phosphatase+3.1.3.2
65490alpha-chymotrypsin+3.4.21.1
65490esterase (C 4)+
65490esterase Lipase (C 8)+
65490cystine arylamidase-3.4.11.3
65490alpha-fucosidase-3.2.1.51
65490alpha-galactosidase-3.2.1.22
65490beta-galactosidase-3.2.1.23
65490N-acetyl-beta-glucosaminidase-3.2.1.52
65490beta-glucosidase-3.2.1.21
65490beta-glucuronidase-3.2.1.31
65490leucine arylamidase-3.4.11.1
65490lipase (C 14)-
65490alpha-mannosidase-3.2.1.24
65490trypsin-3.4.21.4
65490valine arylamidase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65490C15:0 anteiso57
    65490C17:0 anteiso25.2
    65490C16:0 iso6.9
  • type of FA analysis: whole cell analysis
  • incubation medium: TSA supplemented with sea salts
  • incubation temperature: 25
  • incubation time: 2.5
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 65490
  • sample type: marine sediment collected from the Southwest Indian Ridge, a mid-ocean ridge located along the floors, at a depth of 1675.9 m
  • sampling date: June 2016
  • geographic location: Southwest Indian Ocean and Southeast Atlantic Ocean
  • latitude: -54.5589
  • longitude: 34.9489
  • isolation 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

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

Sequence information

16S sequences

  • @ref: 65490
  • description: 16S rRNA gene sequence
  • accession: KY800369
  • database: nuccore

Genome sequences

  • @ref: 66792
  • description: Virgibacillus indicus P2-C2
  • accession: GCA_002266285
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2024554

GC content

  • @ref: 65490
  • GC-content: 38.3
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes88.861no
gram-positiveyes75.814yes
anaerobicno98.421no
aerobicyes89.086no
halophileyes87.343no
spore-formingyes94.09no
glucose-utilyes87.492no
thermophileno90.873yes
motileyes92.817no
glucose-fermentno88.644yes

External links

@ref: 65490

culture collection no.: CGMCC 1.16138, NBRC 113014

literature

  • topic: Phylogeny
  • Pubmed-ID: 29688169
  • title: Virgibacillus indicus sp. nov. and Virgibacillus profundi sp. nov, two moderately halophilic bacteria isolated from marine sediment by using microfluidic streak plates.
  • authors: Xu B, Hu B, Wang J, Lan Y, Zhu Y, Dai X, Huang L, Huang Y, Du W
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002782
  • year: 2018
  • mesh: Archaea/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Indian Ocean, Microfluidics, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Virgibacillus/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
65490Bingxue Xu, Beiyu Hu, Jian Wang, Ying Lan, Yaxin Zhu, Xin Dai, Li Huang, Ying Huang, Wenbin DuVirgibacillus indicus sp. nov. and Virgibacillus profundi sp. nov, two moderately halophilic bacteria isolated from marine sediment by using microfluidic streak plates10.1099/ijsem.0.002782IJSEM 68: 2015-2023 201829688169
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880