Strain identifier

BacDive ID: 1233

Type strain: Yes

Species: Metabacillus indicus

Strain Designation: Sd/3

Strain history: CIP <- 2008, DSMZ <- CCMB, Hyderabad, India: strain Sd/3

NCBI tax ID(s): 1458122 (strain), 246786 (species)

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General

@ref: 6124

BacDive-ID: 1233

DSM-Number: 15820

keywords: mesophilic, spore-forming, aerobe, Bacteria, 16S sequence, genome sequence, gram-positive, rod-shaped

description: Bacillus indicus Sd/3 is an aerobe, spore-forming, mesophilic bacterium that was isolated from sand sample from arsenic-contaminated aquifer.

strain history: <- S. Shivaji, CCMB; Sd/3

doi: 10.13145/bacdive1233.20201210.5

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/firmicutes
  • domain: Bacteria
  • phylum: Firmicutes
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Metabacillus
  • species: Metabacillus indicus
  • full scientific name: Metabacillus indicus (Suresh et al. 2004) Patel and Gupta 2020

  • synonyms

    @refsynonym
    20215Bacillus cibi
    20215Bacillus indicus

@ref: 6124

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Bacillus

species: Bacillus indicus

full scientific name: Bacillus indicus Suresh et al. 2004 emend. Stropko et al. 2014

strain designation: Sd/3

type strain: yes

Morphology

cell morphology

  • @ref: 23315
  • gram stain: positive
  • cell length: 3.3-5.3 µm
  • cell width: 0.9-1.2 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 23315
  • colony size: 3-4 mm
  • colony color: yellowish-orange
  • medium used: Nutrient agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6124CASO AGAR (MERCK 105458) (DSMZ Medium 220), + MnSO4yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium220.pdf
23315Nutrient agar (NA)yes
34014MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
6124positivegrowth30mesophilic
23315positivegrowth15-37
23315nogrowth40thermophilic
23315positiveoptimum30mesophilic
34014positivegrowth30mesophilic

culture pH

  • @ref: 23315
  • ability: positive
  • type: growth
  • pH: 6-7

Physiology and metabolism

oxygen tolerance

  • @ref: 23315
  • oxygen tolerance: aerobe

spore formation

  • @ref: 23315
  • spore description: subterminal, swollen sporangia
  • type of spore: endospore
  • spore formation: yes

halophily

  • @ref: 23315
  • salt: NaCl
  • growth: positive
  • tested relation: resistant
  • concentration: 2 %

murein

  • @ref: 23315
  • type: A4ß L-Orn-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2331516947citrate-carbon source
2331522599arabinose-carbon source
2331529806fumarate-carbon source
2331517859glutaric acid-carbon source
2331517203L-proline-carbon source
2331517115L-serine-carbon source
2331515361pyruvate-carbon source
2331553424tween 20-hydrolysis
2331516199urea-hydrolysis
2331517632nitrate-reduction
2331517057cellobiose+carbon source
2331517306maltose+carbon source
2331516024D-mannose+carbon source
2331528053melibiose+carbon source
2331516988D-ribose+carbon source
2331517113erythritol+carbon source
2331517268myo-inositol+carbon source
2331516467L-arginine+carbon source
2331562345L-rhamnose+carbon source
2331516828L-tryptophan+carbon source
2331517895L-tyrosine+carbon source
2331517716lactose+carbon source
2331516634raffinose+carbon source
2331517992sucrose+carbon source
233154853esculin+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is sensitivesensitivity conc.
233152676amoxicillinyesyes10 µg
2331528971ampicillinyesyes10 µg
2331517076streptomycinyesyes10 µg
2331517698chloramphenicolyesyes30 µg
233156104kanamycinyesyes30 µg
23315100147nalidixic acidyesyes30 µg
233157507neomycinyesyes30 µg
2331528077rifampicinyesyes30 µg
2331527902tetracyclineyesyes30 µg

metabolite production

@refChebi-IDmetaboliteproduction
2331535581indoleno
2331515688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testcitrate test
2331515688acetoin-
2331516947citrate-

enzymes

@refvalueactivityec
23315amylase+
23315arginine dihydrolase+3.5.3.6
23315catalase+1.11.1.6
23315gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture composition
23315sand sample from arsenic-contaminated aquiferChakdah district in West BengalIndiaINDAsia23.0588.5833nutrient agar0.5% peptone, 0.5% NaCl, 0.2% yeast extract, 0.2% beef extract and 1.5% agar, pH 7.0, all w/v containing 5% (w/v) sodium arsenate
6124arsenic polluted sandWest Bengal, Chakda DistrictIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Aquatic
#Environmental#Terrestrial#Sandy

Safety information

risk assessment

  • @ref: 6124
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6124
  • description: Bacillus indicus 16S rRNA gene, type strain Sd/3T
  • accession: AJ583158
  • length: 1505
  • database: ena
  • NCBI tax ID: 246786

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacillus indicus LMG 22858GCA_000708755contigncbi1458122
66792Bacillus indicus LMG 228581458122.18wgspatric1458122

GC content

@refGC-contentmethod
612429
2331541.2thermal denaturation, midpoint method (Tm)

External links

@ref: 6124

culture collection no.: DSM 15820, CIP 108689, LMG 22858, MTCC 4374

straininfo link

@refpassport
20218http://www.straininfo.net/strains/379486
20218http://www.straininfo.net/strains/840221
20218http://www.straininfo.net/strains/381253
20218http://www.straininfo.net/strains/379487

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6124Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15820)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15820
20215D.Gleim, M.Kracht, N.Weiss et. al.http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date.htmlProkaryotic Nomenclature Up-to-date - compilation of all names of Bacteria and Archaea, validly published according to the Bacteriological Code since 1. Jan. 1980, and validly published nomenclatural changes since
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
23315K. Suresh, S. R. Prabagaran, S. Sengupta, S. Shivaji10.1099/ijs.0.03047-0Bacillus indicus sp. nov., an arsenic-resistant bacterium isolated from an aquifer in West Bengal, IndiaIJSEM 54: 1369-1375 2004
34014Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6345
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)