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

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

NCBI tax id

NCBI tax idMatching level
246786species
1458122strain

strain history

@refhistory
6124<- S. Shivaji, CCMB; Sd/3
67770S. Shivaji Sd/3.
120089CIP <- 2008, DSMZ <- CCMB, Hyderabad, India: strain Sd/3

doi: 10.13145/bacdive1233.20230509.8.1

Name and taxonomic classification

LPSN

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

  • synonyms

    @refsynonym
    20215Bacillus indicus
    20215Bacillus cibi

@ref: 6124

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Metabacillus

species: Metabacillus indicus

full scientific name: Metabacillus indicus (Suresh et al. 2004) Patel and Gupta 2020

strain designation: Sd/3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23315positive3.3-5.3 µm0.9-1.2 µmrod-shapedno
69480yes95.743
69480positive100
120089positiverod-shapedno

colony morphology

@refcolony sizecolony colormedium used
233153-4 mmyellowish-orangeNutrient agar
120089

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6124CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
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)
120089CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6124positivegrowth30mesophilic
23315positivegrowth15-37
23315nogrowth40thermophilic
23315positiveoptimum30mesophilic
34014positivegrowth30mesophilic
67770positivegrowth30mesophilic
120089positivegrowth22-45
120089nogrowth10psychrophilic
120089nogrowth55thermophilic

culture pH

@refabilitytypepH
23315positivegrowth6-7
120089positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23315aerobe
120089obligate aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
23315subterminal, swollen sporangiaendosporeyes
69481yes100
69480yes100
120089yes

halophily

@refsaltgrowthtested relationconcentration
23315NaClpositiveresistant2 %
120089NaClpositivegrowth2-10 %
120089NaClnogrowth0 %

murein

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

observation

  • @ref: 67770
  • observation: quinones: MK-7

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
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
12008916947citrate-carbon source
1200894853esculin-hydrolysis
120089606565hippurate-hydrolysis
12008917632nitrate+reduction
12008916301nitrite-reduction
12008917632nitrate-respiration

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
12008935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testcitrate testmethylred-test
2331515688acetoin-
2331516947citrate-
12008915688acetoin-
12008917234glucose-

enzymes

@refvalueactivityec
23315amylase+
23315arginine dihydrolase+3.5.3.6
23315catalase+1.11.1.6
23315gelatinase+
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
120089oxidase+
120089beta-galactosidase-3.2.1.23
120089alcohol dehydrogenase+1.1.1.1
120089gelatinase+/-
120089amylase-
120089DNase+
120089caseinase+3.4.21.50
120089catalase+1.11.1.6
120089tween esterase+
120089gamma-glutamyltransferase+2.3.2.2
120089lecithinase-
120089lipase+
120089lysine decarboxylase-4.1.1.18
120089ornithine decarboxylase-4.1.1.17
120089protease+
120089urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120089-+++-+---+++++-+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120089+--------+/-+++------+/-++++/-+/-+/--+-+++--+++-+/-+------+-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120089++-+---+-++----------++--------+-+++-----+-------++--+--+--++------------+-+--+++---------+++++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionisolation date
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
67770Sand of an arsenic-contaminated aquifer in West BengalIndiaINDAsia
120089Environment, Arsenic polluted sandWest BengalIndiaINDAsia2002

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6832.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3218;97_3948;98_5033;99_6832&stattab=map
  • Last taxonomy: Metabacillus indicus
  • 16S sequence: AJ583158
  • Sequence Identity:
  • Total samples: 508
  • soil counts: 169
  • aquatic counts: 149
  • animal counts: 128
  • plant counts: 62

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61241Risk group (German classification)
1200891Risk group (French 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 228581458122.18wgspatric1458122
66792Bacillus indicus LMG 228582619619114draftimg1458122
67770Metabacillus indicus LMG 22858GCA_000708755contigncbi1458122

GC content

@refGC-contentmethod
612429
6777041.2thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes86.813no
gram-positiveyes89.994yes
anaerobicno97.424yes
halophileyes61.398no
spore-formingyes96.22no
glucose-utilyes89.222no
thermophileno97.957no
aerobicyes91.534yes
flagellatedyes72.358yes
glucose-fermentno94.286no

External links

@ref: 6124

culture collection no.: DSM 15820, CIP 108689, LMG 22858, MTCC 4374, JCM 12168, KCTC 3968

straininfo link

  • @ref: 70889
  • straininfo: 132774

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15280316Bacillus indicus sp. nov., an arsenic-resistant bacterium isolated from an aquifer in West Bengal, India.Suresh K, Prabagaran SR, Sengupta S, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.03047-02004Anti-Bacterial Agents/pharmacology, Arsenic/*pharmacology, Bacillus/*classification/drug effects/*isolation & purification/physiology, DNA, Bacterial/analysis/chemistry/isolation & purification, DNA, Ribosomal/chemistry, Drug Resistance, Bacterial, Fatty Acids/analysis, Genes, rRNA, Gentian Violet, India, Molecular Sequence Data, Movement, Peptidoglycan/chemistry, Phenazines, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, *Soil Microbiology, Spores, Bacterial/cytology, Vitamin K 2/analysis, Water MicrobiologyEnzymology
Metabolism18792057Growth of three bacteria in arsenic solution and their application for arsenic removal from wastewater.Mondal P, Majumder CB, Mohanty BJ Basic Microbiol10.1002/jobm.2008000842008Arsenic/*metabolism, Bacteria/*growth & development/*metabolism, Mining, Water Pollutants, Chemical/*metabolism, Water Purification/methodsEnzymology
Phylogeny25142211Genome-based reclassification of Bacillus cibi as a later heterotypic synonym of Bacillus indicus and emended description of Bacillus indicus.Stropko SJ, Pipes SE, Newman JDInt J Syst Evol Microbiol10.1099/ijs.0.068205-02014Bacillus/*classification, Base Composition, DNA, Bacterial/genetics, Genome, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny28714845Bacillus mangrovi sp. nov., isolated from a sediment sample from a mangrove forest.Gupta V, Singh PK, Korpole S, Tanuku NRS, Pinnaka AKInt J Syst Evol Microbiol10.1099/ijsem.0.0019282017Avicennia/*microbiology, Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *WetlandsTranscriptome
Phylogeny35998028Metabacillus kandeliae sp. nov., isolated from the rhizosphere soil of a decayed mangrove plant Kandelia candel.Cai H, Huang Y, Liu Y, Yang L, Zhou Y, Yang S, Chen X, Jiang C, Jiang M, Jiang Y, Singh PInt J Syst Evol Microbiol10.1099/ijsem.0.0055382022*Bacillaceae, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizophoraceae/microbiology, Rhizosphere, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome

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
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
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 200415280316
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
70889Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132774.1StrainInfo: A central database for resolving microbial strain identifiers
120089Curators of the CIPCollection of Institut Pasteur (CIP 108689)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108689