Strain identifier

BacDive ID: 132389

Type strain: Yes

Species: Domibacillus iocasae

Strain Designation: S6

Strain history: <- Q. Sun, CAS, Inst. of Oceanology; S6 <- Q. Sun and L. Sun

NCBI tax ID(s): 1714016 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 24178

BacDive-ID: 132389

DSM-Number: 29979

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

description: Domibacillus iocasae S6 is an obligate aerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from deep sea sediments.

NCBI tax id

  • NCBI tax id: 1714016
  • Matching level: species

strain history

  • @ref: 24178
  • history: <- Q. Sun, CAS, Inst. of Oceanology; S6 <- Q. Sun and L. Sun

doi: 10.13145/bacdive132389.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Domibacillus
  • species: Domibacillus iocasae
  • full scientific name: Domibacillus iocasae Sun and Sun 2016

@ref: 24178

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Domibacillus

species: Domibacillus iocasae

full scientific name: Domibacillus iocasae Sun and Sun 2016

strain designation: S6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43785positive2.5-3.5 µm0.7-0.8 µmrod-shapedyesperitrichous
69480yes97.596
69480positive100

colony morphology

@refcolony colorcolony shapeincubation periodmedium used
43785Whitishcircular2 daysMarine agar
43785Transparentcircular2 daysTSA agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43785Marine agar (MA)yes
43785Trypticase Soy Agar (TSA)yes
24178BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43785positivegrowth10-45
43785positiveoptimum35mesophilic
24178positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
43785positivegrowth6-11alkaliphile
43785positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 43785
  • oxygen tolerance: obligate aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
43785Spherical to ellipsoidal endospores are formed centrally or paracentrallyendosporeyes
69481yes100
69480yes99.625

halophily

@refsaltgrowthtested relationconcentration
43785NaClpositivegrowth0-8 %(w/v)
43785NaClpositiveoptimum3 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4378517128adipate-assimilation
4378522599arabinose-assimilation
4378527689decanoate-assimilation
4378512936D-galactose-assimilation
4378565327D-xylose-assimilation
4378517268myo-inositol-assimilation
4378515443inulin-assimilation
4378518287L-fucose-assimilation
4378537684mannose-assimilation
43785506227N-acetylglucosamine-assimilation
4378518401phenylacetate-assimilation
4378553258sodium citrate-assimilation
4378532528turanose-assimilation
4378527613amygdalin-builds acid from
4378518305arbutin-builds acid from
4378515963ribitol-builds acid from
4378517108D-arabinose-builds acid from
4378528847D-fucose-builds acid from
4378562318D-lyxose-builds acid from
4378516988D-ribose-builds acid from
4378516443D-tagatose-builds acid from
4378517113erythritol-builds acid from
4378518403L-arabitol-builds acid from
4378517266L-sorbose-builds acid from
4378565328L-xylose-builds acid from
43785320061methyl alpha-D-glucopyranoside-builds acid from
4378543943methyl alpha-D-mannoside-builds acid from
4378574863methyl beta-D-xylopyranoside-builds acid from
43785506227N-acetylglucosamine-builds acid from
43785potassium 2-dehydro-D-gluconate-builds acid from
43785potassium 5-dehydro-D-gluconate-builds acid from
4378517151xylitol-builds acid from
4378517632nitrate-reduction
4378515824D-fructose+builds acid from
4378517634D-glucose+builds acid from
437854853esculin+builds acid from
4378517306maltose+builds acid from
4378529864mannitol+builds acid from
4378517814salicin+builds acid from
4378528017starch+builds acid from
4378517992sucrose+builds acid from
4378527082trehalose+builds acid from
4378515824D-fructose+growth
4378517634D-glucose+growth
4378516899D-mannitol+growth
4378525115malate+growth
4378517306maltose+growth
4378532032potassium gluconate+growth
4378527082trehalose+growth
43785casein+hydrolysis
4378528017starch+hydrolysis
4378553424tween 20+hydrolysis
4378553423tween 40+hydrolysis
4378553425tween 60+hydrolysis
4378553426tween 80+hydrolysis

metabolite production

  • @ref: 43785
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
43785catalase+1.11.1.6
43785esterase (C 4)+
43785esterase Lipase (C 8)+
43785leucine arylamidase+3.4.11.1
43785alpha-chymotrypsin+3.4.21.1
43785acid phosphatase+3.1.3.2
43785alpha-galactosidase+3.2.1.22
43785alpha-glucosidase+3.2.1.20
43785alkaline phosphatase+/-3.1.3.1
43785lipase (C 14)-
43785valine arylamidase-
43785cystine arylamidase-3.4.11.3
43785trypsin-3.4.21.4
43785naphthol-AS-BI-phosphohydrolase-
43785N-acetyl-beta-glucosaminidase-3.2.1.52
43785alpha-fucosidase-3.2.1.51
43785cytochrome oxidase-1.9.3.1
43785gelatinase-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
24178deep sea sedimentsOkinawa Trough (126.88° E 27.64° N at a depth of 1520 m)JapanJPNAsia27.64126.88
43785Deep sea sediment sample (depth, 1520 m) collected at Okinawa TroughOkinawa Trough27.64126.882014-04

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_17604.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1025;97_1195;98_3327;99_17604&stattab=map
  • Last taxonomy: Domibacillus
  • 16S sequence: KT724336
  • Sequence Identity:
  • Total samples: 148
  • soil counts: 130
  • aquatic counts: 14
  • animal counts: 4

Safety information

risk assessment

  • @ref: 24178
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24178
  • description: Domibacillus iocasae strain S6 16S ribosomal RNA gene, partial sequence
  • accession: KT724336
  • length: 1415
  • database: ena
  • NCBI tax ID: 1714016

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Domibacillus iocasae DSM 29979GCA_001750285contigncbi1714016
66792Domibacillus iocasae strain DSM 299791714016.4wgspatric1714016
66792Domibacillus iocasae DSM 299792791354958draftimg1714016

GC content

@refGC-contentmethod
4378544.4genome sequence analysis
2417844.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes90.811yes
gram-positiveyes94.057yes
anaerobicno97.506yes
aerobicyes92.55yes
halophileno84.955no
spore-formingyes92.225yes
glucose-utilyes89.413yes
flagellatedyes88.27yes
thermophileno97.008yes
glucose-fermentno88.757no

External links

@ref: 24178

culture collection no.: DSM 29979, CCTCC AB 2015183

straininfo link

  • @ref: 90732
  • straininfo: 408364

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26637819Description of Domibacillus iocasae sp. nov., isolated from deep-sea sediment, and emended description of the genus Domibacillus.Sun QL, Sun LInt J Syst Evol Microbiol10.1099/ijsem.0.0008232015
Phylogeny27073919Domibacillus antri sp. nov., isolated from the soil of a cave.Xu D, Wang L, Wang G, Zheng SInt J Syst Evol Microbiol10.1099/ijsem.0.0010802016Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24178Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29979Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29979)
43785Qing-Lei Sun, Li SunDescription of Domibacillus iocasae sp. nov., isolated from deep-sea sediment, and emended description of the genus Domibacillus10.1099/ijsem.0.000823IJSEM 66: 982-987 201626637819
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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90732Reimer, 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 identifiers10.60712/SI-ID408364.1