Strain identifier
BacDive ID: 132389
Type strain:
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)
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
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
---|---|---|---|---|---|---|---|
43785 | positive | 2.5-3.5 µm | 0.7-0.8 µm | rod-shaped | yes | peritrichous | |
69480 | yes | 97.596 | |||||
69480 | positive | 100 |
colony morphology
@ref | colony color | colony shape | incubation period | medium used |
---|---|---|---|---|
43785 | Whitish | circular | 2 days | Marine agar |
43785 | Transparent | circular | 2 days | TSA agar |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
43785 | Marine agar (MA) | yes | ||
43785 | Trypticase Soy Agar (TSA) | yes | ||
24178 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
43785 | positive | growth | 10-45 | |
43785 | positive | optimum | 35 | mesophilic |
24178 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
43785 | positive | growth | 6-11 | alkaliphile |
43785 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
- @ref: 43785
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore description | type of spore | spore formation | confidence |
---|---|---|---|---|
43785 | Spherical to ellipsoidal endospores are formed centrally or paracentrally | endospore | yes | |
69481 | yes | 100 | ||
69480 | yes | 99.625 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
43785 | NaCl | positive | growth | 0-8 %(w/v) |
43785 | NaCl | positive | optimum | 3 %(w/v) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43785 | 17128 | adipate | - | assimilation |
43785 | 22599 | arabinose | - | assimilation |
43785 | 27689 | decanoate | - | assimilation |
43785 | 12936 | D-galactose | - | assimilation |
43785 | 65327 | D-xylose | - | assimilation |
43785 | 17268 | myo-inositol | - | assimilation |
43785 | 15443 | inulin | - | assimilation |
43785 | 18287 | L-fucose | - | assimilation |
43785 | 37684 | mannose | - | assimilation |
43785 | 506227 | N-acetylglucosamine | - | assimilation |
43785 | 18401 | phenylacetate | - | assimilation |
43785 | 53258 | sodium citrate | - | assimilation |
43785 | 32528 | turanose | - | assimilation |
43785 | 27613 | amygdalin | - | builds acid from |
43785 | 18305 | arbutin | - | builds acid from |
43785 | 15963 | ribitol | - | builds acid from |
43785 | 17108 | D-arabinose | - | builds acid from |
43785 | 28847 | D-fucose | - | builds acid from |
43785 | 62318 | D-lyxose | - | builds acid from |
43785 | 16988 | D-ribose | - | builds acid from |
43785 | 16443 | D-tagatose | - | builds acid from |
43785 | 17113 | erythritol | - | builds acid from |
43785 | 18403 | L-arabitol | - | builds acid from |
43785 | 17266 | L-sorbose | - | builds acid from |
43785 | 65328 | L-xylose | - | builds acid from |
43785 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
43785 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
43785 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
43785 | 506227 | N-acetylglucosamine | - | builds acid from |
43785 | potassium 2-dehydro-D-gluconate | - | builds acid from | |
43785 | potassium 5-dehydro-D-gluconate | - | builds acid from | |
43785 | 17151 | xylitol | - | builds acid from |
43785 | 17632 | nitrate | - | reduction |
43785 | 15824 | D-fructose | + | builds acid from |
43785 | 17634 | D-glucose | + | builds acid from |
43785 | 4853 | esculin | + | builds acid from |
43785 | 17306 | maltose | + | builds acid from |
43785 | 29864 | mannitol | + | builds acid from |
43785 | 17814 | salicin | + | builds acid from |
43785 | 28017 | starch | + | builds acid from |
43785 | 17992 | sucrose | + | builds acid from |
43785 | 27082 | trehalose | + | builds acid from |
43785 | 15824 | D-fructose | + | growth |
43785 | 17634 | D-glucose | + | growth |
43785 | 16899 | D-mannitol | + | growth |
43785 | 25115 | malate | + | growth |
43785 | 17306 | maltose | + | growth |
43785 | 32032 | potassium gluconate | + | growth |
43785 | 27082 | trehalose | + | growth |
43785 | casein | + | hydrolysis | |
43785 | 28017 | starch | + | hydrolysis |
43785 | 53424 | tween 20 | + | hydrolysis |
43785 | 53423 | tween 40 | + | hydrolysis |
43785 | 53425 | tween 60 | + | hydrolysis |
43785 | 53426 | tween 80 | + | hydrolysis |
metabolite production
- @ref: 43785
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
43785 | catalase | + | 1.11.1.6 |
43785 | esterase (C 4) | + | |
43785 | esterase Lipase (C 8) | + | |
43785 | leucine arylamidase | + | 3.4.11.1 |
43785 | alpha-chymotrypsin | + | 3.4.21.1 |
43785 | acid phosphatase | + | 3.1.3.2 |
43785 | alpha-galactosidase | + | 3.2.1.22 |
43785 | alpha-glucosidase | + | 3.2.1.20 |
43785 | alkaline phosphatase | +/- | 3.1.3.1 |
43785 | lipase (C 14) | - | |
43785 | valine arylamidase | - | |
43785 | cystine arylamidase | - | 3.4.11.3 |
43785 | trypsin | - | 3.4.21.4 |
43785 | naphthol-AS-BI-phosphohydrolase | - | |
43785 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
43785 | alpha-fucosidase | - | 3.2.1.51 |
43785 | cytochrome oxidase | - | 1.9.3.1 |
43785 | gelatinase | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | isolation date |
---|---|---|---|---|---|---|---|---|
24178 | deep sea sediments | Okinawa Trough (126.88° E 27.64° N at a depth of 1520 m) | Japan | JPN | Asia | 27.64 | 126.88 | |
43785 | Deep sea sediment sample (depth, 1520 m) collected at Okinawa Trough | Okinawa Trough | 27.64 | 126.88 | 2014-04 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Domibacillus iocasae DSM 29979 | GCA_001750285 | contig | ncbi | 1714016 |
66792 | Domibacillus iocasae strain DSM 29979 | 1714016.4 | wgs | patric | 1714016 |
66792 | Domibacillus iocasae DSM 29979 | 2791354958 | draft | img | 1714016 |
GC content
@ref | GC-content | method |
---|---|---|
43785 | 44.4 | genome sequence analysis |
24178 | 44.4 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | yes | 90.811 | yes |
gram-positive | yes | 94.057 | yes |
anaerobic | no | 97.506 | yes |
aerobic | yes | 92.55 | yes |
halophile | no | 84.955 | no |
spore-forming | yes | 92.225 | yes |
glucose-util | yes | 89.413 | yes |
flagellated | yes | 88.27 | yes |
thermophile | no | 97.008 | yes |
glucose-ferment | no | 88.757 | no |
External links
@ref: 24178
culture collection no.: DSM 29979, CCTCC AB 2015183
straininfo link
- @ref: 90732
- straininfo: 408364
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 26637819 | Description of Domibacillus iocasae sp. nov., isolated from deep-sea sediment, and emended description of the genus Domibacillus. | Sun QL, Sun L | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000823 | 2015 | ||
Phylogeny | 27073919 | Domibacillus antri sp. nov., isolated from the soil of a cave. | Xu D, Wang L, Wang G, Zheng S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001080 | 2016 | Bacillaceae/*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/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
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 | 10.1099/ijsem.0.004332 | |||
24178 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29979 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29979) | |||
43785 | Qing-Lei Sun, Li Sun | Description of Domibacillus iocasae sp. nov., isolated from deep-sea sediment, and emended description of the genus Domibacillus | 10.1099/ijsem.0.000823 | IJSEM 66: 982-987 2016 | 26637819 | |
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) | https://diaspora-project.de/progress.html#genomes | |||
69479 | João 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 beta | https://microbeatlas.org/ | |||
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) | https://diaspora-project.de/progress.html#genomes | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
90732 | Reimer, 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 identifiers | 10.60712/SI-ID408364.1 |