Strain identifier
BacDive ID: 1406
Type strain:
Species: Amphibacillus sediminis
Strain Designation: Shu-P-Ggiii25-2
Strain history: <- SY Ahn, Tokyo Univ. <- IAM <- Hiroaki Kasai, Marine Biotechnology Institute Co. Ltd.
NCBI tax ID(s): 1220586 (strain), 360185 (species)
General
@ref: 15844
BacDive-ID: 1406
DSM-Number: 21624
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, Gram-positive, rod-shaped, colony-forming
description: Amphibacillus sediminis Shu-P-Ggiii25-2 is a facultative anaerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from Sediment.
NCBI tax id
NCBI tax id | Matching level |
---|---|
360185 | species |
1220586 | strain |
strain history
@ref | history |
---|---|
15844 | <- JCM <- IAM <- S.-Y. An et al.; Shu-P-Ggiii25-2 |
67770 | IAM 15428 <-- S.-Y. An et al. Shu-P-Ggiii25-2. |
67771 | <- SY Ahn, Tokyo Univ. <- IAM <- Hiroaki Kasai, Marine Biotechnology Institute Co. Ltd. |
doi: 10.13145/bacdive1406.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Amphibacillus
- species: Amphibacillus sediminis
- full scientific name: Amphibacillus sediminis An et al. 2007
@ref: 15844
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Amphibacillus
species: Amphibacillus sediminis
full scientific name: Amphibacillus sediminis An et al. 2007
strain designation: Shu-P-Ggiii25-2
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
23032 | positive | rod-shaped | no | |
67771 | rod-shaped | no | ||
67771 | positive | |||
69480 | yes | 96.787 | ||
69480 | positive | 100 |
colony morphology
- @ref: 23032
- colony color: white
- colony shape: circular
- medium used: trypticase soy agar
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
15844 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | Name: 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 |
23032 | trypticase soy agar | yes | trypticase soy agar containing 50 % Herbst’s artificial seawater (l 21 distilled water): 30 g NaCl, 0.7 g KCl, 5.3 g MgSO 4 . 7H 2 O, 1.3 g CaCl 2 . 2H 2 O and 10.8 g MgCl 2 . 6H 2 O.) |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15844 | positive | growth | 30 | mesophilic |
23032 | positive | growth | 17.0-55.0 | |
23032 | no | growth | 10.0 | psychrophilic |
23032 | no | growth | 60.0 | thermophilic |
23032 | positive | optimum | 27.0 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
67771 | positive | growth | 27 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
23032 | positive | optimum | 8.5 | alkaliphile |
23032 | positive | growth | 7.0-9.0 | |
23032 | no | growth | 6.5 | |
23032 | no | growth | 9.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
23032 | facultative anaerobe |
67771 | aerobe |
spore formation
@ref | spore description | type of spore | spore formation | confidence |
---|---|---|---|---|
23032 | spherical,terminal | endospore | yes | |
67771 | endospore | yes | ||
69481 | yes | 100 | ||
69480 | yes | 99.999 |
halophily
- @ref: 23032
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <6.0 %(w/v)
murein
- @ref: 23032
- murein short key: A31
- type: A1gamma m-Dpm-direct
observation
- @ref: 67771
- observation: quinones: MK-7
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
23032 | 16808 | 2-dehydro-D-gluconate | - | builds acid from |
23032 | 17426 | 5-dehydro-D-gluconate | - | builds acid from |
23032 | 15963 | ribitol | - | builds acid from |
23032 | 27613 | amygdalin | - | builds acid from |
23032 | 18305 | arbutin | - | builds acid from |
23032 | 17057 | cellobiose | - | builds acid from |
23032 | 17108 | D-arabinose | - | builds acid from |
23032 | 18333 | D-arabitol | - | builds acid from |
23032 | 28847 | D-fucose | - | builds acid from |
23032 | 62318 | D-lyxose | - | builds acid from |
23032 | 16443 | D-tagatose | - | builds acid from |
23032 | 32528 | turanose | - | builds acid from |
23032 | 65327 | D-xylose | - | builds acid from |
23032 | 16813 | galactitol | - | builds acid from |
23032 | 17113 | erythritol | - | builds acid from |
23032 | 28260 | galactose | - | builds acid from |
23032 | 28066 | gentiobiose | - | builds acid from |
23032 | 24265 | gluconate | - | builds acid from |
23032 | 28087 | glycogen | - | builds acid from |
23032 | 17268 | myo-inositol | - | builds acid from |
23032 | 15443 | inulin | - | builds acid from |
23032 | 30849 | L-arabinose | - | builds acid from |
23032 | 18403 | L-arabitol | - | builds acid from |
23032 | 18287 | L-fucose | - | builds acid from |
23032 | 65328 | L-xylose | - | builds acid from |
23032 | 17716 | lactose | - | builds acid from |
23032 | 29864 | mannitol | - | builds acid from |
23032 | 6731 | melezitose | - | builds acid from |
23032 | 28053 | melibiose | - | builds acid from |
23032 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
23032 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
23032 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
23032 | 506227 | N-acetylglucosamine | - | builds acid from |
23032 | 16634 | raffinose | - | builds acid from |
23032 | 26546 | rhamnose | - | builds acid from |
23032 | 33942 | ribose | - | builds acid from |
23032 | 17814 | salicin | - | builds acid from |
23032 | 30911 | sorbitol | - | builds acid from |
23032 | 27922 | sorbose | - | builds acid from |
23032 | 28017 | starch | - | builds acid from |
23032 | 27082 | trehalose | - | builds acid from |
23032 | 17151 | xylitol | - | builds acid from |
23032 | 16947 | citrate | - | carbon source |
23032 | 17632 | nitrate | - | reduction |
23032 | 4853 | esculin | + | builds acid from |
23032 | 28757 | fructose | + | builds acid from |
23032 | 17234 | glucose | + | builds acid from |
23032 | 17754 | glycerol | + | builds acid from |
23032 | 17306 | maltose | + | builds acid from |
23032 | 37684 | mannose | + | builds acid from |
23032 | 17992 | sucrose | + | builds acid from |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
23032 | 35581 | indole | no |
23032 | 16136 | hydrogen sulfide | no |
23032 | 15688 | acetoin | yes |
metabolite tests
- @ref: 23032
- Chebi-ID: 16947
- metabolite: citrate
- citrate test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
23032 | arginine dihydrolase | + | 3.5.3.6 |
23032 | beta-galactosidase | + | 3.2.1.23 |
23032 | catalase | - | 1.11.1.6 |
23032 | cytochrome oxidase | - | 1.9.3.1 |
23032 | gelatinase | + | |
23032 | lysine decarboxylase | - | 4.1.1.18 |
23032 | ornithine decarboxylase | - | 4.1.1.17 |
23032 | tryptophan deaminase | - | 4.1.99.1 |
23032 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|---|
15844 | Sediment | Lake Hamana, Shizuoka | Japan | JPN | Asia | ||||
23032 | GYPiii medium | 5 g Bacto yeast extract (BD), 1 g Polypepton (soybean, Nihon Pharma), 1 g casein Polypepton (Nihon Pharma), 1 g fish meat extract, 2 g CaCO3 , 1.5 g Na2CO3 , 10 g glucose, 70 g NaCl, 1 mg sodium pyruvate, 20 mg MgSO4.7H2O, 1 mg MnSO4.4H2O, 1 mg FeSO4.7H2O, 10 mg colistin, 10 mg sodium azide, 10 mg cycloheximide, 30 mg bromothymol blue (BTB), 5 mg Tween 80, 900 ml seawater for 1 l medium, pH 10 | 3 days | 25.0 | |||||
67770 | Sediment from Lake Hamana | Shizuoka | Japan | JPN | Asia | ||||
67771 | From sediment | Hamana Lake, Shizuoka City | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Sediment |
#Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_101586.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_230;97_52525;98_69349;99_101586&stattab=map
- Last taxonomy: Amphibacillus sediminis subclade
- 16S sequence: AB243866
- Sequence Identity:
- Total samples: 141
- soil counts: 48
- aquatic counts: 9
- animal counts: 61
- plant counts: 23
Safety information
risk assessment
- @ref: 15844
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Amphibacillus sediminis gene for 16S rRNA, partial sequence, strain: NBRC 103570 | AB682134 | 1493 | ena | 360185 |
15844 | Amphibacillus sediminis rrs gene for 16S rRNA, partial sequence | AB243866 | 1520 | ena | 360185 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Amphibacillus sediminis NBRC 103570 | 1220586.4 | wgs | patric | 1220586 |
66792 | Amphibacillus sediminis NBRC 103570 | 2731957578 | draft | img | 1220586 |
67770 | Amphibacillus sediminis NBRC 103570 | GCA_001552275 | contig | ncbi | 1220586 |
GC content
@ref | GC-content | method |
---|---|---|
15844 | 42.3 | high performance liquid chromatography (HPLC) |
67771 | 42.3 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | yes | 77.705 | yes |
gram-positive | yes | 89.684 | yes |
anaerobic | no | 94.364 | yes |
aerobic | no | 92.662 | no |
halophile | yes | 89.557 | yes |
spore-forming | yes | 87.656 | no |
thermophile | no | 92.486 | no |
glucose-util | yes | 88.018 | no |
flagellated | yes | 53.529 | yes |
glucose-ferment | no | 59.669 | no |
External links
@ref: 15844
culture collection no.: DSM 21624, IAM 15428, JCM 23213, KCTC 13120, MBIC 08269, NBRC 103570
straininfo link
- @ref: 71057
- straininfo: 319362
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17978206 | Amphibacillus sediminis sp. nov., an endospore-forming bacterium isolated from lake sediment in Japan. | An SY, Ishikawa S, Kasai H, Goto K, Yokota A | Int J Syst Evol Microbiol | 10.1099/ijs.0.64926-0 | 2007 | Bacillaceae/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fresh Water/*microbiology, Genes, rRNA, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Spores, Bacterial/*physiology | Genetics |
Phylogeny | 19965990 | Amphibacillus jilinensis sp. nov., a facultatively anaerobic, alkaliphilic bacillus from a soda lake. | Wu XY, Zheng G, Zhang WW, Xu XW, Wu M, Zhu XF | Int J Syst Evol Microbiol | 10.1099/ijs.0.018259-0 | 2009 | Alkalies/*metabolism, Anaerobiosis, Bacillaceae/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Fresh Water/analysis/*microbiology, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/metabolism | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
15844 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21624) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21624 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
23032 | Sun-Young An,Shu Ishikawa,Hiroaki Kasai,Keiichi Goto,Akira Yokota | 10.1099/ijs.0.64926-0 | Amphibacillus sediminis sp. nov., an endospore-forming bacterium isolated from lake sediment in Japan | IJSEM 57: 2489-2492 2007 | 17978206 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
71057 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID319362.1 | StrainInfo: A central database for resolving microbial strain identifiers |