Strain identifier

BacDive ID: 1406

Type strain: Yes

Species: Amphibacillus sediminis

Strain Designation: Shu-P-Ggiii25-2

Strain history: <- SY Ahn, Tokyo Univ. <- IAM <- Hiroaki Kasai, Marine Biotechnology Institute Co. Ltd.

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
360185species
1220586strain

strain history

@refhistory
15844<- JCM <- IAM <- S.-Y. An et al.; Shu-P-Ggiii25-2
67770IAM 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

@refgram staincell shapemotilityconfidence
23032positiverod-shapedno
67771rod-shapedno
67771positive
69480yes96.787
69480positive100

colony morphology

  • @ref: 23032
  • colony color: white
  • colony shape: circular
  • medium used: trypticase soy agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15844CASO 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
23032trypticase soy agaryestrypticase 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

@refgrowthtypetemperaturerange
15844positivegrowth30mesophilic
23032positivegrowth17.0-55.0
23032nogrowth10.0psychrophilic
23032nogrowth60.0thermophilic
23032positiveoptimum27.0mesophilic
67770positivegrowth30mesophilic
67771positivegrowth27mesophilic

culture pH

@refabilitytypepHPH range
23032positiveoptimum8.5alkaliphile
23032positivegrowth7.0-9.0
23032nogrowth6.5
23032nogrowth9.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23032facultative anaerobe
67771aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
23032spherical,terminalendosporeyes
67771endosporeyes
69481yes100
69480yes99.999

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

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23032168082-dehydro-D-gluconate-builds acid from
23032174265-dehydro-D-gluconate-builds acid from
2303215963ribitol-builds acid from
2303227613amygdalin-builds acid from
2303218305arbutin-builds acid from
2303217057cellobiose-builds acid from
2303217108D-arabinose-builds acid from
2303218333D-arabitol-builds acid from
2303228847D-fucose-builds acid from
2303262318D-lyxose-builds acid from
2303216443D-tagatose-builds acid from
2303232528turanose-builds acid from
2303265327D-xylose-builds acid from
2303216813galactitol-builds acid from
2303217113erythritol-builds acid from
2303228260galactose-builds acid from
2303228066gentiobiose-builds acid from
2303224265gluconate-builds acid from
2303228087glycogen-builds acid from
2303217268myo-inositol-builds acid from
2303215443inulin-builds acid from
2303230849L-arabinose-builds acid from
2303218403L-arabitol-builds acid from
2303218287L-fucose-builds acid from
2303265328L-xylose-builds acid from
2303217716lactose-builds acid from
2303229864mannitol-builds acid from
230326731melezitose-builds acid from
2303228053melibiose-builds acid from
23032320061methyl alpha-D-glucopyranoside-builds acid from
2303243943methyl alpha-D-mannoside-builds acid from
2303274863methyl beta-D-xylopyranoside-builds acid from
23032506227N-acetylglucosamine-builds acid from
2303216634raffinose-builds acid from
2303226546rhamnose-builds acid from
2303233942ribose-builds acid from
2303217814salicin-builds acid from
2303230911sorbitol-builds acid from
2303227922sorbose-builds acid from
2303228017starch-builds acid from
2303227082trehalose-builds acid from
2303217151xylitol-builds acid from
2303216947citrate-carbon source
2303217632nitrate-reduction
230324853esculin+builds acid from
2303228757fructose+builds acid from
2303217234glucose+builds acid from
2303217754glycerol+builds acid from
2303217306maltose+builds acid from
2303237684mannose+builds acid from
2303217992sucrose+builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
2303235581indoleno
2303216136hydrogen sulfideno
2303215688acetoinyes

metabolite tests

  • @ref: 23032
  • Chebi-ID: 16947
  • metabolite: citrate
  • citrate test: -

enzymes

@refvalueactivityec
23032arginine dihydrolase+3.5.3.6
23032beta-galactosidase+3.2.1.23
23032catalase-1.11.1.6
23032cytochrome oxidase-1.9.3.1
23032gelatinase+
23032lysine decarboxylase-4.1.1.18
23032ornithine decarboxylase-4.1.1.17
23032tryptophan deaminase-4.1.99.1
23032urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
15844SedimentLake Hamana, ShizuokaJapanJPNAsia
23032GYPiii medium5 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 103 days25.0
67770Sediment from Lake HamanaShizuokaJapanJPNAsia
67771From sedimentHamana Lake, Shizuoka CityJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Amphibacillus sediminis gene for 16S rRNA, partial sequence, strain: NBRC 103570AB6821341493ena360185
15844Amphibacillus sediminis rrs gene for 16S rRNA, partial sequenceAB2438661520ena360185

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amphibacillus sediminis NBRC 1035701220586.4wgspatric1220586
66792Amphibacillus sediminis NBRC 1035702731957578draftimg1220586
67770Amphibacillus sediminis NBRC 103570GCA_001552275contigncbi1220586

GC content

@refGC-contentmethod
1584442.3high performance liquid chromatography (HPLC)
6777142.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes77.705yes
gram-positiveyes89.684yes
anaerobicno94.364yes
aerobicno92.662no
halophileyes89.557yes
spore-formingyes87.656no
thermophileno92.486no
glucose-utilyes88.018no
flagellatedyes53.529yes
glucose-fermentno59.669no

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17978206Amphibacillus sediminis sp. nov., an endospore-forming bacterium isolated from lake sediment in Japan.An SY, Ishikawa S, Kasai H, Goto K, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.64926-02007Bacillaceae/*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/*physiologyGenetics
Phylogeny19965990Amphibacillus jilinensis sp. nov., a facultatively anaerobic, alkaliphilic bacillus from a soda lake.Wu XY, Zheng G, Zhang WW, Xu XW, Wu M, Zhu XFInt J Syst Evol Microbiol10.1099/ijs.0.018259-02009Alkalies/*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/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15844Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21624)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21624
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
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
23032Sun-Young An,Shu Ishikawa,Hiroaki Kasai,Keiichi Goto,Akira Yokota10.1099/ijs.0.64926-0Amphibacillus sediminis sp. nov., an endospore-forming bacterium isolated from lake sediment in JapanIJSEM 57: 2489-2492 200717978206
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
71057Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID319362.1StrainInfo: A central database for resolving microbial strain identifiers