Strain identifier

BacDive ID: 1403

Type strain: Yes

Species: Amphibacillus xylanus

Strain Designation: Ep01

Strain history: Y. Niimura Ep01.

NCBI tax ID(s): 698758 (strain), 1449 (species)

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General

@ref: 2759

BacDive-ID: 1403

DSM-Number: 6626

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, chemoorganotroph, spore-forming, mesophilic, Gram-positive, rod-shaped, colony-forming

description: Amphibacillus xylanus Ep01 is a facultative anaerobe, chemoorganotroph, spore-forming bacterium that forms circular colonies and was isolated from alcaline compost of manure with grass and rice straw.

NCBI tax id

NCBI tax idMatching level
698758strain
1449species

strain history

@refhistory
2759<- JCM <- Y. Niimura, Tokyo Univ. of Agriculture (Ep01)
67770Y. Niimura Ep01.

doi: 10.13145/bacdive1403.20230509.8.1

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 xylanus
  • full scientific name: Amphibacillus xylanus Niimura et al. 1990

@ref: 2759

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Amphibacillus

species: Amphibacillus xylanus

full scientific name: Amphibacillus xylanus Niimura et al. 1990

strain designation: Ep01

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23029positive0.9-1.9 µm0.3-0.5 µmrod-shapedno
69480positive100

colony morphology

  • @ref: 23029
  • colony color: white
  • colony shape: circular
  • incubation period: 1 day
  • medium used: glucose agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2759AMPHIBACILLUS MEDIUM (DSMZ Medium 529)yeshttps://mediadive.dsmz.de/medium/529Name: AMPHIBACILLUS MEDIUM (DSMZ Medium 529) Composition: Agar 15.0 g/l Glucose 10.0 g/l Na2CO3 anhydrous 5.3 g/l NaHCO3 4.2 g/l Yeast extract 3.0 g/l NH4NO3 2.0 g/l K2HPO4 1.0 g/l Polypeptone 0.3 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.1 g/l MnSO4 x 7 H2O 0.005 g/l FeSO4 x 7 H2O 0.005 g/l Distilled water
23029glucose agaryes

culture temp

@refgrowthtypetemperaturerange
2759positivegrowth37mesophilic
23029positivegrowth25.0-44.0
23029nogrowth50.0thermophilic
67770positivegrowth39mesophilic

culture pH

@refabilitytypepHPH range
23029positivegrowth8.0-10.0alkaliphile
23029nogrowth7.0

Physiology and metabolism

oxygen tolerance

  • @ref: 23029
  • oxygen tolerance: facultative anaerobe

nutrition type

  • @ref: 23029
  • type: chemoorganotroph

spore formation

@refspore descriptiontype of sporespore formationconfidence
23029oval,heat-resistantendosporeyes
69481yes98
69480yes97.65

halophily

@refsaltgrowthtested relationconcentration
23029NaClpositivegrowth3.0 %
23029NaClnogrowth6.0 %

murein

  • @ref: 23029
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2302916947citrate-carbon source
2302915443inulin-carbon source
230295291gelatin-hydrolysis
2302917632nitrate-reduction
2302916024D-mannose+carbon source
2302928053melibiose+carbon source
2302937166xylan+carbon source

metabolite production

@refChebi-IDmetaboliteproduction
2302935581indoleno
2302916136hydrogen sulfideno

metabolite tests

  • @ref: 23029
  • Chebi-ID: 16947
  • metabolite: citrate
  • citrate test: -

enzymes

@refvalueactivityec
23029catalase-1.11.1.6
23029cytochrome oxidase-1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample type
2759alcaline compost of manure with grass and rice straw
67770Alkaliphilic compost

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Engineered#Waste#Solid plant waste
#Host#Plants#Herbaceous plants (Grass,Crops)
#Condition#Alkaline

Safety information

risk assessment

  • @ref: 2759
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Amphibacillus xylanus 16S rRNA gene, strain DSM 6626AJ4968071505ena698758
20218Amphibacillus xylanus isolate Ax79 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723603725ena698758
20218Amphibacillus xylanus isolate Ax85 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723604630ena698758
20218Amphibacillus xylanus DNA for 16S ribosomal RNAD820651450ena698758
20218Amphibacillus xylanus gene for 16S rRNA, partial sequence, strain: NBRC 15112AB6807701495ena1449

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amphibacillus xylanus NBRC 15112GCA_000307165completencbi698758
66792Amphibacillus xylanus NBRC 15112698758.3completepatric698758
66792Amphibacillus xylanus NBRC 151122524023219completeimg698758

GC content

@refGC-contentmethod
2302936
6777036thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes98no
motileyes79.432no
flagellatedno50.686no
gram-positiveyes90.534no
anaerobicno94.307yes
aerobicno93.119yes
halophileyes80.204no
spore-formingyes88.334yes
glucose-utilyes88.082no
thermophileno70.403no
glucose-fermentno52.486no

External links

@ref: 2759

culture collection no.: DSM 6626, ATCC 51415, IFO 15112, JCM 7361, NBRC 15112, LMG 17667

straininfo link

  • @ref: 71054
  • straininfo: 9966

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology8836445Unusually stable NAD-specific glutamate dehydrogenase from the alkaliphile Amphibacillus xylanus.Jahns TAntonie Van Leeuwenhoek10.1007/BF003935731996Acetonitriles/pharmacology, Alcohols/pharmacology, Ammonia/metabolism, Bacillus/chemistry/*enzymology, Bacterial Proteins/chemistry/isolation & purification/metabolism, Chromatography, Gel, Electrophoresis, Polyacrylamide Gel, Enzyme Stability, Glutamate Dehydrogenase/*chemistry/isolation & purification/metabolism, Glutamic Acid/metabolism, Hydrogen-Ion Concentration, Kinetics, Molecular Weight, NAD/*metabolism, TemperatureMetabolism
Phylogeny22493173Amphibacillus indicireducens sp. nov., an alkaliphile that reduces an indigo dye.Hirota K, Aino K, Nodasaka Y, Morita N, Yumoto IInt J Syst Evol Microbiol10.1099/ijs.0.037622-02012Bacillaceae/*classification/genetics/isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, Coloring Agents/metabolism, DNA, Bacterial/genetics, Fatty Acids/analysis, Fermentation, Indigo Carmine, Indoles/*metabolism, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Phylogeny26475440Pelagirhabdus alkalitolerans gen. nov., sp. nov., an alkali-tolerant and thermotolerant bacterium isolated from beach sediment, and reclassification of Amphibacillus fermentum as Pelagirhabdus fermentum comb. nov.Sultanpuram VR, Mothe T, Chintalapati S, Chintalapati VRInt J Syst Evol Microbiol10.1099/ijsem.0.0006782015Alkalies, Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2759Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6626)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6626
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
23029Youichi Niimura,Enki Koh,Fujitoshi Yanagida,Ken-Ichiro Suzuki,Kazuo Komagata,Michio Kozaki10.1099/00207713-40-3-297Amphibacillus xylanus gen. nov., sp. nov., a Facultatively Anaerobic Sporeforming Xylan-Digesting Bacterium Which Lacks Cytochrome, Quinone, and CatalaseIJSEM 40: 297-301 1990
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/
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
71054Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9966.1StrainInfo: A central database for resolving microbial strain identifiers