Strain identifier

BacDive ID: 1407

Type strain: Yes

Species: Amphibacillus jilinensis

Strain Designation: Y1

Strain history: X.-Y. Wu Y1.

NCBI tax ID(s): 1216008 (species)

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General

@ref: 17771

BacDive-ID: 1407

DSM-Number: 24783

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

description: Amphibacillus jilinensis Y1 is a facultative anaerobe, halotolerant, spore-forming bacterium that was isolated from sediment from soda lake.

NCBI tax id

  • NCBI tax id: 1216008
  • Matching level: species

strain history

@refhistory
17771<- JCM <- X.-Y. Wu, Zhejiang Univ., Hangzhou, China; Y1
67770X.-Y. Wu Y1.

doi: 10.13145/bacdive1407.20230509.8.1

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 jilinensis
  • full scientific name: Amphibacillus jilinensis Wu et al. 2010

@ref: 17771

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Amphibacillus

species: Amphibacillus jilinensis

full scientific name: Amphibacillus jilinensis Wu et al. 2010

strain designation: Y1

type strain: yes

Morphology

cell morphology

  • @ref: 23033
  • gram stain: positive
  • cell length: 2.0-3.2 µm
  • cell width: 0.4-0.6 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: peritrichous

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17771CASO 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
23033optimized medium JYyescontaining l-1 distilled water: 2.0 g yeast extract (Difco), 5.0 g sucrose, 0.2 g KCl, 0.2 g KH2PO4 , 0.1 g MgCl2.6H2O, 0.5 g NH4Cl, 0.1 g CaCl2 , 0.06 M NaHCO3 and 0.44 M NaCl; final pH 9.0

culture temp

@refgrowthtypetemperaturerange
17771positivegrowth30mesophilic
23033positivegrowth15.0-45.0
23033nogrowth10.0psychrophilic
23033nogrowth50.0thermophilic
23033positiveoptimum32.0mesophilic
67770positivegrowth35mesophilic

culture pH

@refabilitytypepHPH range
23033positiveoptimum9.0alkaliphile
23033positivegrowth7.5-10.5
23033nogrowth7.0
23033nogrowth11.0

Physiology and metabolism

oxygen tolerance

  • @ref: 23033
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 23033
  • spore description: terminal
  • type of spore: endospore
  • spore formation: yes

halophily

  • @ref: 23033
  • halophily level: halotolerant

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2303317234glucose-fermentation
2303330089acetate-growth
2303317968butyrate-growth
23033casamino acids-growth
2303316947citrate-growth
2303316236ethanol-growth
2303315740formate-growth
2303329806fumarate-growth
2303317754glycerol-growth
2303315428glycine-growth
2303316977L-alanine-growth
2303316467L-arginine-growth
2303317561L-cysteine-growth
2303315971L-histidine-growth
2303316643L-methionine-growth
2303324996lactate-growth
2303325115malate-growth
2303317790methanol-growth
2303330623oxalate-growth
2303317272propionate-growth
2303315361pyruvate-growth
2303330031succinate-growth
2303330929tartrate-growth
23033tryptone-growth
2303317368hypoxanthine-hydrolysis
2303318186tyrosine-hydrolysis
2303315318xanthine-hydrolysis
2303317057cellobiose+carbon source
2303315824D-fructose+carbon source
2303312936D-galactose+carbon source
2303317634D-glucose+carbon source
2303316899D-mannitol+carbon source
2303316634raffinose+carbon source
2303317924D-sorbitol+carbon source
2303365327D-xylose+carbon source
2303330849L-arabinose+carbon source
2303317716lactose+carbon source
2303317306maltose+carbon source
2303337684mannose+carbon source
2303328053melibiose+carbon source
2303326546rhamnose+carbon source
2303317992sucrose+carbon source
2303327082trehalose+carbon source
23033yeast extract+growth
23033casein+hydrolysis
2303328017starch+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistantresistance conc.sensitivity conc.
2303328669bacitracinyesnoyes0.04 Unit
230338309polymyxin byesnoyes300 Unit
2303317833gentamicinyesnoyes10 µg (disc)
230337660nystatinyesnoyes100 µg (disc)
230332637amikacinyesnoyes30 µg (disc)
23033100147nalidixic acidyesnoyes30 µg (disc)
230337809oxacillinyesyes1 µg (disc)
230332676amoxicillinyesyes10 µg (disc)
2303328971ampicillinyesyes10 µg (disc)
2303317334penicillinyesyes10 µg (disc)
2303317076streptomycinyesyes10 µg (disc)
2303328864tobramycinyesyes10 µg (disc)
230333393carbenicillinyesyes100 µg (disc)
230332955azithromycinyesyes15 µg (disc)
2303348923erythromycinyesyes15 µg (disc)
2303328915fosfomycinyesyes200 µg (disc)
23033204928cefotaximeyesyes30 µg (disc)
2303317698chloramphenicolyesyes30 µg (disc)
230336104kanamycinyesyes30 µg (disc)
230337507neomycinyesyes30 µg (disc)
2303328368novobiocinyesyes30 µg (disc)
2303327902tetracyclineyesyes30 µg (disc)
2303328001vancomycinyesyes30 µg (disc)
23033209807cefoxitinyesyes300 µg (disc)
2303371415nitrofurantoinyesyes300 µg (disc)
2303328077rifampicinyesyes5 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
2303335581indoleno
2303316136hydrogen sulfideno
2303315688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
2303315688acetoin-
2303317234glucose-

enzymes

@refvalueactivityec
23033catalase-1.11.1.6
23033cytochrome oxidase-1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
17771sediment from soda lakeJilin ProvinceChinaCHNAsia
23033soda lakeJilin ProvinceChinaCHNAsia44.75123.567enrichment culturecontaining (l-1 distilled water) 10.0 g NaCl, 10.0 g Na2CO3, 5.0 g NaHCO3 , 0.2 g KH2PO4, 0.33 g MgCl2.6H2O, 0.5 g NH4Cl, 0.2 g KCl, 2.0 g yeast extract (Difco), 5.0 g glucose, 0.5 g Na2S.9H2O, 0.4 g L-cysteine, 10 ml trace element solution 141 and 0.001 g resazurin3 days32Hungate roll-tube technique
67770Sediment from a soda lake in Jilin ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Aquatic#Lake (large)
#Condition#Alkaline

taxonmaps

  • @ref: 69479
  • File name: preview.99_330.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_230;97_252;98_281;99_330&stattab=map
  • Last taxonomy: Amphibacillus jilinensis
  • 16S sequence: FJ169626
  • Sequence Identity:
  • Total samples: 290
  • soil counts: 96
  • aquatic counts: 41
  • animal counts: 131
  • plant counts: 22

Safety information

risk assessment

  • @ref: 17771
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17771
  • description: Amphibacillus jilinensis Y1 16S ribosomal RNA gene, partial sequence
  • accession: FJ169626
  • length: 1532
  • database: ena
  • NCBI tax ID: 562743

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amphibacillus jilinensis Y1562743.4wgspatric562743
66792Amphibacillus jilinensis Y12547132169draftimg562743
67770Amphibacillus jilinensis Y1GCA_000306965scaffoldncbi562743

GC content

@refGC-contentmethod
1777137.7thermal denaturation, midpoint method (Tm)
6777037.27genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes88.024no
anaerobicno90.332no
halophileyes87.904no
spore-formingyes93.39yes
glucose-utilyes90.526no
thermophileno97.869no
flagellatedyes72.403yes
motileyes86.315yes
aerobicno94.005yes
glucose-fermentno56.558no

External links

@ref: 17771

culture collection no.: DSM 24783, CGMCC 1.5123, JCM 16149

straininfo link

  • @ref: 71058
  • straininfo: 406670

literature

  • topic: Phylogeny
  • Pubmed-ID: 19965990
  • title: Amphibacillus jilinensis sp. nov., a facultatively anaerobic, alkaliphilic bacillus from a soda lake.
  • authors: Wu XY, Zheng G, Zhang WW, Xu XW, Wu M, Zhu XF
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.018259-0
  • year: 2009
  • mesh: 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
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17771Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24783)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24783
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
23033Xiao-Yue Wu,Gang Zheng,Wen-Wu Zhang,Xue-Wei Xu,Min Wu,Xu-Fen Zhu10.1099/ijs.0.018259-0Amphibacillus jilinensis sp. nov., a facultatively anaerobic, alkaliphilic bacillus from a soda lakeIJSEM 60: 2540-2543 201019965990
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/
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
71058Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406670.1StrainInfo: A central database for resolving microbial strain identifiers