Strain identifier

BacDive ID: 164404

Type strain: Yes

Species: Neobacillus piezotolerans

Strain Designation: YLB-04

Strain history: X. Tang; Third Inst. of State Oceanic Admin., China; YLB-04.

NCBI tax ID(s): 2259171 (species)

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General

@ref: 67770

BacDive-ID: 164404

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, rod-shaped, colony-forming

description: Neobacillus piezotolerans YLB-04 is an aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from Deep-sea sediment at 6300 m of the Yap Trench.

NCBI tax id

  • NCBI tax id: 2259171
  • Matching level: species

strain history

  • @ref: 67770
  • history: X. Tang; Third Inst. of State Oceanic Admin., China; YLB-04.

doi: 10.13145/bacdive164404.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Neobacillus
  • species: Neobacillus piezotolerans
  • full scientific name: Neobacillus piezotolerans (Yu et al. 2019) Gupta et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus piezotolerans

@ref: 67770

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Bacillaceae

genus: Neobacillus

species: Neobacillus piezotolerans

full scientific name: Neobacillus piezotolerans (Yu et al. 2019) Gupta et al. 2020

strain designation: YLB-04

type strain: yes

Morphology

cell morphology

  • @ref: 68177
  • gram stain: positive
  • cell length: 1.2-2.2 µm
  • cell width: 0.3-0.6 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: peritrichous

colony morphology

  • @ref: 68177
  • colony size: 0.5-1 mm
  • colony color: cream
  • colony shape: circular
  • incubation period: 1 day
  • medium used: LB (Luria-Bertani) MEDIUM

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
67770positivegrowth37mesophilic
68177positivegrowth15-50
68177positiveoptimum45thermophilic

culture pH

@refabilitytypepHPH range
68177positivegrowth5-10.5alkaliphile
68177positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 68177
  • oxygen tolerance: aerobe

spore formation

  • @ref: 68177
  • type of spore: endospore
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
68177NaClpositivegrowth0-6 %(w/v)
68177NaClpositiveoptimum0 %(w/v)

observation

@refobservation
67770quinones: MK-7
68177Growth occurs within the hydropressure range 0.1-50 MPa (optimum 0.1 MPa)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6817753424tween 20-hydrolysis
6817753423tween 40-hydrolysis
6817753425tween 60-hydrolysis
6817753426tween 80-hydrolysis
6817728017starch-hydrolysis
68177skimmed milk-hydrolysis
6817762968cellulose-hydrolysis
6817759640N-acetylglucosamine+assimilation
6817717306maltose+assimilation
6817717634D-glucose+assimilation
6817717234glucose+fermentation
6817717992sucrose+fermentation
6817727082trehalose+oxidation
6817717992sucrose+oxidation
68177506227N-acetyl-D-glucosamine+oxidation
6817763154N-acetyl-beta-D-mannosamine+oxidation
68177n-acetyl-neuraminic acid+oxidation
6817717925alpha-D-glucose+oxidation
6817715824D-fructose+oxidation
6817717596inosine+oxidation
681771 % sodium lactate+oxidation
6817717754glycerol+oxidation
6817770744glycyl-L-proline+oxidation
6817717309pectin+oxidation
681778391D-gluconate+oxidation
68177100147nalidixic acid+oxidation
6817775248potassium tellurite+oxidation
68177370543-hydroxybutyrate+oxidation
68177161680aztreonam+oxidation
6817764103sodium butyrate+oxidation
681774853esculin+/-hydrolysis
681775291gelatin+/-hydrolysis
6817730849L-arabinose-assimilation
6817732032potassium gluconate-assimilation
6817717120hexanoate-assimilation
6817717128adipate-assimilation
6817725115malate-assimilation
6817753258sodium citrate-assimilation
6817718401phenylacetate-assimilation
6817726546rhamnose-fermentation
6817728053melibiose-fermentation
6817727613amygdalin-fermentation
6817722599arabinose-fermentation
6817729673rifamycin sv+/-assimilation
68177161680aztreonam+assimilation
6817764103sodium butyrate+assimilation
6817775229sodium bromate+/-assimilation
6817723652dextrin-assimilation
6817717057cellobiose-assimilation
6817728066gentiobiose-assimilation
6817732528turanose-assimilation
6817717164stachyose-assimilation
6817716634raffinose-assimilation
6817717716lactose-assimilation
6817728053melibiose-assimilation
6817737657methyl D-glucoside-assimilation
6817717814D-salicin-assimilation
6817728037n-acetyl-D-galactosamine-assimilation
6817716024D-mannose-assimilation
6817712936D-galactose-assimilation
68177739183-O-methyl-D-glucose-assimilation
6817728847D-fucose-assimilation
6817718287L-fucose-assimilation
6817771321fusidate-assimilation
6817717924D-sorbitol-assimilation
6817716899D-mannitol-assimilation
6817718333D-arabitol-assimilation
6817717268myo-inositol-assimilation
6817717665alpha-D-glucose 6-phosphate-assimilation
6817778697D-fructose 6-phosphate-assimilation
6817729990D-aspartate-assimilation
6817716523D-serine-assimilation
6817745735troleandomycin-assimilation
6817750694minocycline-assimilation
6817716977L-alanine-assimilation
6817790350L-arginine-2-naphthylamide-assimilation
6817729991L-aspartate-assimilation
6817729985L-glutamate-assimilation
6817715971L-histidine-assimilation
6817718183L-pyroglutamic acid-assimilation
6817717115L-serine-assimilation
681776472lincomycin-assimilation
6817732735guanidinium chloride-assimilation
6817775273niaproof-assimilation
6817718024D-galacturonic acid-assimilation
6817715895D-galactonic acid lactone-assimilation
6817728860beta-D-glucuronic acid-assimilation
6817732323glucuronamide-assimilation
6817735390galactarate-assimilation
6817717521(-)-quinic acid-assimilation
6817733801D-saccharate-assimilation
6817728001vancomycin-assimilation
6817775193tetrazolium violet-assimilation
6817775198tetrazolium blue-assimilation
68177181014-hydroxyphenylacetic acid-assimilation
6817751850methyl pyruvate-assimilation
68177D-lactic acid methyl ester-assimilation
68177L-lactate-assimilation
6817716947citrate-assimilation
6817715588D-malate-assimilation
6817715589L-malate-assimilation
6817773706bromosuccinate-assimilation
6817748607lithium chloride-assimilation
6817753423tween 40-assimilation
6817716865gamma-aminobutyric acid-assimilation
68177645522-hydroxybutyrate-assimilation
6817713705acetoacetate-assimilation
6817717272propionate-assimilation
6817716411acetic acid-assimilation
6817715740formate-assimilation

metabolite production

@refChebi-IDmetaboliteproduction
6817735581indoleno
6817716136hydrogen sulfideno
6817715688acetoinno

metabolite tests

  • @ref: 68177
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68177catalase+1.11.1.6
68177cytochrome oxidase+1.9.3.1
68177nitrate reductase+1.7.99.4
68177alkaline phosphatase+3.1.3.1
68177leucine arylamidase+3.4.11.1
68177alpha-chymotrypsin+3.4.21.1
68177alpha-glucosidase+3.2.1.20
68177esterase (C 4)+/-
68177esterase Lipase (C 8)+/-
68177lipase (C 14)+/-
68177valine arylamidase+/-
68177cystine arylamidase+/-3.4.11.3
68177trypsin+/-3.4.21.4
68177acid phosphatase+/-3.1.3.2
68177naphthol-AS-BI-phosphohydrolase+/-
68177beta-glucuronidase+/-3.2.1.31
68177beta-glucosidase+/-3.2.1.21
68177alpha-galactosidase-3.2.1.22
68177beta-galactosidase-3.2.1.23
68177N-acetyl-beta-glucosaminidase-3.2.1.52
68177alpha-mannosidase-3.2.1.24
68177alpha-fucosidase-3.2.1.51
68177urease-3.5.1.5
68177ornithine decarboxylase+4.1.1.17
68177arginine dihydrolase-3.5.3.6
68177lysine decarboxylase-4.1.1.18
68177tryptophan deaminase-4.1.99.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68177C14:02.2
    68177C16:021
    68177C18:012.7
    68177C16:1 w7c alcohol2.1
    68177C18:1 w9c2.7
    68177C14:0 iso2.3
    68177C15:0 iso17.6
    68177C16:0 iso4
    68177C17:0 iso3.3
    68177C17:1 iso w10c1.4
    68177C15:0 anteiso13.2
    68177C17:0 anteiso6.2
    68177C17:1 iso / C17:1 anteiso1.3
    68177C18:1 w7c/C18:1 w6c5.1
  • type of FA analysis: whole cell analysis
  • incubation medium: LB
  • incubation temperature: 45
  • incubation time: 2
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA 6.0
  • system: MIS MIDI
  • instrument: Agilent Technologies 6850
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typecountrysampling dategeographic locationlatitudelongitudeenrichment cultureenrichment culture durationisolation procedure
67770Deep-sea sediment at 6300 m of the Yap TrenchPacific Ocean
68177sediment of hadal zonesPacific Ocean2017-06-01West Pacific Yap Trench-9.8661-138.493marine broth7 daysenriched at 60 MPa

Sequence information

16S sequences

  • @ref: 67770
  • description: Bacillus sp. (in: Bacteria) strain ylb-04 16S ribosomal RNA gene, partial sequence
  • accession: MG913994
  • length: 1443
  • database: ena
  • NCBI tax ID: 2259171

Genome sequences

  • @ref: 68177
  • description: Neobacillus piezotolerans YLB-04
  • accession: GCA_003362805
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2259171

GC content

  • @ref: 68177
  • GC-content: 45.4
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes85.615yes
flagellatedyes80.925yes
gram-positiveyes85.335yes
anaerobicno96.702no
aerobicyes88.562yes
halophileno63.66no
spore-formingyes75.059yes
glucose-utilyes87.932yes
thermophileno98.562no
glucose-fermentno88.645yes

External links

@ref: 67770

culture collection no.: JCM 32872, MCCC 1A12711

literature

  • topic: Phylogeny
  • Pubmed-ID: 31364965
  • title: Two novel species of the family Bacillaceae: Oceanobacillus piezotolerans sp. nov. and Bacillus piezotolerans sp. nov., from deep-sea sediment samples of Yap Trench.
  • authors: Yu L, Tang X, Wei S, Qiu Y, Xu X, Xu G, Wang Q, Yang Q
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003559
  • year: 2019
  • mesh: Bacillaceae/*classification/isolation & purification, Bacillus/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Pacific Ocean, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Enzymology

Reference

@idauthorstitledoi/urljournal
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68177Libo Yu, Xixiang Tang, Shiping Wei, Yinkun Qiu, Xiashutong Xu, Guangxin Xu, Qilin Wang and Qian YangTwo novel species of the family Bacillaceae: Oceanobacillus piezotolerans sp. nov. and Bacillus piezotolerans sp. nov., from deep-sea sediment samples of Yap Trench10.1099/ijsem.0.003559IJSEM 69: 3022-3030 2019