Strain identifier

BacDive ID: 140961

Type strain: Yes

Species: Bacillus pacificus

Strain Designation: EB422

Strain history: CIP <- 2017, KCTC <- Y. Liu, Third Inst. State Oceanic Admin.: strain EB422

NCBI tax ID(s): 2026187 (species)

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General

@ref: 43860

BacDive-ID: 140961

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

description: Bacillus pacificus EB422 is a facultative anaerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from sediment of the Pacific Ocean.

NCBI tax id

  • NCBI tax id: 2026187
  • Matching level: species

strain history

@refhistory
67771<- Yang Liu, the Third institute of State Oceanic Administration(SOA)
121503CIP <- 2017, KCTC <- Y. Liu, Third Inst. State Oceanic Admin.: strain EB422

doi: 10.13145/bacdive140961.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Bacillus
  • species: Bacillus pacificus
  • full scientific name: Bacillus pacificus Liu et al. 2017

@ref: 43860

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Bacillaceae

genus: Bacillus

species: Bacillus pacificus

strain designation: EB422

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
43860positive3.0-4.0 µm1.2-1.6 µmrod-shapedno
67771positive
121503positiverod-shapedyes

colony morphology

  • @ref: 43860
  • colony size: 2-3 mm
  • colony color: white
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Luria-Bertani agar

Culture and growth conditions

culture medium

@refnamegrowthlink
43860LB (Luria-Bertani) MEDIUMyes
43860Trypticase soy agaryes
121503CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
43860positivegrowth15-45
43860positiveoptimum30mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43860positivegrowth5.0-10.0alkaliphile
43860positiveoptimum6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43860facultative anaerobe
67771aerobe

spore formation

  • @ref: 43860
  • spore description: central elliptical endospore
  • type of spore: endospore
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
43860NaClpositivegrowth0-9 %(w/v)
43860NaClpositiveoptimum1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43860168082-dehydro-D-gluconate-builds acid from
43860581435-dehydro-D-gluconate-builds acid from
4386027613amygdalin-builds acid from
4386022599arabinose-builds acid from
4386017057cellobiose-builds acid from
4386015963ribitol-builds acid from
4386017108D-arabinose-builds acid from
4386018333D-arabitol-builds acid from
4386028847D-fucose-builds acid from
4386012936D-galactose-builds acid from
4386062318D-lyxose-builds acid from
4386016899D-mannitol-builds acid from
4386016024D-mannose-builds acid from
4386017924D-sorbitol-builds acid from
4386016443D-tagatose-builds acid from
4386016813galactitol-builds acid from
4386017113erythritol-builds acid from
4386028066gentiobiose-builds acid from
4386017234glucose-builds acid from
4386017754glycerol-builds acid from
4386028087glycogen-builds acid from
4386017268myo-inositol-builds acid from
4386015443inulin-builds acid from
4386018403L-arabitol-builds acid from
4386018287L-fucose-builds acid from
4386062345L-rhamnose-builds acid from
4386017266L-sorbose-builds acid from
4386065328L-xylose-builds acid from
4386017716lactose-builds acid from
4386029864mannitol-builds acid from
438606731melezitose-builds acid from
4386028053melibiose-builds acid from
43860320061methyl alpha-D-glucopyranoside-builds acid from
4386043943methyl alpha-D-mannoside-builds acid from
4386074863methyl beta-D-xylopyranoside-builds acid from
4386032032potassium gluconate-builds acid from
4386016634raffinose-builds acid from
4386026546rhamnose-builds acid from
4386017814salicin-builds acid from
4386030911sorbitol-builds acid from
4386028017starch-builds acid from
4386017992sucrose-builds acid from
4386032528turanose-builds acid from
4386017151xylitol-builds acid from
4386028017starch-hydrolysis
4386018305arbutin+builds acid from
4386015824D-fructose+builds acid from
4386017634D-glucose+builds acid from
4386016988D-ribose+builds acid from
4386065327D-xylose+builds acid from
43860esculin ferric citrate+builds acid from
4386017306maltose+builds acid from
43860506227N-acetylglucosamine+builds acid from
4386017992sucrose+builds acid from
4386027082trehalose+builds acid from
4386016947citrate+carbon source
43860casein+hydrolysis
43860skimmed milk+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
4386016136hydrogen sulfideno
4386035581indoleno
4386015688acetoinyes

metabolite tests

  • @ref: 43860
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
43860catalase+1.11.1.6
43860cytochrome oxidase+1.9.3.1
43860arginine dihydrolase+3.5.3.6
43860gelatinase+
43860beta-galactosidase-3.2.1.23
43860lysine decarboxylase-4.1.1.18
43860ornithine decarboxylase-4.1.1.17
43860urease-3.5.1.5
43860tryptophan deaminase-4.1.99.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43860C13:0 anteiso2
    43860C15:0 anteiso6.7
    43860C17:0 anteiso2.7
    43860C12:01.7
    43860C14:06.8
    43860C16:019.9
    43860C16:1ω11c1.7
    43860C16:1ω7c / C15:0 iso 2OH8
    43860C18:02
    43860C18:1ω9c3
    43860C12:0 iso1.2
    43860C13:0 iso6.4
    43860C14:0 iso3.5
    43860C15:0 iso13.8
    43860C16:0 iso5.3
    43860C17:0 iso5.2
    43860C17:1 iso I /C17:1 anteiso B4.6
    43860C17:1 iso ω10c1.7
    43860C17:1 iso ω5c1
  • type of FA analysis: whole cell analysis
  • incubation medium: Tripticase soy agar
  • agar/liquid: agar
  • incubation temperature: 28
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA 6.0
  • system: MIS MIDI
  • instrument: Agilent 6850 gas chromatograph
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountry
43860sediment of the Pacific Ocean
67771From bottom seawater, sedimentthe Pacific OceanPacific Ocean
121503Environment, Bottom seawaterPacific Ocean

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_26.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_21;97_22;98_25;99_26&stattab=map
  • Last taxonomy: Bacillus
  • 16S sequence: KJ812450
  • Sequence Identity:
  • Total samples: 4969
  • soil counts: 1920
  • aquatic counts: 446
  • animal counts: 1524
  • plant counts: 1079

Safety information

risk assessment

  • @ref: 121503
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 43860
  • description: 16S rRNA gene sequence
  • accession: KJ812450
  • database: nuccore

Genome sequences

  • @ref: 66792
  • description: Bacillus pacificus EB422
  • accession: GCA_001884025
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2026187

GC content

  • @ref: 43860
  • GC-content: 35.2
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes70.291yes
gram-positiveyes86.988yes
anaerobicno98.391yes
aerobicyes83.714no
halophileno93.232no
spore-formingyes92.179yes
thermophileno99.682no
glucose-utilyes90.163no
motileyes60.769yes
glucose-fermentno91.083no

External links

@ref: 43860

culture collection no.: MCCC 1A06182, KCTC 33858, CIP 111542, NBRC 113915

straininfo link

  • @ref: 96820
  • straininfo: 413747

literature

  • topic: Phylogeny
  • Pubmed-ID: 28792367
  • title: Proposal of nine novel species of the Bacillus cereus group.
  • authors: Liu Y, Du J, Lai Q, Zeng R, Ye D, Xu J, Shao Z
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001821
  • year: 2017
  • mesh: Bacillus/*classification, Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
43860Yang Liu, Juan Du, Qiliang Lai, Runying Zeng, Dezan Ye, Jun Xu, Zongze ShaoProposal of nine novel species of the Bacillus cereus group10.1099/ijsem.0.001821IJSEM 67: 2499-2508 201728792367
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
96820Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID413747.1
121503Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111542Collection of Institut Pasteur (CIP 111542)