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Strain identifier

BacDive ID: 1303

Type strain: Yes

Species: Cytobacillus oceanisediminis

Strain Designation: H2

Strain history: J. Zhang H2.

NCBI tax ID(s): 665099 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 17755

BacDive-ID: 1303

DSM-Number: 24771

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

description: Cytobacillus oceanisediminis H2 is an aerobe, spore-forming, mesophilic bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 665099
  • Matching level: species

strain history

doi: 10.13145/bacdive1303.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Cytobacillus
  • species: Cytobacillus oceanisediminis
  • full scientific name: Cytobacillus oceanisediminis (Zhang et al. 2010) Patel and Gupta 2020
  • synonyms

    • @ref: 20215
    • synonym: Bacillus oceanisediminis

@ref: 17755

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Cytobacillus

species: Cytobacillus oceanisediminis

full scientific name: Cytobacillus oceanisediminis (Zhang et al. 2010) Patel and Gupta 2020

strain designation: H2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29741positive02-03 µm0.6-0.8 µmrod-shaped
69480yes92.088
69480positive95.129

pigmentation

  • @ref: 29741
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17755BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
37685MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
17755positivegrowth30mesophilic
29741positivegrowth04-45
29741positiveoptimum37mesophilic
37685positivegrowth30mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
29741positivegrowth06-10alkaliphile
29741positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29741
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29741yes
69480yes97.335

halophily

@refsaltgrowthtested relationconcentrationhalophily levelconfidence
29741NaClpositivegrowth0-13 %
29741NaClpositiveoptimum0-13 %
69480non-halophilic82.024

observation

@refobservation
29741aggregates in chains
67770quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2974130089acetate+carbon source
2974117057cellobiose+carbon source
2974117234glucose+carbon source
2974128087glycogen+carbon source
2974124996lactate+carbon source
2974125115malate+carbon source
2974115361pyruvate+carbon source
2974116634raffinose+carbon source
2974126546rhamnose+carbon source
2974130031succinate+carbon source
2974117992sucrose+carbon source
2974117632nitrate+reduction

metabolite production

  • @ref: 29741
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 29741
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
29741catalase+1.11.1.6
29741cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17755marine sedimentSouth China SeaChinaCHNAsia
67770Sediment sample from the South SeaChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1563.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_264;97_962;98_1233;99_1563&stattab=map
  • Last taxonomy: Bacillales
  • 16S sequence: GQ292772
  • Sequence Identity:
  • Total samples: 4254
  • soil counts: 1890
  • aquatic counts: 700
  • animal counts: 1214
  • plant counts: 450

Safety information

risk assessment

  • @ref: 17755
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
29741Bacillus oceanisediminis strain H2 16S ribosomal RNA gene, partial sequenceGQ2927721393nuccore665099
17755CAXO576.rev CAXO Teleopsis dalmanni Early pupal eye-antennal disc EST library Teleopsis dalmanni cDNA clone CAXO576 3', mRNA sequenceGO292772743ena139649

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cytobacillus oceanisediminis CGMCC 1.10115GCA_007830235scaffoldncbi665099
66792Bacillus oceanisediminis strain CGMCC 1.10115665099.9wgspatric665099
66792Bacillus oceanisediminis CGMCC 1.101152596583545draftimg665099

GC content

@refGC-contentmethod
1775544.8thermal denaturation, midpoint method (Tm)
2974144.8

External links

@ref: 17755

culture collection no.: DSM 24771, CGMCC 1.10115, JCM 16506, BCRC 80336

straininfo link

@refpassport
20218http://www.straininfo.net/strains/860679
20218http://www.straininfo.net/strains/860680

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20118297Bacillus oceanisediminis sp. nov., isolated from marine sediment.Zhang J, Wang J, Fang C, Song F, Xin Y, Qu L, Ding KInt J Syst Evol Microbiol10.1099/ijs.0.019851-02010Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny25829330Bacillus taiwanensis sp. nov., isolated from a soil sample from Taiwan.Liu B, Liu GH, Sengonca C, Schumann P, Wang MK, Xiao RF, Zheng XF, Chen ZInt J Syst Evol Microbiol10.1099/ijs.0.0002222015Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Taiwan, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27265352Bacillus oryzisoli sp. nov., isolated from rice rhizosphere.Zhang XX, Gao JS, Zhang L, Zhang CW, Ma XT, Zhang JInt J Syst Evol Microbiol10.1099/ijsem.0.0012152016Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oryza/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny30839250Falsibacillus albus sp. nov., isolated from mangrove soil.Shi SB, Liu C, Jiang MG, Li GD, Yang LF, Wu JF, Jiang LQ, Zhang K, Shen NK, Jiang CL, Jiang YInt J Syst Evol Microbiol10.1099/ijsem.0.0033282019Bacillaceae/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny36478127Cytobacillus pseudoceanisediminis sp. nov., A Novel Facultative Methylotrophic Bacterium with High Heavy Metal Resistance Isolated from the Deep Underground Saline Spring.Tarasov K, Yakhnenko A, Zarubin M, Gangapshev A, Potekhina NV, Avtukh AN, Kravchenko ECurr Microbiol10.1007/s00284-022-03141-82022RNA, Ribosomal, 16S/genetics, Phylogeny, *Metals, Heavy, DNA

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
17755Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24771)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24771
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
2612310.1099/ijs.0.019851-020118297
29741Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126123
37685Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8101
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
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)