Strain identifier

BacDive ID: 1327

Type strain: Yes

Species: Halobacillus halophilus

Strain Designation: 3

Strain history: IAM 13060 <-- M. V. Hao and K. Komagata HK 814 <-- CCM 3527 <-- DSM 2266 <-- H. J. Rolf 3.

NCBI tax ID(s): 866895 (strain), 1570 (species)

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General

@ref: 1011

BacDive-ID: 1327

DSM-Number: 2266

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, moderately halophilic, chemoorganotroph, spore-forming, mesophilic, Gram-positive, motile, rod-shaped, pigmented

description: Halobacillus halophilus 3 is an obligate aerobe, moderately halophilic, chemoorganotroph bacterium that has a orange pigmentation and was isolated from salt marsh soil.

NCBI tax id

NCBI tax idMatching level
1570species
866895strain

strain history

@refhistory
1011<- H.J. Rolf, 3
67770IAM 13060 <-- M. V. Hao and K. Komagata HK 814 <-- CCM 3527 <-- DSM 2266 <-- H. J. Rolf 3.

doi: 10.13145/bacdive1327.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Halobacillus
  • species: Halobacillus halophilus
  • full scientific name: Halobacillus halophilus (Claus et al. 1984) Spring et al. 1996

  • synonyms

    • @ref: 20215
    • synonym: Sporosarcina halophila

@ref: 1011

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Halobacillus

species: Halobacillus halophilus

full scientific name: Halobacillus halophilus (Claus et al. 1984) Spring et al. 1996

strain designation: 3

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
22983positiverod-shapedyes
125439yes91.4

pigmentation

  • @ref: 22983
  • production: yes
  • color: orange

Culture and growth conditions

culture medium

  • @ref: 1011
  • name: MARINE AGAR (DSMZ Medium 123)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/123
  • composition: Name: MARINE AGAR (DSMZ Medium 123) Composition: NaCl 24.0 g/l Agar 15.0 g/l MgCl2 x 6 H2O 11.0 g/l Bacto peptone 5.0 g/l Na2SO4 4.0 g/l CaCl2 x 6 H2O 2.0 g/l Yeast extract 1.0 g/l KCl 0.7 g/l KBr 0.1 g/l SrCl2 x 6 H2O 0.04 g/l H3BO3 0.03 g/l NaSiO3 x 9 H2O 0.005 g/l NaF 0.003 g/l NH4NO3 0.002 g/l Fe(III)PO4 x 4 H2O 0.001 g/l Distilled water

culture temp

@refgrowthtypetemperature
1011positivegrowth30
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
22983obligate aerobe
125439obligate aerobe92.1

nutrition type

  • @ref: 22983
  • type: chemoorganotroph

spore formation

@reftype of sporespore formationconfidence
22983endosporeyes
125438yes95.074
125439yes96.4

halophily

  • @ref: 22983
  • halophily level: moderately halophilic

murein

  • @ref: 1011
  • murein short key: A21.04
  • type: A4ß L-Orn-D-Asp

metabolite utilization

  • @ref: 22983
  • Chebi-ID: 17632
  • metabolite: nitrate
  • utilization activity: -
  • kind of utilization tested: reduction

metabolite production

  • @ref: 22983
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: no

metabolite tests

  • @ref: 22983
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
22983catalase+1.11.1.6
22983cytochrome oxidase+1.9.3.1
22983DNase+
22983urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1011salt marsh soilSyltGermanyDEUEurope
67770Salt marsh soilGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Salt marsh
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_3747.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_469;97_536;98_617;99_3747&stattab=map
  • Last taxonomy: Halobacillus
  • 16S sequence: AB681790
  • Sequence Identity:
  • Total samples: 448
  • soil counts: 116
  • aquatic counts: 246
  • animal counts: 13
  • plant counts: 73

Safety information

risk assessment

  • @ref: 1011
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halobacillus halophilus genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: A492AB367151492nuccore866895
20218Halobacillus halophilus genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: B492AB367152492nuccore866895
20218Halobacillus halophilus genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 740AB367153740nuccore866895
67770Halobacillus halophilus gene for 16S rRNA, partial sequence, strain: NBRC 102448AB6817901492nuccore1570

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halobacillus halophilus DSM 2266 type strain: DSM 2266GCA_000284515completencbi866895
66792Halobacillus halophilus DSM 2266866895.3completepatric866895
66792Halobacillus halophilus DSM 2266 strain type strain: DSM 2266866895.15plasmidpatric866895
66792Halobacillus halophilus DSM 2266 strain type strain: DSM 2266866895.14plasmidpatric866895
66792Halobacillus halophilus DSM 22662513237186completeimg866895

GC content

@refGC-content
2298340-43
101140.8

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes83.316yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no91.644no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes76.718no
125438spore-formingspore-formingAbility to form endo- or exosporesyes95.074yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno92.488yes
125438motile2+flagellatedAbility to perform flagellated movementyes80.427no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes96.4
125439BacteriaNetmotilityAbility to perform movementyes91.4
125439BacteriaNetgram_stainReaction to gram-stainingvariable84.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe92.1

External links

@ref: 1011

culture collection no.: DSM 2266, ATCC 35676, NCIMB 2269, JCM 20832, CCM 3527, CECT 5013, IAM 12846, IAM 13060, KCTC 3685, LMG 17431, NBRC 102448

straininfo link

  • @ref: 70977
  • straininfo: 9982

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23194807Sporosarcina halophila sp. nov., an Obligate, Slightly Halophilic Bacterium from Salt Marsh Soils.Claus D, Fahmy F, Rolf HJ, Tosunoglu NSyst Appl Microbiol10.1016/S0723-2020(83)80007-11983
Phylogeny25795064Halobacillus andaensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soil.Wang K, Zhang L, Yang Y, Pan Y, Meng L, Liu H, Hong S, Huang H, Jiang JInt J Syst Evol Microbiol10.1099/ijs.0.0001982015Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Halobacillus/*classification/genetics/isolation & purification, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1011Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2266)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2266
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
22983S. SPRING,W. LUDWIG,M. C. MARQUEZ,A. VENTOSA,K.-H. SCHLEIFER10.1099/00207713-46-2-492Halobacillus gen. nov., with Descriptions of Halobacillus litoralis sp. nov. and Halobacillus trueperi sp. nov., and Transfer of Sporosarcina halophila to Halobacillus halophilus comb. nov.IJSEM 46: 492-496 1996
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/
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
70977Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9982.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1