Strain identifier

BacDive ID: 1349

Type strain: Yes

Species: Halobacillus kuroshimensis

Strain Designation: JS-Hb7, IS-Hb7

Strain history: CIP <- 2007, JCM <- T. Naganuma, Hiroshima Univ., Hiroshima, Japan: strain IS-Hb7

NCBI tax ID(s): 1121938 (strain), 302481 (species)

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General

@ref: 7522

BacDive-ID: 1349

DSM-Number: 18393

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

description: Halobacillus kuroshimensis JS-Hb7 is a spore-forming, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from carbonate rock collected from a 642 m-deep methane cold seep.

NCBI tax id

NCBI tax idMatching level
1121938strain
302481species

strain history

@refhistory
7522<- Takeshi Naganuma <- Ngoc-Phuc Hua, IS-Hb7
67770T. Naganuma IS-Hb7.
120515CIP <- 2007, JCM <- T. Naganuma, Hiroshima Univ., Hiroshima, Japan: strain IS-Hb7

doi: 10.13145/bacdive1349.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Halobacillus
  • species: Halobacillus kuroshimensis
  • full scientific name: Halobacillus kuroshimensis Hua et al. 2007

@ref: 7522

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Halobacillus

species: Halobacillus kuroshimensis

full scientific name: Halobacillus kuroshimensis Hua et al. 2007

strain designation: JS-Hb7, IS-Hb7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
22985positive1.6-3.3 µm0.5-1.0 µmrod-shapedno
120515positiveovoid-shapedno

colony morphology

  • @ref: 22985
  • colony size: 1.5-2.5 mm
  • colony color: yellow-orange
  • colony shape: circular
  • incubation period: 3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7522BACTO 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
37807Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120515CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
7522positivegrowth30
22985positivegrowth9.0-48.0
22985positiveoptimum25.0
37807positivegrowth30
67770positivegrowth30

culture pH

@refabilitytypepHPH range
22985positivegrowth5.5-10.0alkaliphile
22985positiveoptimum7.5-8.0

Physiology and metabolism

spore formation

@refspore descriptiontype of sporespore formationconfidence
22985spherical or ellipsoidal, terminal positionendosporeyes
120515no
69480yes93.448
69481yes100

halophily

@refsaltgrowthtested relationconcentration
22985NaClpositivegrowth0.5-25.0 %(w/v)
22985NaCloptimum6.0 %

murein

  • @ref: 7522
  • murein short key: A21.04
  • type: A4ß L-Orn-D-Asp

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2298512936D-galactose-builds acid from
2298516899D-mannitol-builds acid from
2298516443D-tagatose-builds acid from
2298516551D-trehalose-builds acid from
2298565327D-xylose-builds acid from
2298528053melibiose-builds acid from
2298517814salicin-builds acid from
2298540585alpha-cyclodextrin-hydrolysis
2298523652dextrin-hydrolysis
2298528087glycogen-hydrolysis
2298517632nitrate-reduction
2298517057cellobiose+builds acid from
2298515824D-fructose+builds acid from
2298517634D-glucose+builds acid from
2298517754glycerol+builds acid from
2298517268myo-inositol+builds acid from
2298517306maltose+builds acid from
2298537684mannose+builds acid from
22985506227N-acetylglucosamine+builds acid from
2298517992sucrose+builds acid from
2298517925alpha-D-glucose+carbon source
2298516024D-mannose+carbon source
2298565327D-xylose+carbon source
2298517306maltose+carbon source
2298517268myo-inositol+carbon source
2298553423tween 40+carbon source
2298553426tween 80+carbon source
22985casein+hydrolysis
229854853esculin+hydrolysis
229855291gelatin+hydrolysis
2298528017starch+hydrolysis
2298553424tween 20+hydrolysis
2298553423tween 40+hydrolysis
2298553426tween 80+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
12051517632nitrate-reduction
12051516301nitrite-reduction

metabolite production

  • @ref: 120515
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
22985catalase+1.11.1.6
22985cytochrome oxidase+1.9.3.1
22985phenylalanine deaminase-4.3.1.5
22985urease-3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
120515oxidase+
120515catalase+1.11.1.6
120515urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120515-+++------++-+------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120515+---+----++++-+/---+---+----++--++--+++--+----+/-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment culture
22985carbonate rock collected from a 642 m-deep methane cold seepKuroshima KnollJapanJPNAsia24.13124.187enrichment medium containing 0.5 % (w/v) Bacto-peptone (Difco),0.25 % yeast extract (Difco),0.1 % D-glucose (Wako) and 15 % NaCl
7522deep-sea carbonate rockKuroshima KnollJapanJPNAsia
67770Deep-sea carbonate rock at a methane cold seep in Kuroshima KnollJapanJPNAsia
120515Environment, Deep sea carbonate rockCarbonate rocks authentically formed in a methane seep of the Kuroshima Knoll, located at 642 m depth (Fujikuraet al., 2003, Inagakiet al., 2004), were collected with the remotely operated vehicle Dolphin 3K, operated by the Japan Agency for Marine Earth Science and Technology (JAMSTEC).JapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Environmental#Terrestrial#Geologic
#Condition#Psychrophilic (<10°C)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
75221Risk group (German classification)
1205151Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7522
  • description: Halobacillus kuroshimensis gene for 16S rRNA, partial sequence
  • accession: AB195680
  • length: 1544
  • database: nuccore
  • NCBI tax ID: 302481

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halobacillus kuroshimensis DSM 183931121938.3wgspatric1121938
66792Halobacillus kuroshimensis DSM 183932523533634draftimg1121938
67770Halobacillus kuroshimensis DSM 18393 DSM 18393GCA_000425705scaffoldncbi1121938

GC content

@refGC-contentmethod
752242.1
6777042.1capillary zone electrophoresis (CZE)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes81.931no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.86no
69480spore-formingspore-formingAbility to form endo- or exosporesyes93.448no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes76.568no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.268yes
69480flagellatedmotile2+Ability to perform flagellated movementyes84.704no

External links

@ref: 7522

culture collection no.: DSM 18393, JCM 14155, CIP 109650

straininfo link

  • @ref: 70999
  • straininfo: 309457

literature

  • topic: Phylogeny
  • Pubmed-ID: 17551037
  • title: Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov., moderately halophilic bacteria isolated from a deep-sea methane cold seep.
  • authors: Hua NP, Kanekiyo A, Fujikura K, Yasuda H, Naganuma T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64817-0
  • year: 2007
  • mesh: Bacillaceae/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cold Temperature, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hydrostatic Pressure, Japan, Locomotion, Microscopy, Phase-Contrast, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Spores, Bacterial
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7522Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18393)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18393
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
22985Ngoc-Phuc Hua,Atsuko Kanekiyo,Katsunori Fujikura,Hisato Yasuda,Takeshi Naganuma10.1099/ijs.0.64817-0Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov., moderately halophilic bacteria isolated from a deep-sea methane cold seepIJSEM 57: 1243-1249 200717551037
37807Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7417
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/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
70999Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309457.1StrainInfo: A central database for resolving microbial strain identifiers
120515Curators of the CIPCollection of Institut Pasteur (CIP 109650)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109650