Strain identifier

BacDive ID: 1252

Type strain: Yes

Species: Halalkalibacter krulwichiae

Strain Designation: AM31D

Strain history: CIP <- 2003, JCM <- 2002, I. Yumoto: strain AM31D

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General

@ref: 7441

BacDive-ID: 1252

DSM-Number: 18225

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, motile

description: Halalkalibacter krulwichiae AM31D is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1220588strain
199441species

strain history

@refhistory
7441<- NCIMB
67770I. Yumoto AM31D.
120507CIP <- 2003, JCM <- 2002, I. Yumoto: strain AM31D

doi: 10.13145/bacdive1252.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Halalkalibacter
  • species: Halalkalibacter krulwichiae
  • full scientific name: Halalkalibacter krulwichiae (Yumoto et al. 2003) Joshi et al. 2022
  • synonyms

    @refsynonym
    20215Alkalihalobacillus krulwichiae
    20215Bacillus krulwichiae

@ref: 7441

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Bacillaceae

genus: Halalkalibacter

species: Halalkalibacter krulwichiae

full scientific name: Halalkalibacter krulwichiae (Yumoto et al. 2003) Joshi et al. 2022

strain designation: AM31D

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes92.817
69480100positive
120507yespositiverod-shaped

colony morphology

  • @ref: 120507

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7441ALKALINE NUTRIENT AGAR (DSMZ Medium 31)yeshttps://mediadive.dsmz.de/medium/31Name: ALKALINE NUTRIENT AGAR (DSMZ Medium 31) Composition: Agar 15.0 g/l Na2CO3 anhydrous 5.3 g/l Peptone 5.0 g/l NaHCO3 4.2 g/l Meat extract 3.0 g/l Distilled water
32895MEDIUM 291 - for Bacillus hortiyesDistilled water make up to (900.000 ml);Magnesium sulphate heptahydrate (0.200 g);Agar (15.000 g);Glucose (10.000 g);Yeast extract (5.000 g);Potassium di-hydrogen phosphate (1.000 g);Polypeptone (5.000 g);Sodium carbonate solution - M00442 (100.000 ml)
120507CIP Medium 291yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=291

culture temp

@refgrowthtypetemperaturerange
7441positivegrowth30mesophilic
32895positivegrowth30mesophilic
67770positivegrowth27mesophilic
120507positivegrowth22-45
120507nogrowth10psychrophilic
120507nogrowth55thermophilic

culture pH

  • @ref: 120507
  • ability: no
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 120507
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
120507NaClnogrowth0 %
120507NaClnogrowth2 %
120507NaClnogrowth4 %
120507NaClnogrowth6 %
120507NaClnogrowth8 %
120507NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-7, MK-6, MK-5

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12050716947citrate-carbon source
1205074853esculin-hydrolysis
120507606565hippurate-hydrolysis
12050717632nitrate+reduction
12050716301nitrite-reduction
12050717632nitrate-respiration

metabolite production

  • @ref: 120507
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12050715688acetoin-
12050717234glucose-

enzymes

@refvalueactivityec
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
120507oxidase-
120507beta-galactosidase-3.2.1.23
120507alcohol dehydrogenase-1.1.1.1
120507gelatinase-
120507amylase-
120507DNase-
120507caseinase-3.4.21.50
120507catalase+1.11.1.6
120507tween esterase-
120507gamma-glutamyltransferase+2.3.2.2
120507lecithinase-
120507lipase-
120507lysine decarboxylase-4.1.1.18
120507ornithine decarboxylase-4.1.1.17
120507urease-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
120507--+-----------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7441soilIbaraki, TsukubaJapanJPNAsia
67770Soil sample obtained from TsukubaIbaraki Pref.JapanJPNAsia
120507Environment, SoilTsukuba, IbarakiJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1542.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_880;97_1028;98_1217;99_1542&stattab=map
  • Last taxonomy: Alkalihalobacillus krulwichiae
  • 16S sequence: AB681754
  • Sequence Identity:
  • Total samples: 97
  • soil counts: 34
  • aquatic counts: 14
  • animal counts: 40
  • plant counts: 9

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
74411Risk group (German classification)
1205071Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7441Bacillus krulwichiae gene for 16S rRNA, partial sequenceAB0868971507ena199441
67770Bacillus krulwichiae gene for 16S rRNA, partial sequence, strain: NBRC 102362AB6817541412ena199441

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halalkalibacter krulwichiae AM31DGCA_002109385completencbi199441
66792Bacillus krulwichiae NBRC 1023621220588.3wgspatric1220588
66792Bacillus krulwichiae NBRC 1023622731957674draftimg1220588
66792Bacillus krulwichiae NBRC 1023622773857802completeimg1220588
67770Halalkalibacter krulwichiae NBRC 102362GCA_001591945contigncbi1220588

GC content

@refGC-contentmethod
744141.5
6777041.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: yes
  • confidence: 100
  • training_data: no

External links

@ref: 7441

culture collection no.: DSM 18225, IAM 15000, JCM 11691, NCIMB 13904, CIP 108137, NBRC 102362

straininfo link

  • @ref: 70908
  • straininfo: 127980

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny13130043Bacillus krulwichiae sp. nov., a halotolerant obligate alkaliphile that utilizes benzoate and m-hydroxybenzoate.Yumoto I, Yamaga S, Sogabe Y, Nodasaka Y, Matsuyama H, Nakajima K, Suemori AInt J Syst Evol Microbiol10.1099/ijs.0.02596-02003Bacillus/*classification/genetics/isolation & purification/*metabolism, Benzoates/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Hydroxybenzoates/metabolism, Japan, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sodium Chloride, Soil Microbiology, Vitamin K 2/analysisMetabolism
Phylogeny20833886Bacillus alkalisediminis sp. nov., an alkaliphilic and moderately halophilic bacterium isolated from sediment of extremely shallow soda ponds.Borsodi AK, Pollak B, Keki Z, Rusznyak A, Kovacs AL, Sproer C, Schumann P, Marialigeti K, Toth EMInt J Syst Evol Microbiol10.1099/ijs.0.019489-02010Alkalies/*metabolism, Bacillus/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/*metabolism, *Water MicrobiologyMetabolism
Metabolism31126948A Pathway for Isethionate Dissimilation in Bacillus krulwichiae.Tong Y, Wei Y, Hu Y, Ang EL, Zhao H, Zhang YAppl Environ Microbiol10.1128/AEM.00793-192019Acetaldehyde/*analogs & derivatives/metabolism, Acetyltransferases/*genetics, Bacillus/*metabolism, Bacterial Proteins/*genetics, Isethionic Acid/*metabolism, Multigene Family
Enzymology34021568Molecular and biochemical characteristics of inulosucrase InuBK from Alkalihalobacillus krulwichiae JCM 11691.Yokoi KJ, Tsutsui S, Arakawa GY, Takaba M, Fujii K, Kaneko SBiosci Biotechnol Biochem10.1093/bbb/zbab0942021Bacillaceae/*enzymology/genetics, Chromatography, High Pressure Liquid/methods, Cloning, Molecular, Culture Media, Genes, Bacterial, Hexosyltransferases/genetics/isolation & purification/*metabolism, Inulin/biosynthesis, Magnetic Resonance Spectroscopy/methods, Molecular Weight, Phylogeny, TemperaturePhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7441Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18225)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18225
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
32895Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5726
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/
68382Automatically annotated from API zym
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)
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
70908Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID127980.1StrainInfo: A central database for resolving microbial strain identifiers
120507Curators of the CIPCollection of Institut Pasteur (CIP 108137)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108137