Strain identifier

BacDive ID: 424

Type strain: Yes

Species: Alicyclobacillus pomorum

Strain Designation: 3A, 3AT

Strain history: CIP <- 2003, K. Goto, Shizuoka, Japan: strain3AT

NCBI tax ID(s): 1111479 (strain), 204470 (species)

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General

@ref: 5618

BacDive-ID: 424

DSM-Number: 14955

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, thermophilic, Gram-positive, rod-shaped

description: Alicyclobacillus pomorum 3A is an obligate aerobe, thermophilic, Gram-positive bacterium that was isolated from mixed fruit juice.

NCBI tax id

NCBI tax idMatching level
204470species
1111479strain

strain history

@refhistory
5618<- K. Goto; 3A
397752003, K. Goto, Shizuoka, Japan: strain3AT
67770IAM 14988 <-- K. Goto 3A.
121937CIP <- 2003, K. Goto, Shizuoka, Japan: strain3AT

doi: 10.13145/bacdive424.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Alicyclobacillaceae
  • genus: Alicyclobacillus
  • species: Alicyclobacillus pomorum
  • full scientific name: Alicyclobacillus pomorum Goto et al. 2003

@ref: 5618

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Alicyclobacillaceae

genus: Alicyclobacillus

species: Alicyclobacillus pomorum

full scientific name: Alicyclobacillus pomorum Goto et al. 2003

strain designation: 3A, 3AT

type strain: yes

Morphology

cell morphology

  • @ref: 121937
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 121937

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5618ALICYCLOBACILLUS MEDIUM (DSMZ Medium 402)yeshttps://mediadive.dsmz.de/medium/402Name: ALICYCLOBACILLUS MEDIUM (DSMZ Medium 402) Composition: Agar 15.0 g/l Glucose 5.0 g/l KH2PO4 3.0 g/l Yeast extract 2.0 g/l MgSO4 x 7 H2O 0.5 g/l CaCl2 x 2 H2O 0.25 g/l (NH4)2SO4 0.2 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
39775MEDIUM 313 - for Alicyclobacillus acidoterrestrisyesDistilled water make up to (500.000 ml);Magnesium sulphate heptahydrate (0.180 g);Calcium chloride dihydrate (0.660 g);Glucose (5.000 g);Yeast extract (1.000 g);Ammonium sulphate (0.200 g);Potassium di-hydrogen phosphate (3.000 g);Agar solution - M0614(50
121937CIP Medium 313yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=313
121937CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5618positivegrowth45thermophilic
39775positivegrowth45thermophilic
67770positivegrowth45thermophilic
121937positivegrowth37-55
121937nogrowth10psychrophilic
121937nogrowth22psychrophilic
121937nogrowth30mesophilic

culture pH

  • @ref: 121937
  • ability: no
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 121937
  • oxygen tolerance: obligate aerobe

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12193716947citrate-carbon source
1219374853esculin-hydrolysis
121937606565hippurate+hydrolysis
12193717632nitrate-reduction
12193716301nitrite-reduction
12193717632nitrate-respiration

metabolite production

  • @ref: 121937
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12193715688acetoin-
12193717234glucose-

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
121937oxidase+
121937beta-galactosidase+3.2.1.23
121937alcohol dehydrogenase-1.1.1.1
121937gelatinase+
121937catalase-1.11.1.6
121937gamma-glutamyltransferase+2.3.2.2
121937lysine decarboxylase-4.1.1.18
121937ornithine decarboxylase-4.1.1.17
121937urease-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
121937-+++------++---++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5618mixed fruit juicefruit juice imported into Japan from USAUSAUSANorth America
67770Spoiled mixed fruit juice
121937Fruit juiceUnited States of AmericaUSANorth America2000

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Beverage
#Host Body-Site#Plant#Fruit (Seed)

taxonmaps

  • @ref: 69479
  • File name: preview.99_24084.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_313;96_11483;97_14664;98_18131;99_24084&stattab=map
  • Last taxonomy: Alicyclobacillus pomorum subclade
  • 16S sequence: AB681267
  • Sequence Identity:
  • Total samples: 11299
  • soil counts: 7189
  • aquatic counts: 2531
  • animal counts: 755
  • plant counts: 824

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
56181Risk group (German classification)
1219371Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Alicyclobacillus pomorum gene for 16S rRNAAB0898401528ena1111479
20218Alicyclobacillus pomorum gene for 16S rRNA, partial sequence, strain: NBRC 100861AB6812671470ena1111479

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Alicyclobacillus pomorum DSM 149551111479.4wgspatric1111479
66792Alicyclobacillus pomorum DSM 149552513237116draftimg1111479
67770Alicyclobacillus pomorum DSM 14955GCA_000472905scaffoldncbi1111479

GC content

  • @ref: 67770
  • GC-content: 53.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno71.218no
flagellatedno93.899no
gram-positiveyes90.918no
anaerobicno98.532no
aerobicyes90.179no
halophileno88.003no
spore-formingyes91.641no
glucose-utilyes91.499no
thermophileyes99.427yes
glucose-fermentno88.465no

External links

@ref: 5618

culture collection no.: DSM 14955, IAM 14988, JCM 21459, CIP 108162, NBRC 100861

straininfo link

  • @ref: 70104
  • straininfo: 126421

literature

  • topic: Phylogeny
  • Pubmed-ID: 13130044
  • title: Alicyclobacillus pomorum sp. nov., a novel thermo-acidophilic, endospore-forming bacterium that does not possess omega-alicyclic fatty acids, and emended description of the genus Alicyclobacillus.
  • authors: Goto K, Mochida K, Asahara M, Suzuki M, Kasai H, Yokota A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02546-0
  • year: 2003
  • mesh: Base Composition, Base Sequence, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Fruit/microbiology, Gram-Positive Endospore-Forming Rods/*classification/genetics/isolation & purification/*metabolism, Hot Temperature, Hydrogen-Ion Concentration, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics
  • topic2: Stress

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5618Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14955)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14955
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
39775Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5754
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/
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
70104Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID126421.1StrainInfo: A central database for resolving microbial strain identifiers
121937Curators of the CIPCollection of Institut Pasteur (CIP 108162)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108162