Strain identifier

BacDive ID: 131

Type strain: Yes

Species: Acidobacterium capsulatum

Strain Designation: 161

Strain history: N. Kishimoto 161.

NCBI tax ID(s): 240015 (strain), 33075 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 4255

BacDive-ID: 131

DSM-Number: 11244

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, rod-shaped, pigmented

description: Acidobacterium capsulatum 161 is a mesophilic, rod-shaped bacterium that has a orange pigmentation and was isolated from acidic mineral environment.

NCBI tax id

NCBI tax idMatching level
240015strain
33075species

strain history

@refhistory
4255<- JCM <- N. Kishimoto, strain 161
67770N. Kishimoto 161.

doi: 10.13145/bacdive131.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/acidobacteriota
  • domain: Bacteria
  • phylum: Acidobacteriota
  • class: Terriglobia
  • order: Terriglobales
  • family: Acidobacteriaceae
  • genus: Acidobacterium
  • species: Acidobacterium capsulatum
  • full scientific name: Acidobacterium capsulatum Kishimoto et al. 1991

@ref: 4255

domain: Bacteria

phylum: Acidobacteria

class: Acidobacteriia

order: Acidobacteriales

family: Acidobacteriaceae

genus: Acidobacterium

species: Acidobacterium capsulatum

full scientific name: Acidobacterium capsulatum Kishimoto et al. 1991 emend. Pankratov et al. 2012

strain designation: 161

type strain: yes

Morphology

cell morphology

@refcell lengthcell shapegram stainconfidence
228871.1-2.3 µmrod-shaped
69480negative99.971

colony morphology

  • @ref: 4255
  • incubation period: 3-7 days

pigmentation

  • @ref: 22887
  • production: yes
  • name: orange

Culture and growth conditions

culture medium

  • @ref: 4255
  • name: ACIDIPHILIUM MEDIUM (DSMZ Medium 269)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/269
  • composition: Name: ACIDIPHILIUM MEDIUM (DSMZ Medium 269; with strain-specific modifications) Composition: (NH4)2SO4 2.0 g/l D-Glucose 1.0 g/l MgSO4 x 7 H2O 0.5 g/l K2HPO4 0.5 g/l Yeast extract 0.1 g/l KCl 0.1 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
4255positivegrowth30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
22887positivemaximum6
22887positiveminimum3acidophile

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no93
69480no99.986

observation

  • @ref: 67770
  • observation: quinones: MK-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
4255catalase-1.11.1.6
4255cytochrome-c oxidase-1.9.3.1
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
68382beta-glucuronidase+3.2.1.31
68382beta-galactosidase+3.2.1.23
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-
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382alkaline phosphatase-3.1.3.1
68369cytochrome oxidase-1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
4255--+/---+/-----+++/-+++/-++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4255-----+-+/--------------
4255-----+-+------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
4255acidic mineral environmentJapanJPNAsia
67770Mine at Okayama Pref.JapanJPNAsia

isolation source categories

Cat1Cat2
#Environmental
#Condition#Acidic

taxonmaps

  • @ref: 69479
  • File name: preview.99_5007.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_236;96_2449;97_2988;98_3743;99_5007&stattab=map
  • Last taxonomy: Acidobacterium capsulatum subclade
  • 16S sequence: NR_074106
  • Sequence Identity:
  • Total samples: 14423
  • soil counts: 2976
  • aquatic counts: 835
  • animal counts: 10178
  • plant counts: 434

Safety information

risk assessment

  • @ref: 4255
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Acidobacterium capsulatum gene for 16S rRNA, partial sequenceD261711422ena33075
67770Acidobacterium capsulatum ATCC 51196 16S ribosomal RNA, partial sequenceNR_0433861424nuccore240015
67770Acidobacterium capsulatum ATCC 51196 16S ribosomal RNA, partial sequenceNR_0741061493nuccore240015

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acidobacterium capsulatum ATCC 51196GCA_000022565completencbi240015
66792Acidobacterium capsulatum ATCC 51196240015.3completepatric240015
66792Acidobacterium capsulatum ATCC 51196643692001completeimg240015

GC content

@refGC-content
2288759.9-60.8
425560

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno93no
motileno62.044no
flagellatedno91.157no
gram-positiveno97.756no
anaerobicno97.612no
aerobicyes79.585no
halophileno91.979no
spore-formingno92.968no
glucose-utilyes72.368no
thermophileno89.588yes
glucose-fermentno90.499yes

External links

@ref: 4255

culture collection no.: DSM 11244, ATCC 51196, JCM 7670, NCIMB 13165, BCRC 80197, IFO 15755, NBRC 15755

straininfo link

  • @ref: 69814
  • straininfo: 42853

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism22486608Comparative genomic and physiological analysis provides insights into the role of Acidobacteria in organic carbon utilization in Arctic tundra soils.Rawat SR, Mannisto MK, Bromberg Y, Haggblom MMFEMS Microbiol Ecol10.1111/j.1574-6941.2012.01381.x2012Acidobacteria/genetics/*metabolism/physiology, Arctic Regions, Carbohydrate Metabolism, Carbon/*metabolism, Comparative Genomic Hybridization, DNA, Bacterial/genetics, Ecosystem, Genome Size, *Genome, Bacterial, Phylogeny, Plasmids/genetics, Polysaccharides, Bacterial/metabolism, RNA, Ribosomal, 16S/genetics, Soil/*chemistry, *Soil MicrobiologyGenetics
25210600Discovery of a novel (R)-selective bacterial hydroxynitrile lyase from Acidobacterium capsulatum.Wiedner R, Gruber-Khadjawi M, Schwab H, Steiner KComput Struct Biotechnol J10.1016/j.csbj.2014.07.0022014
Phylogeny26774420Silvibacterium bohemicum gen. nov. sp. nov., an acidobacterium isolated from coniferous soil in the Bohemian Forest National Park.Llado S, Benada O, Cajthaml T, Baldrian P, Garcia-Fraile PSyst Appl Microbiol10.1016/j.syapm.2015.12.0052015Acidobacteria/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition/genetics, Base Sequence, Carbohydrate Metabolism/genetics, Czech Republic, DNA, Bacterial/genetics, Fatty Acids/analysis, Forests, Genome, Bacterial/genetics, Parks, Recreational, Phylogeny, Polysaccharides/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, TracheophytaMetabolism
Phylogeny27692038Isolation and characterization of Acidobacterium ailaaui sp. nov., a novel member of Acidobacteria subdivision 1, from a geothermally heated Hawaiian microbial mat.Myers MR, King GMInt J Syst Evol Microbiol10.1099/ijsem.0.0015162016Acidobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hawaii, Hot Temperature, *Microbial Consortia, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAStress
Phylogeny35679110Paracidobacterium acidisoli gen. nov., sp. nov. and Alloacidobacterium dinghuense gen. nov., sp. nov., two acidobacteria isolated from forest soil, and reclassification of Acidobacterium ailaaui and Acidipila dinghuensis as Pseudacidobacterium ailaaui gen. nov., comb. nov. and Silvibacterium dinghuense comb. nov.Zhang QM, Fu JC, Chen ZQ, Qiu LHInt J Syst Evol Microbiol10.1099/ijsem.0.0054152022*Acidobacteria, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Glycolipids, *Phosphatidylethanolamines, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4255Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11244)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11244
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
22887Timofey A. Pankratov, Lilia A. Kirsanova, Elena N. Kaparullina, Vadim V. Kevbrin, Svetlana N. Dedysh10.1099/ijs.0.029629-0Telmatobacter bradus gen. nov., sp. nov., a cellulolytic facultative anaerobe from subdivision 1 of the Acidobacteria, and emended description of Acidobacterium capsulatum Kishimoto et al. 1991IJSEM 62: 430-437 201221460138
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/
68369Automatically annotated from API 20NE
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
69814Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42853.1StrainInfo: A central database for resolving microbial strain identifiers