Strain identifier
BacDive ID: 131
Type strain:
Species: Acidobacterium capsulatum
Strain Designation: 161
Strain history: N. Kishimoto 161.
NCBI tax ID(s): 240015 (strain), 33075 (species)
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 id | Matching level |
---|---|
240015 | strain |
33075 | species |
strain history
@ref | history |
---|---|
4255 | <- JCM <- N. Kishimoto, strain 161 |
67770 | N. 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
@ref | cell length | cell shape | gram stain | confidence |
---|---|---|---|---|
22887 | 1.1-2.3 µm | rod-shaped | ||
69480 | negative | 99.971 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
4255 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
22887 | positive | maximum | 6 | |
22887 | positive | minimum | 3 | acidophile |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 93 |
69480 | no | 99.986 |
observation
- @ref: 67770
- observation: quinones: MK-8
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | - | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | - | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
4255 | catalase | - | 1.11.1.6 |
4255 | cytochrome-c oxidase | - | 1.9.3.1 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | beta-glucuronidase | + | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68369 | cytochrome oxidase | - | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
4255 | - | - | +/- | - | - | +/- | - | - | - | - | + | + | +/- | + | + | +/- | + | + | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
4255 | - | - | - | - | - | + | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - |
4255 | - | - | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
4255 | acidic mineral environment | Japan | JPN | Asia |
67770 | Mine at Okayama Pref. | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 |
---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Acidobacterium capsulatum gene for 16S rRNA, partial sequence | D26171 | 1422 | ena | 33075 |
67770 | Acidobacterium capsulatum ATCC 51196 16S ribosomal RNA, partial sequence | NR_043386 | 1424 | nuccore | 240015 |
67770 | Acidobacterium capsulatum ATCC 51196 16S ribosomal RNA, partial sequence | NR_074106 | 1493 | nuccore | 240015 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Acidobacterium capsulatum ATCC 51196 | GCA_000022565 | complete | ncbi | 240015 |
66792 | Acidobacterium capsulatum ATCC 51196 | 240015.3 | complete | patric | 240015 |
66792 | Acidobacterium capsulatum ATCC 51196 | 643692001 | complete | img | 240015 |
GC content
@ref | GC-content |
---|---|
22887 | 59.9-60.8 |
4255 | 60 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 93 | no |
motile | no | 62.044 | no |
flagellated | no | 91.157 | no |
gram-positive | no | 97.756 | no |
anaerobic | no | 97.612 | no |
aerobic | yes | 79.585 | no |
halophile | no | 91.979 | no |
spore-forming | no | 92.968 | no |
glucose-util | yes | 72.368 | no |
thermophile | no | 89.588 | yes |
glucose-ferment | no | 90.499 | yes |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Metabolism | 22486608 | Comparative 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 MM | FEMS Microbiol Ecol | 10.1111/j.1574-6941.2012.01381.x | 2012 | Acidobacteria/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 Microbiology | Genetics |
25210600 | Discovery of a novel (R)-selective bacterial hydroxynitrile lyase from Acidobacterium capsulatum. | Wiedner R, Gruber-Khadjawi M, Schwab H, Steiner K | Comput Struct Biotechnol J | 10.1016/j.csbj.2014.07.002 | 2014 | |||
Phylogeny | 26774420 | Silvibacterium 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 P | Syst Appl Microbiol | 10.1016/j.syapm.2015.12.005 | 2015 | Acidobacteria/*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, Tracheophyta | Metabolism |
Phylogeny | 27692038 | Isolation and characterization of Acidobacterium ailaaui sp. nov., a novel member of Acidobacteria subdivision 1, from a geothermally heated Hawaiian microbial mat. | Myers MR, King GM | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001516 | 2016 | Acidobacteria/*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, DNA | Stress |
Phylogeny | 35679110 | Paracidobacterium 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 LH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005415 | 2022 | *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 Microbiology | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4255 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11244) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11244 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
22887 | Timofey A. Pankratov, Lilia A. Kirsanova, Elena N. Kaparullina, Vadim V. Kevbrin, Svetlana N. Dedysh | 10.1099/ijs.0.029629-0 | Telmatobacter bradus gen. nov., sp. nov., a cellulolytic facultative anaerobe from subdivision 1 of the Acidobacteria, and emended description of Acidobacterium capsulatum Kishimoto et al. 1991 | IJSEM 62: 430-437 2012 | 21460138 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
69814 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42853.1 | StrainInfo: A central database for resolving microbial strain identifiers |