Strain identifier
BacDive ID: 17798
Type strain:
Species: Caldisericum exile
Strain Designation: AZM16c01
Strain history: <- K. Mori, NBRC; AZM16c01 <- K. Mori {2007}
NCBI tax ID(s): 693075 (species)
General
@ref: 15992
BacDive-ID: 17798
DSM-Number: 21853
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative, motile
description: Caldisericum exile AZM16c01 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from hot spring.
NCBI tax id
- NCBI tax id: 693075
- Matching level: species
strain history
- @ref: 15992
- history: <- K. Mori, NBRC; AZM16c01 <- K. Mori {2007}
doi: 10.13145/bacdive17798.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/caldisericota
- domain: Bacteria
- phylum: Caldisericota
- class: Caldisericia
- order: Caldisericales
- family: Caldisericaceae
- genus: Caldisericum
- species: Caldisericum exile
- full scientific name: Caldisericum exile Mori et al. 2009
@ref: 15992
domain: Bacteria
phylum: Caldiserica
class: Caldisericia
order: Caldisericales
family: Caldisericaceae
genus: Caldisericum
species: Caldisericum exile
full scientific name: Caldisericum exile Mori et al. 2009
strain designation: AZM16c01
type strain: yes
Morphology
cell morphology
- @ref: 29275
- gram stain: negative
- cell length: 4.95 µm
- cell width: 0.3 µm
- motility: yes
Culture and growth conditions
culture medium
- @ref: 15992
- name: CALDISERICUM MEDIUM (DSMZ Medium 1211)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1211
- composition: Name: CALDISERICUM MEDIUM (DSMZ Medium 1211) Composition: Yeast extract 4.98504 g/l Na2S2O3 x 5 H2O 2.49252 g/l Na2S x 9 H2O 0.249252 g/l L-Cysteine HCl x H2O 0.249252 g/l NH4Cl 0.249252 g/l MgSO4 x 7 H2O 0.249252 g/l Na2CO3 0.249252 g/l KH2PO4 0.0897308 g/l K2HPO4 0.0498504 g/l Nitrilotriacetic acid 0.0127617 g/l FeCl2 x 4 H2O 0.000997009 g/l NaCl 0.000997009 g/l Sodium resazurin 0.000498504 g/l CaCl2 x 2 H2O 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 9.97009e-05 g/l NiCl2 x 6 H2O 9.97009e-05 g/l Na2WO4 x 2 H2O 3.98804e-05 g/l Na2SeO3 x 5 H2O 2.99103e-05 g/l CoCl2 x 6 H2O 2.99103e-05 g/l Na2MoO4 x 2 H2O 2.99103e-05 g/l CuCl2 1.99402e-05 g/l Pyridoxine hydrochloride 1.99402e-05 g/l p-Aminobenzoic acid 9.97009e-06 g/l Calcium D-(+)-pantothenate 9.97009e-06 g/l Nicotinic acid 9.97009e-06 g/l Riboflavin 9.97009e-06 g/l Thiamine HCl 9.97009e-06 g/l (DL)-alpha-Lipoic acid 9.97009e-06 g/l H3BO3 9.97009e-06 g/l Biotin 3.98804e-06 g/l Folic acid 3.98804e-06 g/l Vitamin B12 1.99402e-07 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15992 | positive | growth | 65 | thermophilic |
29275 | positive | growth | 55-70 | thermophilic |
29275 | positive | optimum | 65 | thermophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
29275 | positive | growth | 5.5-7.5 |
29275 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
15992 | anaerobe |
29275 | anaerobe |
spore formation
- @ref: 29275
- spore formation: no
halophily
- @ref: 29275
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <1 %
Isolation, sampling and environmental information
isolation
- @ref: 15992
- sample type: hot spring
- geographic location: Nagano
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Thermal spring |
#Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_3466.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_407;96_1810;97_2169;98_2661;99_3466&stattab=map
- Last taxonomy: Caldisericum exile subclade
- 16S sequence: JQ346734
- Sequence Identity:
- Total samples: 457
- soil counts: 11
- aquatic counts: 367
- animal counts: 74
- plant counts: 5
Safety information
risk assessment
- @ref: 15992
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Caldisericum exile strain AZM16c01 16S ribosomal RNA gene, partial sequence | JQ346734 | 1426 | ena | 693075 |
15992 | Caldisericum exile AZM16c01 gene for 16S rRNA, partial sequence | AB428365 | 1481 | ena | 511051 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Caldisericum exile AZM16c01 | GCA_000284335 | complete | ncbi | 511051 |
66792 | Caldisericum exile AZM16c01 | 511051.3 | complete | patric | 511051 |
66792 | Caldisericum exile AZM16c01, NBRC 104410 | 2513237181 | complete | img | 511051 |
GC content
@ref | GC-content | method |
---|---|---|
15992 | 34.6 | high performance liquid chromatography (HPLC) |
29275 | 34.6 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 84.082 | yes |
flagellated | no | 98.784 | no |
gram-positive | no | 91.702 | yes |
anaerobic | yes | 99.195 | yes |
aerobic | no | 98.753 | no |
halophile | no | 86.714 | yes |
spore-forming | no | 96.3 | yes |
glucose-util | yes | 79.177 | no |
thermophile | yes | 99.598 | no |
glucose-ferment | no | 60.7 | no |
External links
@ref: 15992
culture collection no.: DSM 21853, NBRC 104410
straininfo link
- @ref: 86790
- straininfo: 407941
literature
- topic: Phylogeny
- Pubmed-ID: 19628600
- title: Caldisericum exile gen. nov., sp. nov., an anaerobic, thermophilic, filamentous bacterium of a novel bacterial phylum, Caldiserica phyl. nov., originally called the candidate phylum OP5, and description of Caldisericaceae fam. nov., Caldisericales ord. nov. and Caldisericia classis nov.
- authors: Mori K, Yamaguchi K, Sakiyama Y, Urabe T, Suzuki K
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.010033-0
- year: 2009
- mesh: Anaerobiosis, Bacteria/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Hot Springs/*microbiology, Hot Temperature, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics
- topic2: Metabolism
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
15992 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21853) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21853 | ||||
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 | ||
29275 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 25692 | ||
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) | ||||
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 | ||||
86790 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407941.1 | StrainInfo: A central database for resolving microbial strain identifiers |