Strain identifier
BacDive ID: 17632
Type strain: 
Species: Caldilinea aerophila
Strain Designation: STL-6-01
Strain history: Y. Sekiguchi STL-6-O1.
NCBI tax ID(s): 926550 (strain), 133453 (species)
version 9.3 (current version)
General
@ref: 5287
BacDive-ID: 17632
DSM-Number: 14535
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic
description: Caldilinea aerophila STL-6-01 is an anaerobe, thermophilic bacterium that was isolated from sulfur-turf sample in a hot spring.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 133453 | species |
| 926550 | strain |
strain history
| @ref | history |
|---|---|
| 5287 | <- Y. Sekiguchi, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan; STL-6-01 <- A. Sukegawa and Y. Kamagata; {2000} |
| 67770 | Y. Sekiguchi STL-6-O1. |
doi: 10.13145/bacdive17632.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/chloroflexota
- domain: Bacteria
- phylum: Chloroflexota
- class: Caldilineae
- order: Caldilineales
- family: Caldilineaceae
- genus: Caldilinea
- species: Caldilinea aerophila
- full scientific name: Caldilinea aerophila Sekiguchi et al. 2003
@ref: 5287
domain: Bacteria
phylum: Chloroflexi
class: Caldilineae
order: Caldilineales
family: Caldilineaceae
genus: Caldilinea
species: Caldilinea aerophila
full scientific name: Caldilinea aerophila Sekiguchi et al. 2003 emend. Nouioui et al. 2018
strain designation: STL-6-01
type strain: yes
Morphology
cell morphology
- @ref: 125439
- gram stain: negative
- confidence: 96.4
colony morphology
- @ref: 5287
- incubation period: 3-7 days
multimedia
- @ref: 66793
- multimedia content: EM_DSM_14535_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 5287
- name: ANAEROLINEA MEDIUM (DSMZ Medium 1004)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1004
- composition: Name: ANAEROLINEA MEDIUM (DSMZ Medium 1004) Composition: NaHCO3 2.49252 g/l Yeast extract 2.29312 g/l D-Glucose 2.19342 g/l NH4Cl 0.538385 g/l Na2S x 9 H2O 0.249252 g/l L-Cysteine HCl x H2O 0.249252 g/l MgCl2 x 6 H2O 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l KH2PO4 0.139581 g/l Na2-EDTA x 2 H2O 0.00518445 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 5287 | positive | growth | 55 |
| 67770 | positive | growth | 55 |
Physiology and metabolism
oxygen tolerance
- @ref: 5287
- oxygen tolerance: anaerobe
spore formation
- @ref: 125439
- spore formation: no
- confidence: 96.2
observation
- @ref: 67770
- observation: quinones: MK-10
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 5287 | sulfur-turf sample in a hot spring | Gifu prefecture, Nakao hot spring | Japan | JPN | Asia |
| 67770 | Hot spring sulfur-turf | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_7178.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_628;96_3360;97_4124;98_5277;99_7178&stattab=map
- Last taxonomy: Caldilinea aerophila subclade
- 16S sequence: AB067647
- Sequence Identity:
- Total samples: 1069
- soil counts: 195
- aquatic counts: 620
- animal counts: 234
- plant counts: 20
Safety information
risk assessment
- @ref: 5287
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5287
- description: Caldilinea aerophila gene for 16S rRNA, partial sequence
- accession: AB067647
- length: 1427
- database: nuccore
- NCBI tax ID: 926550
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Caldilinea aerophila DSM 14535 = NBRC 104270 | GCA_000281175 | complete | ncbi | 926550 |
| 66792 | Caldilinea aerophila DSM 14535 = NBRC 104270 | 926550.5 | complete | patric | 926550 |
| 66792 | Caldilinea aerophila STL-6-O1, DSM 14535 | 2513020048 | draft | img | 926550 |
| 66792 | Caldilinea aerophila STL-6-O1, DSM 14535 | 2540341085 | complete | img | 926550 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 5287 | 59 | |
| 67770 | 59 | high performance liquid chromatography (HPLC) |
| 67770 | 58.8 | genome sequence analysis |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 51.282 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 50.681 | yes |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 50.997 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 55.64 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | yes | 54.047 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 82 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 96.2 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 51.4 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 96.4 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 75.5 |
External links
@ref: 5287
culture collection no.: DSM 14535, JCM 11387, NBRC 104270
straininfo link
- @ref: 86624
- straininfo: 127976
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 14657113 | Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. | Sekiguchi Y, Yamada T, Hanada S, Ohashi A, Harada H, Kamagata Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.02699-0 | 2003 | Bacteria/classification, Chloroflexi/*classification/*genetics/growth & development/ultrastructure, Microscopy, Electron, Molecular Sequence Data, *Phylogeny | Genetics |
| Phylogeny | 20584812 | Caldilinea tarbellica sp. nov., a filamentous, thermophilic, anaerobic bacterium isolated from a deep hot aquifer in the Aquitaine Basin. | Gregoire P, Bohli M, Cayol JL, Joseph M, Guasco S, Dubourg K, Cambar J, Michotey V, Bonin P, Fardeau ML, Ollivier B | Int J Syst Evol Microbiol | 10.1099/ijs.0.025676-0 | 2010 | Anaerobiosis, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Chloroflexi/*classification/genetics/isolation & purification/*physiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, France, Hot Temperature, Hydrogen-Ion Concentration, Molecular Sequence Data, Nitrates/metabolism, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Sulfates/metabolism, *Water Microbiology | Metabolism |
| Enzymology | 32732042 | Characteristics of a fructose 6-phosphate 4-epimerase from Caldilinea aerophila DSM 14535 and its application for biosynthesis of tagatose. | Dai Y, Zhang J, Zhang T, Chen J, Hassanin HA, Jiang B | Enzyme Microb Technol | 10.1016/j.enzmictec.2020.109594 | 2020 | Carbohydrate Epimerases/genetics/*metabolism, Chloroflexi/*enzymology/genetics, Cloning, Molecular, Crystallography, X-Ray, Fructosephosphates/*metabolism, Hexoses/*biosynthesis, Hydrogen-Ion Concentration, Kinetics, Polysaccharides/metabolism, Substrate Specificity | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5287 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14535) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14535 | |||
| 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 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 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/ | ||||
| 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 | |||
| 86624 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID127976.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |