Strain identifier
BacDive ID: 18090
Type strain: 
Species: Caldithrix abyssi
Strain Designation: LF13
Strain history: <- M. L. Miroshnichenko, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; LF13 <- M. L. Miroshnichenko
NCBI tax ID(s): 880073 (strain), 187145 (species)
version 8.1 (current version)
General
@ref: 5067
BacDive-ID: 18090
DSM-Number: 13497
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative
description: Caldithrix abyssi LF13 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from deep-sea hot vent.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 187145 | species |
| 880073 | strain |
strain history
- @ref: 5067
- history: <- M. L. Miroshnichenko, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; LF13 <- M. L. Miroshnichenko
doi: 10.13145/bacdive18090.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/calditrichota
- domain: Bacteria
- phylum: Calditrichota
- class: Calditrichia
- order: Calditrichales
- family: Calditrichaceae
- genus: Caldithrix
- species: Caldithrix abyssi
- full scientific name: Caldithrix abyssi Miroshnichenko et al. 2003
@ref: 5067
domain: Bacteria
phylum: Calditrichaeota
class: Calditrichae
order: Deferribacterales
family: Calditrichaceae
genus: Caldithrix
species: Caldithrix abyssi
full scientific name: Caldithrix abyssi Miroshnichenko et al. 2003
strain designation: LF13
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 100
multimedia
- @ref: 66793
- multimedia content: EM_DSM_13497_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 5067
- name: CALDITHRIX MEDIUM (DSMZ Medium 946a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/946a
- composition: Name: CALDITHRIX MEDIUM (DSMZ Medium 946a) Composition: MgCl2 x 6 H2O 5.44016 g/l Yeast extract 2.96736 g/l Na2CO3 0.98912 g/l KCl 0.642928 g/l Na2S x 9 H2O 0.593472 g/l NH4Cl 0.326409 g/l KH2PO4 0.326409 g/l NaBr 0.098912 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l SrCl2 x 6 H2O 0.0148368 g/l Na3-citrate 0.0098912 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l CoSO4 x 7 H2O 0.00178042 g/l ZnSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l FeSO4 x 7 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l H3BO3 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l KI 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water
culture temp
- @ref: 5067
- growth: positive
- type: growth
- temperature: 60
- range: thermophilic
Physiology and metabolism
oxygen tolerance
- @ref: 5067
- oxygen tolerance: anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.809 |
Isolation, sampling and environmental information
isolation
- @ref: 5067
- sample type: deep-sea hot vent
- geographic location: Mid-Atlantic Ridge, Logatchev hydrothermal field
- latitude: 14.75
- longitude: -44.9833
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Environmental | #Aquatic | #Marine |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_3404.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16128;96_1779;97_2129;98_2609;99_3404&stattab=map
- Last taxonomy: Caldithrix abyssi subclade
- 16S sequence: AJ430587
- Sequence Identity:
- Total samples: 734
- soil counts: 55
- aquatic counts: 665
- animal counts: 10
- plant counts: 4
Safety information
risk assessment
- @ref: 5067
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5067
- description: Caldothrix abyssi 16S rRNA gene, strain LF13T
- accession: AJ430587
- length: 1504
- database: ena
- NCBI tax ID: 880073
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Caldithrix abyssi DSM 13497 LF13 | GCA_001886815 | complete | ncbi | 880073 |
| 66792 | Caldithrix abyssi DSM 13497 | GCA_000241815 | chromosome | ncbi | 880073 |
| 66792 | Caldithrix abyssi DSM 13497 | 880073.11 | complete | patric | 880073 |
| 66792 | Caldithrix abyssi DSM 13497 | 880073.4 | wgs | patric | 880073 |
| 66792 | Caldithrix abyssi LF13, DSM 13497 | 2561511127 | draft | img | 880073 |
| 66792 | Caldithrix abyssi LF13, DSM 13497 | 2718218154 | complete | img | 880073 |
| 66792 | Caldithrix abyssi LF13, DSM 13497 | 2643221409 | draft | img | 880073 |
| 66792 | Caldithrix abyssi DSM 13497 TH-08apr19-15 | GCA_945865405 | contig | ncbi | 880073 |
| 66792 | Caldithrix abyssi DSM 13497 strain TH-08apr19-15 | 880073.23 | wgs | patric | 880073 |
GC content
- @ref: 5067
- GC-content: 42.5
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 77.776 | no |
| gram-positive | no | 99.317 | no |
| anaerobic | yes | 93.101 | yes |
| aerobic | no | 94.074 | yes |
| halophile | no | 73.18 | no |
| spore-forming | no | 91.062 | no |
| glucose-util | yes | 78.369 | no |
| thermophile | yes | 96.906 | no |
| motile | yes | 73.01 | no |
| glucose-ferment | no | 82.898 | no |
External links
@ref: 5067
culture collection no.: DSM 13497, VKM B-2286
straininfo link
- @ref: 87078
- straininfo: 100576
literature
- topic: Phylogeny
- Pubmed-ID: 12656191
- title: Caldithrix abyssi gen. nov., sp. nov., a nitrate-reducing, thermophilic, anaerobic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent, represents a novel bacterial lineage.
- authors: Miroshnichenko ML, Kostrikina NA, Chernyh NA, Pimenov NV, Tourova TP, Antipov AN, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02390-0
- year: 2003
- mesh: Atlantic Ocean, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*classification/genetics/*isolation & purification/metabolism, Hot Temperature, Microscopy, Electron, Molecular Sequence Data, Nitrates/metabolism, Oxidation-Reduction, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5067 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13497) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13497 | |||
| 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 | |
| 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 | |||
| 87078 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100576.1 | StrainInfo: A central database for resolving microbial strain identifiers |