Strain identifier
BacDive ID: 109
Type strain:
Species: Ferrithrix thermotolerans
Strain Designation: Y005
Strain history: <- D. B. Johnson, School Biol. Sci., Bangor Univ., United Kingdom; Y005
NCBI tax ID(s): 1121881 (strain), 209649 (species)
General
@ref: 8142
BacDive-ID: 109
DSM-Number: 19514
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, filament-shaped
description: Ferrithrix thermotolerans Y005 is a mesophilic, Gram-negative, filament-shaped bacterium that was isolated from mineral sample .
NCBI tax id
NCBI tax id | Matching level |
---|---|
1121881 | strain |
209649 | species |
strain history
- @ref: 8142
- history: <- D. B. Johnson, School Biol. Sci., Bangor Univ., United Kingdom; Y005
doi: 10.13145/bacdive109.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Acidimicrobiia
- order: Acidimicrobiales
- family: Acidimicrobiaceae
- genus: Ferrithrix
- species: Ferrithrix thermotolerans
- full scientific name: Ferrithrix thermotolerans Johnson et al. 2009
@ref: 8142
domain: Bacteria
phylum: Actinobacteria
class: Acidimicrobiia
order: Acidimicrobiales
family: Acidimicrobiaceae
genus: Ferrithrix
species: Ferrithrix thermotolerans
full scientific name: Ferrithrix thermotolerans Johnson et al. 2009 emend. Nouioui et al. 2018
strain designation: Y005
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell shape | motility | confidence |
---|---|---|---|---|---|
22969 | negative | 1.0-3.0 mm | filament-shaped | no | |
69480 | negative | 90.162 |
colony morphology
@ref | incubation period | colony size | colony shape |
---|---|---|---|
8142 | 2-3 days | ||
22969 | 1.0-2.0 mm | rhizoid |
Culture and growth conditions
culture medium
- @ref: 8142
- name: FERROUS SULFATE/YEAST EXTRACT MEDIUM (DSMZ Medium 1190)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1190
- composition: Name: FERROUS SULFATE/YEAST EXTRACT MEDIUM (DSMZ Medium 1190) Composition: FeSO4 x 7 H2O 5.56 g/l MgSO4 x 7 H2O 0.5 g/l (NH4)2SO4 0.45 g/l Yeast extract 0.2 g/l Na2SO4 x 10 H2O 0.15 g/l KH2PO4 0.05 g/l KCl 0.05 g/l Ca(NO3)2 x 4 H2O 0.014 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8142 | positive | growth | 37 | mesophilic |
22969 | maximum | 50.0 | thermophilic | |
22969 | positive | optimum | 43.0 | thermophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
22969 | positive | optimum | 1.8 | acidophile |
22969 | positive | minimum | 1.6 |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
22969 | no | |
69480 | no | 99.999 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
22969 | 33403 | elemental sulfur | - | oxidation |
22969 | 17754 | glycerol | + | carbon source |
22969 | 17754 | glycerol | + | electron donor |
22969 | 17754 | glycerol | + | energy source |
22969 | 16236 | ethanol | + | growth |
22969 | 17754 | glycerol | + | growth |
22969 | yeast extract | + | growth | |
22969 | 18248 | iron | + | oxidation |
22969 | 18248 | iron | + | reduction |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture composition | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|
8142 | mineral sample (pH 2.7; 31 °C) | Yellowstone National Park, Beryl Spring/Gibbon river area | USA | USA | North America | |||
22969 | geothermal site | solid media | ferrous iron,ferrous iron,tryptone soya broth,potassium tetrathionate | 45.0 |
isolation source categories
Cat1 | Cat2 |
---|---|
#Environmental | #Terrestrial |
#Condition | #Acidic |
taxonmaps
- @ref: 69479
- File name: preview.99_6890.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_568;96_3237;97_3974;98_5072;99_6890&stattab=map
- Last taxonomy: Ferrithrix thermotolerans subclade
- 16S sequence: AY140237
- Sequence Identity:
- Total samples: 728
- soil counts: 99
- aquatic counts: 160
- animal counts: 461
- plant counts: 8
Safety information
risk assessment
- @ref: 8142
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8142
- description: Ferrithrix thermotolerans strain Y005 16S ribosomal RNA gene, partial sequence
- accession: AY140237
- length: 1331
- database: ena
- NCBI tax ID: 209649
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Ferrithrix thermotolerans DSM 19514 | GCA_900128965 | scaffold | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain DSM 19514 | 1121881.3 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 | 2582580746 | draft | img | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 AE-24oct19-111 | GCA_945860575 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 LH-05nov19-135 | GCA_945860855 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 LH-02apr19-314 | GCA_945861025 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 LH-02apr19-234 | GCA_945861285 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 MaH-04nov19-128 | GCA_945861325 | scaffold | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 MaE-04nov19-347 | GCA_945861475 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 ME-08apr19-91 | GCA_945862025 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 MH-08apr19-197 | GCA_945862115 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 LH-05nov19-18 | GCA_945872865 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 TE-08apr19-108 | GCA_945875775 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 AE-03may19-179 | GCA_945875945 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 LE-02apr19-120 | GCA_945878475 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 MsH-30apr19-214 | GCA_945878705 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 TE-11nov19-233 | GCA_945878815 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 MH-21oct19-164 | GCA_945885515 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 MH-09jul19-56 | GCA_945889085 | scaffold | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 MoH-02may19-17 | GCA_945897405 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 TH-08apr19-274 | GCA_945899535 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 TH-08apr19-218 | GCA_945906305 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 TrE-25oct19-114 | GCA_945906845 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 TrH-03may19-239 | GCA_945906865 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 TrH-25oct19-82 | GCA_945906955 | contig | ncbi | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain TrH-25oct19-82 | 1121881.17 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain TrE-25oct19-114 | 1121881.16 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain TH-08apr19-274 | 1121881.14 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain TH-08apr19-218 | 1121881.15 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain TE-11nov19-233 | 1121881.10 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain TE-08apr19-108 | 1121881.7 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain MsH-30apr19-214 | 1121881.9 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain MoH-02may19-17 | 1121881.13 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain MaH-04nov19-128 | 1121881.22 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain MaE-04nov19-347 | 1121881.23 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain MH-21oct19-164 | 1121881.11 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain MH-09jul19-56 | 1121881.12 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain MH-08apr19-197 | 1121881.25 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain ME-08apr19-91 | 1121881.24 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain LH-05nov19-135 | 1121881.19 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain LH-02apr19-314 | 1121881.20 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain LH-02apr19-234 | 1121881.21 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain AE-24oct19-111 | 1121881.18 | wgs | patric | 1121881 |
66792 | Ferrithrix thermotolerans DSM 19514 strain AE-03may19-179 | 1121881.8 | wgs | patric | 1121881 |
GC content
@ref | GC-content | method |
---|---|---|
8142 | 50.2±0.8 | thermal denaturation, midpoint method (Tm) |
22969 | 59.4-51 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 80 | no |
motile | yes | 64.807 | no |
flagellated | no | 95.248 | no |
gram-positive | no | 63.382 | yes |
anaerobic | no | 96.679 | no |
aerobic | yes | 89.274 | no |
halophile | no | 94.327 | no |
spore-forming | no | 93.971 | yes |
glucose-ferment | no | 83.386 | no |
thermophile | yes | 84.24 | no |
glucose-util | yes | 86.16 | no |
External links
@ref: 8142
culture collection no.: DSM 19514, ATCC BAA 1645
straininfo link
- @ref: 69792
- straininfo: 404349
literature
- topic: Phylogeny
- Pubmed-ID: 19406797
- title: Ferrimicrobium acidiphilum gen. nov., sp. nov. and Ferrithrix thermotolerans gen. nov., sp. nov.: heterotrophic, iron-oxidizing, extremely acidophilic actinobacteria.
- authors: Johnson DB, Bacelar-Nicolau P, Okibe N, Thomas A, Hallberg KB
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.65409-0
- year: 2009
- mesh: Actinobacteria/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Culture Media, DNA, Bacterial/analysis, Fresh Water/microbiology, *Heterotrophic Processes, Hot Springs/microbiology, Hydrogen-Ion Concentration, Iron/*metabolism, Mining, Molecular Sequence Data, Oxidation-Reduction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Sulfur, Wales, Wyoming
- topic2: Cultivation
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8142 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19514) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19514 | |||
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 | |||
22969 | D. Barrie Johnson,Paula Bacelar-Nicolau,Naoko Okibe,Angharad Thomas,Kevin B. Hallberg | 10.1099/ijs.0.65409-0 | Ferrimicrobium acidiphilum gen. nov., sp. nov. and Ferrithrix thermotolerans gen. nov., sp. nov.: heterotrophic, iron-oxidizing, extremely acidophilic actinobacteria | IJSEM 59: 1082-1089 2009 | 19406797 | |
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 | |||
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) | |||
69792 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID404349.1 | StrainInfo: A central database for resolving microbial strain identifiers |