Strain identifier

BacDive ID: 109

Type strain: Yes

Species: Ferrithrix thermotolerans

Strain Designation: Y005

Strain history: <- D. B. Johnson, School Biol. Sci., Bangor Univ., United Kingdom; Y005

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
1121881strain
209649species

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

@refgram staincell lengthcell shapemotilityconfidence
22969negative1.0-3.0 mmfilament-shapedno
69480negative90.162

colony morphology

@refincubation periodcolony sizecolony shape
81422-3 days
229691.0-2.0 mmrhizoid

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

@refgrowthtypetemperaturerange
8142positivegrowth37mesophilic
22969maximum50.0thermophilic
22969positiveoptimum43.0thermophilic

culture pH

@refabilitytypepHPH range
22969positiveoptimum1.8acidophile
22969positiveminimum1.6

Physiology and metabolism

spore formation

@refspore formationconfidence
22969no
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2296933403elemental sulfur-oxidation
2296917754glycerol+carbon source
2296917754glycerol+electron donor
2296917754glycerol+energy source
2296916236ethanol+growth
2296917754glycerol+growth
22969yeast extract+growth
2296918248iron+oxidation
2296918248iron+reduction

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture temperature
8142mineral sample (pH 2.7; 31 °C)Yellowstone National Park, Beryl Spring/Gibbon river areaUSAUSANorth America
22969geothermal sitesolid mediaferrous iron,ferrous iron,tryptone soya broth,potassium tetrathionate45.0

isolation source categories

Cat1Cat2
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ferrithrix thermotolerans DSM 19514GCA_900128965scaffoldncbi1121881
66792Ferrithrix thermotolerans DSM 19514 strain DSM 195141121881.3wgspatric1121881
66792Ferrithrix thermotolerans DSM 195142582580746draftimg1121881
66792Ferrithrix thermotolerans DSM 19514 AE-24oct19-111GCA_945860575contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 LH-05nov19-135GCA_945860855contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 LH-02apr19-314GCA_945861025contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 LH-02apr19-234GCA_945861285contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 MaH-04nov19-128GCA_945861325scaffoldncbi1121881
66792Ferrithrix thermotolerans DSM 19514 MaE-04nov19-347GCA_945861475contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 ME-08apr19-91GCA_945862025contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 MH-08apr19-197GCA_945862115contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 LH-05nov19-18GCA_945872865contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 TE-08apr19-108GCA_945875775contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 AE-03may19-179GCA_945875945contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 LE-02apr19-120GCA_945878475contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 MsH-30apr19-214GCA_945878705contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 TE-11nov19-233GCA_945878815contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 MH-21oct19-164GCA_945885515contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 MH-09jul19-56GCA_945889085scaffoldncbi1121881
66792Ferrithrix thermotolerans DSM 19514 MoH-02may19-17GCA_945897405contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 TH-08apr19-274GCA_945899535contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 TH-08apr19-218GCA_945906305contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 TrE-25oct19-114GCA_945906845contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 TrH-03may19-239GCA_945906865contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 TrH-25oct19-82GCA_945906955contigncbi1121881
66792Ferrithrix thermotolerans DSM 19514 strain TrH-25oct19-821121881.17wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain TrE-25oct19-1141121881.16wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain TH-08apr19-2741121881.14wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain TH-08apr19-2181121881.15wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain TE-11nov19-2331121881.10wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain TE-08apr19-1081121881.7wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain MsH-30apr19-2141121881.9wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain MoH-02may19-171121881.13wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain MaH-04nov19-1281121881.22wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain MaE-04nov19-3471121881.23wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain MH-21oct19-1641121881.11wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain MH-09jul19-561121881.12wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain MH-08apr19-1971121881.25wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain ME-08apr19-911121881.24wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain LH-05nov19-1351121881.19wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain LH-02apr19-3141121881.20wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain LH-02apr19-2341121881.21wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain AE-24oct19-1111121881.18wgspatric1121881
66792Ferrithrix thermotolerans DSM 19514 strain AE-03may19-1791121881.8wgspatric1121881

GC content

@refGC-contentmethod
814250.2±0.8thermal denaturation, midpoint method (Tm)
2296959.4-51thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno80no
motileyes64.807no
flagellatedno95.248no
gram-positiveno63.382yes
anaerobicno96.679no
aerobicyes89.274no
halophileno94.327no
spore-formingno93.971yes
glucose-fermentno83.386no
thermophileyes84.24no
glucose-utilyes86.16no

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

@idauthorscataloguedoi/urltitlejournalpubmed
8142Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19514)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19514
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
22969D. Barrie Johnson,Paula Bacelar-Nicolau,Naoko Okibe,Angharad Thomas,Kevin B. Hallberg10.1099/ijs.0.65409-0Ferrimicrobium acidiphilum gen. nov., sp. nov. and Ferrithrix thermotolerans gen. nov., sp. nov.: heterotrophic, iron-oxidizing, extremely acidophilic actinobacteriaIJSEM 59: 1082-1089 200919406797
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69792Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404349.1StrainInfo: A central database for resolving microbial strain identifiers