Strain identifier

BacDive ID: 17083

Type strain: Yes

Species: Thiothrix caldifontis

Strain Designation: G1

Strain history: <- G. Dubinina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; G1 <- M. Grabovich et al., Dept. Biology, Univ. Voronezh, Russia

NCBI tax ID(s): 1123398 (strain), 525918 (species)

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General

@ref: 15527

BacDive-ID: 17083

DSM-Number: 21228

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped

description: Thiothrix caldifontis G1 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from bacterial mat from a sulfide spring at 33-40 °C.

NCBI tax id

NCBI tax idMatching level
525918species
1123398strain

strain history

  • @ref: 15527
  • history: <- G. Dubinina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; G1 <- M. Grabovich et al., Dept. Biology, Univ. Voronezh, Russia

doi: 10.13145/bacdive17083.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Beggiatoales
  • family: Leucotrichaceae
  • genus: Thiothrix
  • species: Thiothrix caldifontis
  • full scientific name: Thiothrix caldifontis Chernousova et al. 2009

@ref: 15527

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Thiotrichales

family: Thiotrichaceae

genus: Thiothrix

species: Thiothrix caldifontis

full scientific name: Thiothrix caldifontis Chernousova et al. 2009

strain designation: G1

type strain: yes

Morphology

cell morphology

  • @ref: 29249
  • gram stain: negative
  • cell length: 4.85 µm
  • cell width: 1.55 µm
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 29249
  • production: no

Culture and growth conditions

culture medium

  • @ref: 15527
  • name: Thiothrix medium II (DSMZ Medium 1774)
  • growth: yes
  • link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1774.pdf

culture temp

@refgrowthtypetemperaturerange
29249positivegrowth07-37
29249positiveoptimum25mesophilic
15527positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
29249positivegrowth7-8.6alkaliphile
29249positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 29249
  • oxygen tolerance: aerobe

halophily

  • @ref: 29249
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <3 %

observation

  • @ref: 29249
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2924930089acetate+carbon source
2924935391aspartate+carbon source
2924924996lactate+carbon source
2924925017leucine+carbon source
2924915361pyruvate+carbon source
2924930031succinate+carbon source
2924916199urea+carbon source
2924917632nitrate+reduction

enzymes

@refvalueactivityec
29249cytochrome oxidase+1.9.3.1
29249urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 15527
  • sample type: bacterial mat from a sulfide spring at 33-40 °C
  • geographic location: Northern Caucasus, Petushok spring
  • country: Russia
  • origin.country: RUS
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Spring
#Host#Microbial#Bacteria
#Condition#Sulfuric

taxonmaps

  • @ref: 69479
  • File name: preview.99_98112.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_524;96_3712;97_4564;98_5857;99_98112&stattab=map
  • Last taxonomy: Thiothrix
  • 16S sequence: EU642573
  • Sequence Identity:
  • Total samples: 901
  • soil counts: 27
  • aquatic counts: 820
  • animal counts: 47
  • plant counts: 7

Safety information

risk assessment

  • @ref: 15527
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15527
  • description: Thiothrix caldifontis strain G1 16S ribosomal RNA gene, partial sequence
  • accession: EU642573
  • length: 1404
  • database: ena
  • NCBI tax ID: 525918

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thiothrix caldifontis DSM 21228GCA_900107695scaffoldncbi525918
66792Thiothrix caldifontis strain DSM 21228525918.3wgspatric525918
66792Thiothrix caldifontis DSM 212282599185268draftimg525918

GC content

@refGC-contentmethod
1552752thermal denaturation, midpoint method (Tm)
2924952

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno79.739yes
glucose-fermentno86.102no
flagellatedno86.062yes
gram-positiveno99.423yes
anaerobicno94.009yes
aerobicyes71.574yes
halophileno92.156no
spore-formingno92.696no
thermophileno98.828yes
glucose-utilyes63.908no

External links

@ref: 15527

culture collection no.: DSM 21228

straininfo link

  • @ref: 86083
  • straininfo: 404309

literature

  • topic: Phylogeny
  • Pubmed-ID: 19643883
  • title: Thiothrix caldifontis sp. nov. and Thiothrix lacustris sp. nov., gammaproteobacteria isolated from sulfide springs.
  • authors: Chernousova E, Gridneva E, Grabovich M, Dubinina G, Akimov V, Rossetti S, Kuever J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.009456-0
  • year: 2009
  • mesh: DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Hot Springs/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sulfides/*metabolism, Thiothrix/*classification/genetics/*isolation & purification/metabolism
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15527Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21228)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21228
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
29249Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2566928776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
86083Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404309.1StrainInfo: A central database for resolving microbial strain identifiers