Strain identifier

BacDive ID: 14339

Type strain: Yes

Species: Thiospirochaeta perfilievii

Strain Designation: P

Strain history: <- G. A. Dubinina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; strain P <- G. A. Dubinina {1991}

NCBI tax ID(s): 252967 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7967

BacDive-ID: 14339

DSM-Number: 19205

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, motile, spiral-shaped

description: Thiospirochaeta perfilievii P is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from "Thiodendron" bacterial sulfur mat .

NCBI tax id

  • NCBI tax id: 252967
  • Matching level: species

strain history

  • @ref: 7967
  • history: <- G. A. Dubinina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; strain P <- G. A. Dubinina {1991}

doi: 10.13145/bacdive14339.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/spirochaetota
  • domain: Bacteria
  • phylum: Spirochaetota
  • class: Spirochaetia
  • order: Spirochaetales
  • family: Spirochaetaceae
  • genus: Thiospirochaeta
  • species: Thiospirochaeta perfilievii
  • full scientific name: Thiospirochaeta perfilievii (Dubinina et al. 2011) Dubinina et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Spirochaeta perfilievii

@ref: 7967

domain: Bacteria

phylum: Spirochaetes

class: Spirochaetia

order: Spirochaetales

family: Spirochaetaceae

genus: Thiospirochaeta

species: Thiospirochaeta perfilievii

full scientific name: Thiospirochaeta perfilievii (Dubinina et al. 2011) Dubinina et al. 2020

strain designation: P

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
29667negative105 µm0.3 µmspiral-shapedyesgliding
69480yes90.119
69480negative99.806

colony morphology

  • @ref: 7967
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

  • @ref: 7967
  • name: SEDIMINISPIROCHAETA MEDIUM (DSMZ Medium 1008)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1008
  • composition: Name: SEDIMINISPIROCHAETA MEDIUM (DSMZ Medium 1008; with strain-specific modifications) Composition: D-Glucose 5.0 g/l Trypticase peptone 2.0 g/l Na-thioglycolate 1.0 g/l Yeast extract 1.0 g/l Sodium resazurin 0.0005 g/l Charcoal-filtered, natural seawater Distilled water

culture temp

@refgrowthtypetemperaturerange
7967positivegrowth28mesophilic
29667positivegrowth04-32
29667positiveoptimum29mesophilic

culture pH

@refabilitytypepHPH range
29667positivegrowth6.5-8.5alkaliphile
29667positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7967anaerobe
29667anaerobe
69480anaerobe98.651

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.957

halophily

@refsaltgrowthtested relationconcentration
29667NaClpositivegrowth0.58-5.8 %
29667NaClpositiveoptimum2.03 %

observation

  • @ref: 29667
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2966722653asparagine+carbon source
2966717057cellobiose+carbon source
2966717234glucose+carbon source
2966728087glycogen+carbon source
2966717306maltose+carbon source
2966717992sucrose+carbon source
2966727082trehalose+carbon source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380alanine arylamidase+3.4.11.2
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
7967---+/--++--+-------+--+/-+/--+/-++/----

Isolation, sampling and environmental information

isolation

  • @ref: 7967
  • sample type: "Thiodendron" bacterial sulfur mat (mineral sulfide spring)
  • geographic location: Novgorod Region, Staraya Russa resort
  • country: Russia
  • origin.country: RUS
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Spring
#Environmental#Microbial community#Microbial mat
#Condition#Sulfuric

taxonmaps

  • @ref: 69479
  • File name: preview.99_88261.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3699;96_36603;97_46517;98_60961;99_88261&stattab=map
  • Last taxonomy: Thiospirochaeta perfilievii subclade
  • 16S sequence: AY337318
  • Sequence Identity:
  • Total samples: 4592
  • soil counts: 99
  • aquatic counts: 4385
  • animal counts: 48
  • plant counts: 60

Safety information

risk assessment

  • @ref: 7967
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7967
  • description: Spirochaeta perfilievii strain P 16S ribosomal RNA gene, partial sequence
  • accession: AY337318
  • length: 1428
  • database: ena
  • NCBI tax ID: 252967

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thiospirochaeta perfilievii PGCA_008329945completencbi252967
66792Spirochaeta perfilievii strain P252967.3completepatric252967

GC content

@refGC-contentmethod
796741.7thermal denaturation, midpoint method (Tm)
2966741.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno53no
motileyes84.208no
flagellatedno80.529yes
gram-positiveno95.34yes
anaerobicyes98.264yes
aerobicno98.25yes
halophileno78.312no
spore-formingno79.426no
glucose-utilyes87.028no
thermophileno92.944no
glucose-fermentyes70.73no

External links

@ref: 7967

culture collection no.: DSM 19205, VKM B-2514

straininfo link

  • @ref: 83484
  • straininfo: 398000

literature

  • topic: Phylogeny
  • Pubmed-ID: 20173011
  • title: Spirochaeta perfilievii sp. nov., an oxygen-tolerant, sulfide-oxidizing, sulfur- and thiosulfate-reducing spirochaete isolated from a saline spring.
  • authors: Dubinina G, Grabovich M, Leshcheva N, Rainey FA, Gavrish E
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.018333-0
  • year: 2010
  • mesh: Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Hydrogen-Ion Concentration, Molecular Sequence Data, Oxidation-Reduction, Oxygen/*toxicity, Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, Sodium Chloride/metabolism, Spirochaeta/*classification/genetics/*isolation & purification/metabolism, Sulfides/*metabolism, Sulfur/*metabolism, Temperature, Thiosulfates/*metabolism, *Water Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7967Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19205)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19205
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
29667Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2605428776041
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)
68380Automatically annotated from API rID32A
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)
83484Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398000.1StrainInfo: A central database for resolving microbial strain identifiers