Strain identifier
BacDive ID: 14339
Type strain:
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)
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
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
---|---|---|---|---|---|---|---|
29667 | negative | 105 µm | 0.3 µm | spiral-shaped | yes | gliding | |
69480 | yes | 90.119 | |||||
69480 | negative | 99.806 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
7967 | positive | growth | 28 | mesophilic |
29667 | positive | growth | 04-32 | |
29667 | positive | optimum | 29 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29667 | positive | growth | 6.5-8.5 | alkaliphile |
29667 | positive | optimum | 7.25 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
7967 | anaerobe | |
29667 | anaerobe | |
69480 | anaerobe | 98.651 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.957
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29667 | NaCl | positive | growth | 0.58-5.8 % |
29667 | NaCl | positive | optimum | 2.03 % |
observation
- @ref: 29667
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29667 | 22653 | asparagine | + | carbon source |
29667 | 17057 | cellobiose | + | carbon source |
29667 | 17234 | glucose | + | carbon source |
29667 | 28087 | glycogen | + | carbon source |
29667 | 17306 | maltose | + | carbon source |
29667 | 17992 | sucrose | + | carbon source |
29667 | 27082 | trehalose | + | carbon source |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | 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
@ref | value | activity | ec |
---|---|---|---|
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | alanine arylamidase | + | 3.4.11.2 |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucyl glycin arylamidase | - | 3.4.11.1 |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | L-arginine arylamidase | + | |
68380 | alkaline phosphatase | - | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | + | 3.2.1.21 |
68380 | alpha-glucosidase | + | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Thiospirochaeta perfilievii P | GCA_008329945 | complete | ncbi | 252967 |
66792 | Spirochaeta perfilievii strain P | 252967.3 | complete | patric | 252967 |
GC content
@ref | GC-content | method |
---|---|---|
7967 | 41.7 | thermal denaturation, midpoint method (Tm) |
29667 | 41.7 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 53 | no |
motile | yes | 84.208 | no |
flagellated | no | 80.529 | yes |
gram-positive | no | 95.34 | yes |
anaerobic | yes | 98.264 | yes |
aerobic | no | 98.25 | yes |
halophile | no | 78.312 | no |
spore-forming | no | 79.426 | no |
glucose-util | yes | 87.028 | no |
thermophile | no | 92.944 | no |
glucose-ferment | yes | 70.73 | no |
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
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7967 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19205) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19205 | |||
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 | |||
29667 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26054 | 28776041 | |
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) | |||
68380 | Automatically annotated from API rID32A | |||||
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) | |||
83484 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID398000.1 | StrainInfo: A central database for resolving microbial strain identifiers |