Strain identifier
BacDive ID: 17159
Type strain:
Species: Selenomonas sputigena
Strain history: <- ATCC <- W.E.C. Moore, VPI D19B-28
NCBI tax ID(s): 546271 (strain), 69823 (species)
General
@ref: 9065
BacDive-ID: 17159
DSM-Number: 20758
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, human pathogen
description: Selenomonas sputigena DSM 20758 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from subgingival sulcus.
NCBI tax id
NCBI tax id | Matching level |
---|---|
69823 | species |
546271 | strain |
strain history
- @ref: 9065
- history: <- ATCC <- W.E.C. Moore, VPI D19B-28
doi: 10.13145/bacdive17159.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Negativicutes
- order: Selenomonadales
- family: Selenomonadaceae
- genus: Selenomonas
- species: Selenomonas sputigena
- full scientific name: Selenomonas sputigena (Flügge 1886) Boskamp 1922 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Spirillum sputigenum
@ref: 9065
domain: Bacteria
phylum: Firmicutes
class: Negativicutes
order: Selenomonadales
family: Selenomonadaceae
genus: Selenomonas
species: Selenomonas sputigena
full scientific name: Selenomonas sputigena (Flügge 1886) Boskamp 1922 emend. Judicial Commission 1992
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.993
colony morphology
@ref | incubation period |
---|---|
9065 | 2-3 days |
56553 | 2-3 days |
multimedia
- @ref: 66793
- multimedia content: EM_DSM_20758_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
9065 | CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) | yes | https://mediadive.dsmz.de/medium/110 | Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water |
9065 | PYG MEDIUM (MODIFIED) (DSMZ Medium 104) | yes | https://mediadive.dsmz.de/medium/104 | Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
9065 | positive | growth | 37 | mesophilic |
56553 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
9065 | anaerobe | |
56553 | anaerobe | |
69480 | anaerobe | 100 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.706 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
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 | glycin arylamidase | - | |
68380 | alanine arylamidase | - | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | - | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | - | 3.4.11.1 |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | L-arginine arylamidase | - | |
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 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | + | 3.2.1.23 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
9065 | - | - | + | + | - | +/- | - | - | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
9065 | subgingival sulcus |
56553 | Subgingival sulcus |
isolation source categories
- Cat1: #Host Body-Site
- Cat2: #Oral cavity and airways
- Cat3: #Gingiva
taxonmaps
- @ref: 69479
- File name: preview.99_160.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_55;96_119;97_126;98_141;99_160&stattab=map
- Last taxonomy: Selenomonas sputigena subclade
- 16S sequence: CP002637
- Sequence Identity:
- Total samples: 987
- soil counts: 21
- aquatic counts: 28
- animal counts: 923
- plant counts: 15
Safety information
risk assessment
- @ref: 9065
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Selenomonas sputigena 16S ribosomal RNA gene, partial sequence | AF287793 | 1497 | ena | 546271 |
20218 | Selenomonas sputigena strain ATCC35185 16S ribosomal RNA gene, partial sequence | AF373023 | 1499 | ena | 546271 |
9065 | Selenomonas sputigena ATCC 35185, complete genome | CP002637 | 2568361 | ena | 546271 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Selenomonas sputigena ATCC 35185 | GCA_000208405 | complete | ncbi | 546271 |
66792 | Selenomonas sputigena ATCC 35185 | GCA_000160495 | scaffold | ncbi | 546271 |
66792 | Selenomonas sputigena ATCC 35185 | 546271.3 | wgs | patric | 546271 |
66792 | Selenomonas sputigena ATCC 35185 | 546271.5 | complete | patric | 546271 |
66792 | Selenomonas sputigena DSM 20758 | 2504557006 | complete | img | 546271 |
66792 | Selenomonas sputigena ATCC 35185 | 645951802 | draft | img | 546271 |
GC content
- @ref: 9065
- GC-content: 57.0
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 75.626 | no |
flagellated | no | 78.212 | no |
gram-positive | no | 98.192 | no |
anaerobic | yes | 99.999 | yes |
aerobic | no | 99.338 | yes |
halophile | no | 92.8 | no |
spore-forming | no | 83.179 | no |
glucose-util | yes | 66.373 | no |
glucose-ferment | yes | 55.799 | no |
thermophile | no | 78.286 | no |
External links
@ref: 9065
culture collection no.: DSM 20758, ATCC 35185, CCUG 44933, VPI D 19B-28, VPI D19B-28
straininfo link
- @ref: 86158
- straininfo: 46379
literature
- topic: Phylogeny
- Pubmed-ID: 30508628
- title: Microbial biomarkers of common tongue coatings in patients with gastric cancer.
- authors: Xu J, Xiang C, Zhang C, Xu B, Wu J, Wang R, Yang Y, Shi L, Zhang J, Zhan Z
- journal: Microb Pathog
- DOI: 10.1016/j.micpath.2018.11.051
- year: 2018
- mesh: Aged, Bacteria/*classification/genetics, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Fungal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Female, Fungi/*classification/genetics, Humans, Male, *Microbiota, Middle Aged, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 18S/genetics, ROC Curve, Sequence Analysis, DNA, Stomach Neoplasms/*microbiology/*pathology, Tongue/*microbiology
- topic2: Pathogenicity
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9065 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20758) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20758 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
56553 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 44933) | https://www.ccug.se/strain?id=44933 | |||
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) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
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) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
86158 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID46379.1 | StrainInfo: A central database for resolving microbial strain identifiers |