Strain identifier
BacDive ID: 17165
Type strain:
Species: Selenomonas noxia
Strain history: ATCC 43541 <-- L. V. H. Moore VPI D9B-5.
NCBI tax ID(s): 585503 (strain), 135083 (species)
General
@ref: 8189
BacDive-ID: 17165
DSM-Number: 19578
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Selenomonas noxia DSM 19578 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human gingival crevice.
NCBI tax id
NCBI tax id | Matching level |
---|---|
135083 | species |
585503 | strain |
strain history
@ref | history |
---|---|
8189 | <- JCM <- ATCC <- L. V. Moore; VPI D9B-5 <- W. E. C. Moore |
67770 | ATCC 43541 <-- L. V. H. Moore VPI D9B-5. |
doi: 10.13145/bacdive17165.20230509.8.1
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 noxia
- full scientific name: Selenomonas noxia Moore et al. 1987
@ref: 8189
domain: Bacteria
phylum: Firmicutes
class: Negativicutes
order: Selenomonadales
family: Selenomonadaceae
genus: Selenomonas
species: Selenomonas noxia
full scientific name: Selenomonas noxia Moore et al. 1987
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.981
colony morphology
- @ref: 60046
- incubation period: 2-3 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8189 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
8189 | CHOPPED MEAT MEDIUM (DSMZ Medium 78) | yes | https://mediadive.dsmz.de/medium/78 | Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8189 | positive | growth | 37 | mesophilic |
60046 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
8189 | anaerobe | |
60046 | anaerobe | |
69480 | anaerobe | 99.999 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.916 |
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 | 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 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8189 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
8189 | human gingival crevice | USA | USA | North America |
60046 | Human gingival crevice,severe periodontitis | |||
67770 | Gingival crevice of an affected site in a person with rapidly progressive periodontitis |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body-Site | #Oral cavity and airways | #Gingiva |
#Host Body-Site | #Oral cavity and airways | #Tooth |
taxonmaps
- @ref: 69479
- File name: preview.99_10812.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_55;96_1405;97_1676;98_2041;99_10812&stattab=map
- Last taxonomy: Selenomonas noxia subclade
- 16S sequence: LC037221
- Sequence Identity:
- Total samples: 2843
- soil counts: 23
- aquatic counts: 60
- animal counts: 2746
- plant counts: 14
Safety information
risk assessment
- @ref: 8189
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
8189 | Selenomonas noxia 16S ribosomal RNA gene, partial sequence | AF287799 | 1491 | ena | 135083 |
67770 | Selenomonas noxia gene for 16S ribosomal RNA, partial sequence, strain: JCM 8546 | LC037221 | 1505 | ena | 135083 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Selenomonas noxia ATCC 43541 | 585503.3 | wgs | patric | 585503 |
66792 | Selenomonas noxia ATCC 43541 | 645951808 | draft | img | 585503 |
67770 | Selenomonas noxia ATCC 43541 | GCA_000160555 | scaffold | ncbi | 585503 |
GC content
@ref | GC-content | method |
---|---|---|
8189 | 57 | |
67770 | 57 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 97.754 | no |
anaerobic | yes | 99.665 | no |
halophile | no | 90.573 | no |
spore-forming | no | 86.201 | no |
glucose-util | yes | 65.394 | no |
thermophile | no | 83.661 | no |
flagellated | no | 72.793 | no |
aerobic | no | 98.774 | yes |
motile | yes | 80.607 | no |
glucose-ferment | yes | 53.618 | no |
External links
@ref: 8189
culture collection no.: DSM 19578, ATCC 43541, JCM 8546, CCUG 53876, BCRC 14410, VPI D9B-5
straininfo link
- @ref: 86164
- straininfo: 41902
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8189 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19578) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19578 | |||
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 | |||
60046 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 53876) | https://www.ccug.se/strain?id=53876 | |||
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) | |||
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 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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 | |||
86164 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID41902.1 | StrainInfo: A central database for resolving microbial strain identifiers |