Strain identifier
BacDive ID: 4059
Type strain: 
Species: Desulfomicrobium orale
Strain Designation: NY678
Strain history: DSM 12838 <-- P. S. Langendijk NY678.
NCBI tax ID(s): 888061 (strain), 132132 (species)
version 8.1 (current version)
General
@ref: 4846
BacDive-ID: 4059
DSM-Number: 12838
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Desulfomicrobium orale NY678 is an anaerobe, mesophilic, motile bacterium that was isolated from subgingival plaque of a patient with periodontitis.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 132132 | species |
| 888061 | strain |
strain history
| @ref | history |
|---|---|
| 4846 | <- P. S. Langendijk; NY678 <- P. S. Langendijk {1993} |
| 67770 | DSM 12838 <-- P. S. Langendijk NY678. |
doi: 10.13145/bacdive4059.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfovibrionales
- family: Desulfomicrobiaceae
- genus: Desulfomicrobium
- species: Desulfomicrobium orale
- full scientific name: Desulfomicrobium orale Langendijk et al. 2001
@ref: 4846
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfovibrionales
family: Desulfomicrobiaceae
genus: Desulfomicrobium
species: Desulfomicrobium orale
full scientific name: Desulfomicrobium orale Langendijk et al. 2001
strain designation: NY678
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 96.556 | |
| 69480 | 99.999 | negative |
Culture and growth conditions
culture medium
- @ref: 4846
- name: DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63)
- growth: yes
- link: https://mediadive.dsmz.de/medium/63
- composition: Name: DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63; with strain-specific modifications) Composition: Meat extract 3.0 g/l MgSO4 x 7 H2O 2.0 g/l Na-DL-lactate 2.0 g/l Yeast extract 1.0 g/l NH4Cl 1.0 g/l Na2SO4 1.0 g/l K2HPO4 0.5 g/l FeSO4 x 7 H2O 0.5 g/l Ascorbic acid 0.1 g/l CaCl2 x 2 H2O 0.1 g/l Na-thioglycolate 0.1 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 4846 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 4846 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.983 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 4846 | subgingival plaque of a patient with periodontitis | Netherlands | NLD | Europe |
| 67770 | Subgingival plaque of a patient with periodontitis |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Inflammation | |
| #Infection | #Patient | |
| #Host Body-Site | #Oral cavity and airways | #Subgingival plaque |
taxonmaps
- @ref: 69479
- File name: preview.99_6536.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_533;96_3097;97_3798;98_4824;99_6536&stattab=map
- Last taxonomy: Desulfomicrobium orale subclade
- 16S sequence: AJ251623
- Sequence Identity:
- Total samples: 6194
- soil counts: 199
- aquatic counts: 470
- animal counts: 5462
- plant counts: 63
Safety information
risk assessment
- @ref: 4846
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Desulfomicrobium orale gene for 16S ribosomal RNA, partial sequence, strain: JCM 17150 | AB573871 | 1513 | ena | 132132 |
| 4846 | Desulfomicrobium orale 16S rRNA gene, strain DSM12838 | AJ251623 | 1475 | ena | 888061 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfomicrobium orale DSM 12838 | GCA_001553625 | complete | ncbi | 888061 |
| 66792 | Desulfomicrobium orale DSM 12838 | 888061.5 | complete | patric | 888061 |
| 66792 | Desulfomicrobium orale DSM 12838 | 2684623057 | complete | img | 888061 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 4846 | 59.7 | high performance liquid chromatography (HPLC) |
| 67770 | 59.5 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 57.282 | no |
| gram-positive | no | 99.145 | no |
| anaerobic | yes | 99.457 | yes |
| halophile | no | 72.566 | no |
| spore-forming | no | 96.242 | no |
| thermophile | no | 75.804 | yes |
| glucose-util | no | 72.026 | no |
| motile | yes | 88.042 | no |
| aerobic | no | 98.661 | yes |
| glucose-ferment | no | 77.048 | no |
External links
@ref: 4846
culture collection no.: DSM 12838, JCM 17150
straininfo link
- @ref: 73564
- straininfo: 49378
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 11411671 | Isolation of Desulfomicrobium orale sp. nov. and Desulfovibrio strain NY682, oral sulfate-reducing bacteria involved in human periodontal disease. | Langendijk PS, Kulik EM, Sandmeier H, Meyer J, van der Hoeven JS | Int J Syst Evol Microbiol | 10.1099/00207713-51-3-1035 | 2001 | Bacterial Infections/microbiology, Cytochrome c Group/analysis, DNA, Ribosomal/genetics, Deltaproteobacteria/*classification/genetics/isolation & purification, Dental Plaque/*microbiology, Desulfovibrio/*classification/genetics/isolation & purification, Humans, Hydrogensulfite Reductase, Molecular Sequence Data, Oxidoreductases Acting on Sulfur Group Donors/analysis, Periodontitis/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics | Enzymology |
| Phylogeny | 25013226 | Oligoflexus tunisiensis gen. nov., sp. nov., a Gram-negative, aerobic, filamentous bacterium of a novel proteobacterial lineage, and description of Oligoflexaceae fam. nov., Oligoflexales ord. nov. and Oligoflexia classis nov. | Nakai R, Nishijima M, Tazato N, Handa Y, Karray F, Sayadi S, Isoda H, Naganuma T | Int J Syst Evol Microbiol | 10.1099/ijs.0.060798-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Desert Climate, Fatty Acids/chemistry, Gram-Negative Bacteria/classification, Molecular Sequence Data, *Phylogeny, Proteobacteria/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Tunisia, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4846 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12838) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12838 | |||
| 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 | |
| 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) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 73564 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49378.1 | StrainInfo: A central database for resolving microbial strain identifiers |