Strain identifier
BacDive ID: 4051
Type strain:
Species: Desulfomicrobium baculatum
Strain Designation: X
Strain history: <- M.B. Vainstein <- E.P. Rozanova and T.N. Nazina, strain X
NCBI tax ID(s): 525897 (strain), 899 (species)
General
@ref: 1577
BacDive-ID: 4051
DSM-Number: 4028
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Desulfomicrobium baculatum X is an anaerobe, mesophilic, motile bacterium that was isolated from manganese ore.
NCBI tax id
NCBI tax id | Matching level |
---|---|
899 | species |
525897 | strain |
strain history
- @ref: 1577
- history: <- M.B. Vainstein <- E.P. Rozanova and T.N. Nazina, strain X
doi: 10.13145/bacdive4051.20230509.8.1
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 baculatum
- full scientific name: Desulfomicrobium baculatum corrig. (Rozanova and Nazina 1984) Rozanova et al. 1994
synonyms
@ref synonym 20215 Desulfomicrobium baculatus 20215 Desulfovibrio baculatus
@ref: 1577
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfovibrionales
family: Desulfomicrobiaceae
genus: Desulfomicrobium
species: Desulfomicrobium baculatum
full scientific name: Desulfomicrobium baculatum (Rozanova and Nazina 1984) Rozanova et al. 1994
strain designation: X
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 96.713 | |
69480 | 99.992 | negative |
multimedia
- @ref: 66793
- multimedia content: EM_DSM_4028_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 1577
- name: DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63)
- growth: yes
- link: https://mediadive.dsmz.de/medium/63
- composition: Name: DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63) Composition: MgSO4 x 7 H2O 2.0 g/l Na-DL-lactate 2.0 g/l NH4Cl 1.0 g/l Yeast extract 1.0 g/l Na2SO4 1.0 g/l FeSO4 x 7 H2O 0.5 g/l K2HPO4 0.5 g/l CaCl2 x 2 H2O 0.1 g/l Na-thioglycolate 0.1 g/l Ascorbic acid 0.1 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
- @ref: 1577
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
1577 | anaerobe | |
69480 | anaerobe | 99.999 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.997 |
Isolation, sampling and environmental information
isolation
- @ref: 1577
- sample type: manganese ore
- country: USSR
- continent: Asia
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Geologic
taxonmaps
- @ref: 69479
- File name: preview.99_5694.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_533;96_2736;97_3363;98_4242;99_5694&stattab=map
- Last taxonomy: Desulfomicrobium
- 16S sequence: AJ277894
- Sequence Identity:
- Total samples: 2243
- soil counts: 172
- aquatic counts: 1917
- animal counts: 82
- plant counts: 72
Safety information
risk assessment
- @ref: 1577
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Desulfomicrobium baculatum 16S ribosomal RNA gene, complete sequence | AF030438 | 1540 | ena | 525897 |
20218 | Desulfomicrobium baculatum 16S rRNA gene, strain DSM 4028T | AJ277894 | 1517 | ena | 525897 |
20218 | Desulfomicrobium baculatum DSM 4028 16S ribosomal RNA gene, partial sequence | JX293692 | 225 | ena | 525897 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Desulfomicrobium baculatum DSM 4028 | GCA_000023225 | complete | ncbi | 525897 |
66792 | Desulfomicrobium baculatum DSM 4028 | 525897.5 | complete | patric | 525897 |
66792 | Desulfomicrobium baculatum X, DSM 4028 | 644736350 | complete | img | 525897 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 91.569 | no |
flagellated | yes | 52.187 | no |
gram-positive | no | 98.836 | no |
anaerobic | yes | 98.717 | yes |
aerobic | no | 98.443 | no |
halophile | no | 80.891 | no |
spore-forming | no | 94.568 | no |
thermophile | no | 97.511 | yes |
glucose-util | no | 67.818 | no |
glucose-ferment | no | 79.791 | no |
External links
@ref: 1577
culture collection no.: DSM 4028, VKM B-1378, CCUG 34229
straininfo link
- @ref: 73556
- straininfo: 93044
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 25792369 | Desulfoplanes formicivorans gen. nov., sp. nov., a novel sulfate-reducing bacterium isolated from a blackish meromictic lake, and emended description of the family Desulfomicrobiaceae. | Watanabe M, Kojima H, Fukui M | Int J Syst Evol Microbiol | 10.1099/ijs.0.000197 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deltaproteobacteria/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Japan, Lakes/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfur-Reducing Bacteria/*classification/genetics/isolation & purification | Enzymology |
31154126 | A novel biological sulfur reduction process for mercury-contaminated wastewater treatment. | Wang J, Hong Y, Lin Z, Zhu C, Da J, Chen G, Jiang F | Water Res | 10.1016/j.watres.2019.05.066 | 2019 | Bioreactors, *Mercury, *Methylmercury Compounds, Sulfur, *Sulfur-Reducing Bacteria, Waste Water |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1577 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4028) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4028 | |||
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) | |||
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 | |
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 | |||
73556 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID93044.1 | StrainInfo: A central database for resolving microbial strain identifiers |