Strain identifier

BacDive ID: 4051

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
899species
525897strain

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

    @refsynonym
    20215Desulfomicrobium baculatus
    20215Desulfovibrio 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

@refmotilityconfidencegram stain
69480yes96.713
6948099.992negative

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

@refoxygen toleranceconfidence
1577anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
69481no100
69480no99.997

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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Desulfomicrobium baculatum 16S ribosomal RNA gene, complete sequenceAF0304381540ena525897
20218Desulfomicrobium baculatum 16S rRNA gene, strain DSM 4028TAJ2778941517ena525897
20218Desulfomicrobium baculatum DSM 4028 16S ribosomal RNA gene, partial sequenceJX293692225ena525897

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Desulfomicrobium baculatum DSM 4028GCA_000023225completencbi525897
66792Desulfomicrobium baculatum DSM 4028525897.5completepatric525897
66792Desulfomicrobium baculatum X, DSM 4028644736350completeimg525897

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.569no
flagellatedyes52.187no
gram-positiveno98.836no
anaerobicyes98.717yes
aerobicno98.443no
halophileno80.891no
spore-formingno94.568no
thermophileno97.511yes
glucose-utilno67.818no
glucose-fermentno79.791no

External links

@ref: 1577

culture collection no.: DSM 4028, VKM B-1378, CCUG 34229

straininfo link

  • @ref: 73556
  • straininfo: 93044

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25792369Desulfoplanes 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 MInt J Syst Evol Microbiol10.1099/ijs.0.0001972015Bacterial 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 & purificationEnzymology
31154126A novel biological sulfur reduction process for mercury-contaminated wastewater treatment.Wang J, Hong Y, Lin Z, Zhu C, Da J, Chen G, Jiang FWater Res10.1016/j.watres.2019.05.0662019Bioreactors, *Mercury, *Methylmercury Compounds, Sulfur, *Sulfur-Reducing Bacteria, Waste Water

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1577Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4028)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4028
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
73556Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID93044.1StrainInfo: A central database for resolving microbial strain identifiers