Strain identifier

BacDive ID: 133072

Type strain: Yes

Species: Desulfobulbus oligotrophicus

Strain Designation: Prop6

Strain history: A. Ranchou-Peyruse; Univ. of Pau & Pays de l'Adour, France; Prop6.

NCBI tax ID(s): 1909699 (species)

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General

@ref: 24860

BacDive-ID: 133072

DSM-Number: 103420

keywords: genome sequence, 16S sequence, Bacteria, obligate anaerobe, mesophilic, Gram-negative, motile, oval-shaped

description: Desulfobulbus oligotrophicus Prop6 is an obligate anaerobe, mesophilic, Gram-negative bacterium that was isolated from municipal mesophilic anaerobic sewage sludge digester.

NCBI tax id

  • NCBI tax id: 1909699
  • Matching level: species

strain history

@refhistory
24860<- A. Ranchou-Peyruse, Université de Pau et des Pays de l'Adour, Pau, France; Prop6 <- A. El Houari and A. I. Qatibi {2015}
67770A. Ranchou-Peyruse; Univ. of Pau & Pays de l'Adour, France; Prop6.

doi: 10.13145/bacdive133072.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfobacterales
  • family: Desulfobulbaceae
  • genus: Desulfobulbus
  • species: Desulfobulbus oligotrophicus
  • full scientific name: Desulfobulbus oligotrophicus El Houari et al. 2017

@ref: 24860

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfobacterales

family: Desulfobulbaceae

genus: Desulfobulbus

species: Desulfobulbus oligotrophicus

full scientific name: Desulfobulbus oligotrophicus El Houari et al. 2017

strain designation: Prop6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
25179negative1.6-2.2 µm0.9-1.0 µmoval-shapedyesamphitrichous
69480yes92.82
69480negative99.957

colony morphology

  • @ref: 25179
  • colony size: 0.5-1.0 mm
  • colony color: brown
  • incubation period: 49-54 days
  • medium used: basal medium (agar roll-tubes)

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
25179basal medium (agar roll-tubes)yescontaining 1 % (w/v) glucose, 1 % (w/v) casamino acids, 1 % (w/v) peptone, 1 % (w/v) yeast extract supplemented with 20 mM propionate and 20 mM sulfate and 1 % (w/v) biotrypticase
24860DESULFOBULBUS SP. MEDIUM (FRESHWATER) (DSMZ Medium 194)yesName: DESULFOBULBUS SP. MEDIUM (FRESHWATER) (DSMZ Medium 194) Composition: Na2SO4 2.99103 g/l Na2CO3 1.49551 g/l Na-propionate 1.49551 g/l NaCl 0.997009 g/l KCl 0.498504 g/l MgCl2 x 6 H2O 0.398804 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled waterhttps://mediadive.dsmz.de/medium/194

culture temp

@refgrowthtypetemperaturerange
25179positiveoptimum35mesophilic
24860positivegrowth35mesophilic
67770positivegrowth35mesophilic

culture pH

  • @ref: 25179
  • ability: positive
  • type: optimum
  • pH: 7.6

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
25179obligate anaerobe
69480anaerobe98.648

spore formation

@refspore formationconfidence
25179no
69481no100
69480no99.986

halophily

  • @ref: 25179
  • salt: NaCl
  • tested relation: optimum
  • concentration: 2.0-5.0 g/L

observation

  • @ref: 67770
  • observation: quinones: MK-5(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25179169971,2-propandiol-carbon source
251791,4-propandiol-carbon source
25179356862-butanol-carbon source
25179620642,3-butanediol-carbon source
251792,4-butanediol-carbon source
2517930089acetate-carbon source
2517915347acetone-carbon source
2517916449alanine-carbon source
2517929016arginine-carbon source
2517935391aspartate-carbon source
2517916150benzoate-carbon source
2517928885butanol-carbon source
2517917968butyrate-carbon source
25179casamino acids-carbon source
2517917057cellobiose-carbon source
2517916947citrate-carbon source
2517935899crotonate-carbon source
2517916236ethanol-carbon source
2517916236ethanol-fermentation
2517916236ethanol-electron donor
2517930742ethylene glycol-carbon source
2517929034ferric iron-electron acceptor
2517915740formate-carbon source
2517928757fructose-carbon source
2517929806fumarate-carbon source
2517929806fumarate-fermentation
2517929806fumarate-electron donor
2517928260galactose-carbon source
2517924265gluconate-carbon source
2517917234glucose-carbon source
2517929987glutamate-carbon source
2517917754glycerol-carbon source
2517915428glycine-carbon source
2517929805glycolate-carbon source
251797896hexadecanoate-carbon source
2517917716lactose-carbon source
2517925017leucine-carbon source
2517925115malate-carbon source
2517925115malate-fermentation
2517925115malate-electron donor
2517937684mannose-carbon source
2517917790methanol-carbon source
2517916811methionine-carbon source
2517917632nitrate-electron acceptor
2517925629octadecanoate-carbon source
2517925646octanoate-carbon source
2517944884pentanol-carbon source
25179peptone-carbon source
2517915882phenol-carbon source
2517928831propanol-carbon source
2517928831propanol-fermentation
2517928831propanol-electron donor
25179178242-propanol-carbon source
2517916109propane-1,3-diol-carbon source
2517917272propionate-fermentation
2517933942ribose-carbon source
2517917822serine-carbon source
2517930031succinate-carbon source
2517917992sucrose-carbon source
25179132950tartrate-carbon source
2517932497thioacetamide-carbon source
2517931011valerate-carbon source
2517927266valine-carbon source
25179yeast extract-carbon source
2517930089acetate+carbon source
2517924996lactate+oxidation
2517924996lactate+fermentation
2517924996lactate+electron donor
2517917272propionate+oxidation
2517917272propionate+electron donor
2517915361pyruvate+oxidation
2517915361pyruvate+fermentation
2517915361pyruvate+electron donor
2517916189sulfate+electron acceptor
2517917359sulfite+electron acceptor
2517916094thiosulfate+electron acceptor

enzymes

@refvalueactivityec
25179catalase+1.11.1.6
25179cytochrome oxidase+1.9.3.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25179C14:08.7
    25179C15:02.2
    25179C16:017
    25179C16:1ω59.9
    25179C16:1ω77.2
    25179C17:1ω69
    25179C18:01.2
    25179C18:1ω741.9
  • type of FA analysis: whole cell analysis
  • incubation medium: basal medium
  • incubation temperature: 35
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
24860municipal mesophilic anaerobic sewage sludge digesterMarrakechMoroccoMARAfrica
25179February 2015basal mediumcontaining 1 % (w/v) glucose, 1 % (w/v) casamino acids, 1 % (w/v) peptone, 1 % (w/v) yeast extract supplemented with 20 mM propionate and 20 mM sulfate and 1 % (w/v) biotrypticase28-35 days35
67770Municipal mesophilic anaerobic sewage sludge digester of the wastewater treatment plantMarrakechMoroccoMARAfrica

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Anaerobic digestor
#Engineered#Waste#Sewage sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_133863.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_128;96_43415;97_55568;98_73559;99_133863&stattab=map
  • Last taxonomy: Desulfobulbus oligotrophicus subclade
  • 16S sequence: KU845305
  • Sequence Identity:
  • Total samples: 113
  • soil counts: 4
  • aquatic counts: 79
  • animal counts: 18
  • plant counts: 12

Safety information

risk assessment

  • @ref: 24860
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24860
  • description: Desulfobulbus oligotrophicus strain Prop6 16S ribosomal RNA gene, partial sequence
  • accession: KU845305
  • length: 1385
  • database: ena
  • NCBI tax ID: 1909699

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Desulfobulbus oligotrophicus Prop6GCA_016446285completencbi1909699
66792Desulfobulbus oligotrophicus strain Prop61909699.3completepatric1909699

GC content

@refGC-contentmethod
2486051.7high performance liquid chromatography (HPLC)
6777051.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno86.458no
gram-positiveno99.086yes
anaerobicyes98.699yes
aerobicno97.555yes
halophileno90.976no
spore-formingno91.965yes
thermophileno89.161yes
glucose-utilno84.288yes
motileyes82.646yes
glucose-fermentno85.445no

External links

@ref: 24860

culture collection no.: DSM 103420, JCM 31535

straininfo link

  • @ref: 91337
  • straininfo: 396983

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27902225Desulfobulbus oligotrophicus sp. nov., a sulfate-reducing and propionate-oxidizing bacterium isolated from a municipal anaerobic sewage sludge digester.El Houari A, Ranchou-Peyruse M, Ranchou-Peyruse A, Dakdaki A, Guignard M, Idouhammou L, Bennisse R, Bouterfass R, Guyoneaud R, Qatibi AIInt J Syst Evol Microbiol10.1099/ijsem.0.0016152017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Deltaproteobacteria/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Morocco, Oxidation-Reduction, *Phylogeny, Propionates/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sulfur-Reducing Bacteria/classification/genetics/isolation & purificationEnzymology
Genetics33541869Complete Genome Sequence of Desulfobulbus oligotrophicus Prop6, an Anaerobic Deltabacterota Strain That Lacks Mercury Methylation Capability.Podar PT, Peyton K, Soren A, Wilpiszeski RL, Gilmour CC, Elias DA, Podar MMicrobiol Resour Announc10.1128/MRA.00002-212021

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24860Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103420Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103420)
25179A. R.-P. El Houari, M.,Ranchou-Peyruse, A.,Dakdaki, A.,Guignard, M.,Idouhammou, L.,Bennisse, R.,Bouterfass, R.,Guyoneaud, R.,Qatibi, A. I.Desulfobulbus oligotrophicus sp. nov., a sulfate-reducing and propionate-oxidizing bacterium isolated from a municipal anaerobic sewage sludge digester10.1099/ijsem.0.001615IJSEM 67: 275-281 201727902225
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91337Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID396983.1