Strain identifier

BacDive ID: 133124

Type strain: Yes

Species: Beggiatoa leptomitoformis

Strain Designation: D-402

Strain history: <- G. A. Dubinina, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; D-402 <- A.S. Savichev {1981}

NCBI tax ID(s): 288004 (species)

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General

@ref: 5613

BacDive-ID: 133124

DSM-Number: 14946

keywords: genome sequence, 16S sequence, Bacteria, chemolithoautotroph, mesophilic, Gram-negative, motile

description: Beggiatoa leptomitoformis D-402 is a chemolithoautotroph, mesophilic, Gram-negative bacterium that was isolated from freshwater spring contaminated with residential and agricultural wastewater.

NCBI tax id

  • NCBI tax id: 288004
  • Matching level: species

strain history

  • @ref: 5613
  • history: <- G. A. Dubinina, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; D-402 <- A.S. Savichev {1981}

doi: 10.13145/bacdive133124.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Beggiatoales
  • family: Beggiatoaceae
  • genus: Beggiatoa
  • species: Beggiatoa leptomitoformis
  • full scientific name: Beggiatoa leptomitoformis Dubinina et al. 2017

@ref: 5613

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Thiotrichales

family: Beggiatoaceae

genus: Beggiatoa

species: Beggiatoa leptomitoformis

full scientific name: Beggiatoa leptomitoformis Dubinina et al. 2017

strain designation: D-402

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityconfidence
25176negative3.5-4.0 µm1.0-2.5 µmyes
69480negative100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5613EGGC (DSMZ Medium 1191)yeshttps://mediadive.dsmz.de/medium/1191Name: EGGC (DSMZ Medium 1191) Composition: Agar 15.0 g/l Glucose 0.6 g/l Casamino acids 0.3 g/l Na-acetate 0.3 g/l Na2HPO4 0.248 g/l NaH2PO4 0.0308 g/l (NH4)2SO4 0.01 g/l MgSO4 x 7 H2O 0.005 g/l KCl 0.005 g/l Thiamine-HCl x 2 H2O 0.0025 g/l Nicotinic acid 0.0025 g/l Pyridoxine hydrochloride 0.0025 g/l Calcium pantothenate 0.0025 g/l CaCl2 x 2 H2O 0.002 g/l CaCO3 0.002 g/l Riboflavin 0.0005 g/l FeCl3 x 6 H2O 5e-05 g/l Vitamin B12 5e-05 g/l Folic acid 1e-05 g/l Biotin 5e-06 g/l Demineralized water
25176agar mediumyescontaining the following (g l-1 distilled water): NaNO3 (0.62); NaH2PO4 (0.125); CaCl2.2H2O (0.03); Na2SO4 (0.5); KCl (0.125);MgCl2.6H2O (0.05); agar (Difco; 15.0); pH 7.2.; Prior to inoculation, the following components were added to 1 litre of the medium as sterile solutions: trace elements and vitamins [16, 17], 1 ml; NaHCO3 , 0.125 g; Na2S2O3.5H2O, 1.0g; sodium lactate, 0.5 g

culture temp

@refgrowthtypetemperaturerange
5613positivegrowth25mesophilic
25176positivegrowth8.0-35.0
25176positiveoptimum28mesophilic

culture pH

@refabilitytypepH
25176positivegrowth6.0-8.2
25176positiveoptimum7.5-7.8

Physiology and metabolism

nutrition type

  • @ref: 25176
  • type: chemolithoautotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.981

halophily

  • @ref: 25176
  • salt: NaCl
  • tested relation: maximum
  • concentration: 0.3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2517630089acetate+growth
2517622210aconitate+growth
2517616449alanine+nitrogen source
2517616449alanine+growth
2517628938ammonium+nitrogen source
2517622599arabinose+growth
2517629016arginine+growth
2517622653asparagine+growth
2517635391aspartate+nitrogen source
2517628885butanol+growth
25176casein hydrolysate+nitrogen source
2517615356cysteine+nitrogen source
2517617376cystine+nitrogen source
2517615824D-fructose+growth
2517617437dimethyl sulfide+oxidation
2517628262dimethyl sulfoxide+oxidation
2517633403elemental sulfur+growth
2517616236ethanol+growth
2517615740formate+growth
2517628260galactose+growth
2517617234glucose+growth
2517629987glutamate+nitrogen source
2517627570histidine+growth
2517624996lactate+growth
2517617716lactose+growth
2517625115malate+growth
2517617306maltose+growth
2517617790methanol+growth
2517616811methionine+nitrogen source
2517617632nitrate+nitrogen source
25176peptone+nitrogen source
25176peptone+growth
2517628044phenylalanine+growth
2517615361pyruvate+growth
2517616634raffinose+growth
2517633942ribose+growth
2517617822serine+nitrogen source
2517617822serine+growth
2517627922sorbose+growth
2517628017starch+hydrolysis
2517630031succinate+growth
2517617992sucrose+growth
2517615138sulfide+growth
2517615226tetrathionate+growth
2517632497thioacetamide+oxidation
2517675184thiodiglycol+oxidation
2517616094thiosulfate+growth
2517615987trithionate+growth
2517627897tryptophan+growth
2517627266valine+growth
2517618222xylose+growth
25176yeast extract+growth

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.
2517628077rifampicinyesyes100 µg/mL
251767507neomycinyesyes10 µg/mL

enzymes

@refvalueactivityec
25176catalase-1.11.1.6
25176cytochrome oxidase+1.9.3.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25176C12:02.3
    25176C12:0 3OH1.1
    25176C14:02.2
    25176C16:015.5
    25176C16:132.9
    25176C18:146.1
  • type of FA analysis: whole cell analysis
  • incubation medium: See reference
  • agar/liquid: agar
  • software version: Sherlock 6.1
  • library/peak naming table: ANAER 6
  • system: MIS MIDI
  • method/protocol: Sasser 1990

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture composition
25176freshwater spring contaminated with residential and agricultural wastewaterMoscow regionRussiaRUSEuropeagar mediumcontaining the following (g l-1 distilled water): NaNO3 (0.62); NaH2PO4 (0.125); CaCl2.2H2O (0.03); Na2SO4 (0.5); KCl (0.125);MgCl2.6H2O (0.05); agar (Difco; 15.0); pH 7.2.; Prior to inoculation, the following components were added to 1 litre of the medium as sterile solutions: trace elements and vitamins [16, 17], 1 ml; NaHCO3 , 0.125 g; Na2S2O3.5H2O, 1.0g; sodium lactate, 0.5 g
5613sulfur mat in a freshwater spring contaminated with residential and agricultural wastewaterMoscow regionRussiaRUSEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Engineered#Waste#Wastewater
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Spring

taxonmaps

  • @ref: 69479
  • File name: preview.99_6494.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16706;96_2716;97_3337;98_4790;99_6494&stattab=map
  • Last taxonomy: Beggiatoa leptomitoformis subclade
  • 16S sequence: AY583996
  • Sequence Identity:
  • Total samples: 371
  • soil counts: 50
  • aquatic counts: 268
  • animal counts: 49
  • plant counts: 4

Safety information

risk assessment

  • @ref: 5613
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
25176Beggiatoa sp. 402 16S ribosomal RNA gene, partial sequenceAY583996.11416nuccore288004
5613Beggiatoa leptomitoformis strain D-402 16S ribosomal RNA gene, partial sequenceAY5839961416ena288004

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Beggiatoa leptomitoformis D-402GCA_001305575completencbi288004
66792Beggiatoa leptomitiformis strain D-402319938.3completepatric288004
66792Beggiatoa leptomitoformis D-4022654588010completeimg288004

GC content

  • @ref: 5613
  • GC-content: 42.1
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno78.344yes
motileno78.344yes
motileno78.344yes
flagellatedno85.748no
flagellatedno85.748no
flagellatedno85.748no
gram-positiveno99.168yes
gram-positiveno99.168yes
gram-positiveno99.168yes
anaerobicno91.459no
anaerobicno91.459no
anaerobicno91.459no
aerobicno74.049no
aerobicno74.049no
aerobicno74.049no
halophileno91.544no
halophileno91.544no
halophileno91.544no
spore-formingno93.561no
spore-formingno93.561no
spore-formingno93.561no
glucose-utilno50.772yes
glucose-utilno50.772yes
glucose-utilno50.772yes
thermophileno92.907yes
thermophileno92.907yes
thermophileno92.907yes
glucose-fermentno88.756no
glucose-fermentno88.756no
glucose-fermentno88.756no

External links

@ref: 5613

culture collection no.: DSM 14946, UNIQEM U 779

straininfo link

  • @ref: 91372
  • straininfo: 397716

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics26659680Complete Genome Sequence of the Freshwater Colorless Sulfur Bacterium Beggiatoa leptomitoformis [corrected] Neotype Strain D-402T.Fomenkov A, Vincze T, Grabovich MY, Dubinina G, Orlova M, Belousova E, Roberts RJGenome Announc10.1128/genomeA.01436-152015
Phylogeny27902215Beggiatoa leptomitoformis sp. nov., the first freshwater member of the genus capable of chemolithoautotrophic growth.Dubinina G, Savvichev A, Orlova M, Gavrish E, Verbarg S, Grabovich MInt J Syst Evol Microbiol10.1099/ijsem.0.0015842017Bacterial Typing Techniques, Base Composition, Beggiatoa/*classification/genetics/isolation & purification, *Chemoautotrophic Growth, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Nucleic Acid Hybridization, Oxidation-Reduction, *Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, Sulfides/chemistryTranscriptome
Genetics29700149Complete Genome Sequence of the Freshwater Bacterium Beggiatoa leptomitoformis Strain D-401.Fomenkov A, Sun Z, Vincze T, Dubinina G, Orlova M, Tarlachkov SV, Anton BP, Grabovich MY, Roberts RJGenome Announc10.1128/genomeA.00311-182018
Genetics30262951Genomics and Biochemistry of Metabolic Pathways for the C1 Compounds Utilization in Colorless Sulfur Bacterium Beggiatoa leptomitoformis D-402.Orlova MV, Tarlachkov SV, Kulinchenko EI, Dubinina GA, Tutukina MN, Grabovich MYIndian J Microbiol10.1007/s12088-018-0737-x2018
Genetics32575621Comparative Genomics of Beggiatoa leptomitoformis Strains D-401 and D-402(T) with Contrasting Physiology but Extremely High Level of Genomic Identity.Rudenko TS, Tarlachkov SV, Shatskiy ND, Grabovich MYMicroorganisms10.3390/microorganisms80609282020Physiology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5613Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14946)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14946
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
25176G. S. Dubinina, A.,Orlova, M.,Gavrish, E.,Verbarg, S.,Grabovich, M.10.1099/ijsem.0.001584Beggiatoa leptomitoformis sp. nov., the first freshwater member of the genus capable of chemolithoautotrophic growthIJSEM 67: 197-204 201727902215
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)
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
91372Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397716.1StrainInfo: A central database for resolving microbial strain identifiers