Strain identifier

BacDive ID: 24814

Type strain: Yes

Species: Chthoniobacter flavus

Strain Designation: Ellin428

Strain history: <- M. Sait, Dept. Molecular Biology, Univ. Wyoming, Laramie, USA <- P. H. Janssen; Ellin428

NCBI tax ID(s): 191863 (species)

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General

@ref: 21325

BacDive-ID: 24814

DSM-Number: 22515

keywords: genome sequence, 16S sequence, Bacteria, aerobe, heterotroph, mesophilic, Gram-negative, oval-shaped

description: Chthoniobacter flavus Ellin428 is an aerobe, heterotroph, mesophilic bacterium that was isolated from pasture soil.

NCBI tax id

  • NCBI tax id: 191863
  • Matching level: species

strain history

  • @ref: 21325
  • history: <- M. Sait, Dept. Molecular Biology, Univ. Wyoming, Laramie, USA <- P. H. Janssen; Ellin428

doi: 10.13145/bacdive24814.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/verrucomicrobiota
  • domain: Bacteria
  • phylum: Verrucomicrobiota
  • class: Terrimicrobiia
  • order: Terrimicrobiales
  • family: Chthoniobacteraceae
  • genus: Chthoniobacter
  • species: Chthoniobacter flavus
  • full scientific name: Chthoniobacter flavus Sangwan et al. 2004

@ref: 21325

domain: Bacteria

phylum: Verrucomicrobia

class: Terrimicrobia

order: Spartobacteria, not assigned to order

family: Chthoniobacteraceae

genus: Chthoniobacter

species: Chthoniobacter flavus

full scientific name: Chthoniobacter flavus Sangwan et al. 2004

strain designation: Ellin428

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43403negative1.4 µm0.9 µmoval-shapedno
69480negative99.993

colony morphology

  • @ref: 43403
  • colony size: 4 mm
  • colony color: Yellow
  • medium used: VL55 (liquid media)

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
43403VL55 (liquid media)yes1.95 g of 2-[N-morpholino]ethanesulfonic acid, 0.2 mmol MgSO4, 0.3 mmol CaCl2, 0.2 mmol (NH 4) 2HPO4, 1 ml of selenite-tungstate solution (50), 1 ml of trace element solution SL-10 (55) per liter, and the pH was adjusted to 5.5
43403full strength and 1/100-strength nutrient agaryes
43403full strength and 1/10-strength Trypticase soy agaryes
43403Reasoner's 2A agar (R2A)yes
43403cold-extracted soil extract agaryes
43403Winogradsky's sal solution agaryes
21325MEDIUM VL55 (DSMZ Medium 1266)yesName: MEDIUM VL55 (DSMZ Medium 1266) Composition: MES 1.9403 g/l FeCl2 x 4 H2O 0.00149254 g/l NaOH 0.000497512 g/l CoCl2 x 6 H2O 0.000189055 g/l Pyridoxamine hydrochloride 0.000149254 g/l MnCl2 x 4 H2O 9.95025e-05 g/l Nicotinic acid 9.85075e-05 g/l Thiamine-HCl x 2 H2O 9.85075e-05 g/l ZnCl2 6.96517e-05 g/l Vitamin B12 5.07463e-05 g/l Hemicalcium D-(+)-pantothenate 5.07463e-05 g/l 4-aminobenzoate 3.8806e-05 g/l Na2MoO4 x 2 H2O 3.58209e-05 g/l Riboflavin 2.98507e-05 g/l DL-6,8-thioctic acid 2.98507e-05 g/l NiCl2 x 6 H2O 2.38806e-05 g/l Folic acid 1.19403e-05 g/l Biotin 8.95522e-06 g/l H3BO3 5.97015e-06 g/l Na2WO4 x 2 H2O 3.9801e-06 g/l Na2SeO3 x 5 H2O 2.98507e-06 g/l CuCl2 x 2 H2O 1.99005e-06 g/l HCl (NH4)2HPO4 CaCl2 x 2 H2O MgSO4 x 7 H2O Glucose Distilled waterhttps://mediadive.dsmz.de/medium/1266

culture temp

@refgrowthtypetemperaturerange
21325positivegrowth25mesophilic
43403nogrowth37mesophilic
43403positivegrowth34mesophilic
43403positivegrowth30mesophilic
43403positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
43403positivegrowth4-7acidophile
43403nogrowth7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43403
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 43403
  • type: heterotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.582

halophily

@refsaltgrowthtested relationconcentration
43403NaClpositivegrowth5 g/L
43403NaClnogrowth10 g/L

observation

  • @ref: 43403
  • observation: does not appear able to grow with amino acids or organic acids other than pyruvate

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4340330089acetate-growth
4340330089acetate-carbon source
4340330089acetate-energy source
4340316449alanine-growth
4340316449alanine-carbon source
4340316449alanine-energy source
4340358187alginate+aerobic growth
4340322599arabinose-growth
4340322599arabinose-carbon source
4340322599arabinose-energy source
4340329016arginine-growth
4340329016arginine-carbon source
4340329016arginine-energy source
4340335391aspartate-growth
4340335391aspartate-carbon source
4340335391aspartate-energy source
4340316150benzoate-growth
4340316150benzoate-carbon source
4340316150benzoate-energy source
4340317750betaine-growth
4340317750betaine-carbon source
4340317750betaine-energy source
4340328885butanol-growth
4340328885butanol-carbon source
4340328885butanol-energy source
4340317968butyrate-growth
4340317968butyrate-carbon source
4340317968butyrate-energy source
4340318135catechol-growth
4340318135catechol-carbon source
4340318135catechol-energy source
4340317057cellobiose+aerobic growth
4340362968cellulose+aerobic growth
4340316947citrate-growth
4340316947citrate-carbon source
4340316947citrate-energy source
4340325115malate-growth
4340325115malate-carbon source
4340325115malate-energy source
4340316236ethanol-growth
4340316236ethanol-carbon source
4340316236ethanol-energy source
4340315740formate-growth
4340315740formate-carbon source
4340315740formate-energy source
4340328757fructose+aerobic growth
4340329806fumarate-growth
4340329806fumarate-carbon source
4340329806fumarate-energy source
4340328260galactose+aerobic growth
4340324175galacturonate+aerobic growth
4340317234glucose-anaerobic growth
4340317234glucose+aerobic growth
4340324297glucuronate+aerobic growth
4340329987glutamate-growth
4340329987glutamate-carbon source
4340329987glutamate-energy source
4340317754glycerol-growth
4340317754glycerol-carbon source
4340317754glycerol-energy source
4340315428glycine-growth
4340315428glycine-carbon source
4340315428glycine-energy source
4340329805glycolate-growth
4340329805glycolate-carbon source
4340329805glycolate-energy source
4340324996lactate-growth
4340324996lactate-carbon source
4340324996lactate-energy source
4340317716lactose+aerobic growth
4340325017leucine-growth
4340325017leucine-carbon source
4340325017leucine-energy source
4340325094lysine-growth
4340325094lysine-carbon source
4340325094lysine-energy source
4340315792malonate-growth
4340315792malonate-carbon source
4340315792malonate-energy source
4340329864mannitol-growth
4340329864mannitol-carbon source
4340329864mannitol-energy source
4340337684mannose+aerobic growth
4340317790methanol-growth
4340317790methanol-carbon source
4340317790methanol-energy source
4340317309pectin+aerobic growth
4340328831propanol-growth
4340328831propanol-carbon source
4340328831propanol-energy source
4340317272propionate-growth
4340317272propionate-carbon source
4340317272propionate-energy source
4340315361pyruvate+aerobic growth
4340333942ribose-growth
4340333942ribose-carbon source
4340333942ribose-energy source
4340317822serine-growth
4340317822serine-carbon source
4340317822serine-energy source
4340328017starch+aerobic growth
4340330031succinate-growth
4340330031succinate-carbon source
4340330031succinate-energy source
4340317992sucrose+aerobic growth
4340330929tartrate-growth
4340330929tartrate-carbon source
4340330929tartrate-energy source
4340326986threonine-growth
4340326986threonine-carbon source
4340326986threonine-energy source
4340316199urea-growth
4340316199urea-carbon source
4340316199urea-energy source
4340327266valine-growth
4340327266valine-carbon source
4340327266valine-energy source
4340316632vanillate-growth
4340316632vanillate-carbon source
4340316632vanillate-energy source
4340337166xylan+aerobic growth
4340318222xylose+aerobic growth

enzymes

@refvalueactivityec
43403catalase-1.11.1.6
43403cytochrome oxidase-1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
21325pasture soilVictoria, EllinbankAustraliaAUSAustralia and Oceania
43403a rye grass and clover pasture soilVictoriaAustraliaAUSAustralia and Oceania-37144.984

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Grassland
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2198.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_301;96_1195;97_1409;98_1715;99_2198&stattab=map
  • Last taxonomy: Chthoniobacter flavus subclade
  • 16S sequence: AY388649
  • Sequence Identity:
  • Total samples: 1009
  • soil counts: 845
  • aquatic counts: 77
  • animal counts: 10
  • plant counts: 77

Sequence information

16S sequences

  • @ref: 21325
  • description: Bacterium Ellin428 16S ribosomal RNA gene, partial sequence
  • accession: AY388649
  • length: 1360
  • database: ena
  • NCBI tax ID: 497964

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chthoniobacter flavus DSM 22515GCA_004341915scaffoldncbi191863
66792Chthoniobacter flavus Ellin428GCA_000173075scaffoldncbi497964
66792Chthoniobacter flavus Ellin428497964.5wgspatric497964
66792Chthoniobacter flavus strain DSM 22515191863.3wgspatric191863
66792Chthoniobacter flavus DSM 225152795385450draftimg191863
66792Chthoniobacter flavus Ellin428642791618draftimg497964

GC content

  • @ref: 43403
  • GC-content: 60.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.307no
flagellatedno95.856no
gram-positiveno95.715yes
anaerobicno98.738yes
aerobicyes85.069yes
halophileno93.636yes
spore-formingno91.68no
thermophileno99.448yes
glucose-utilyes88.996no
glucose-fermentno84.025no

External links

@ref: 21325

culture collection no.: DSM 22515

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15466527Chthoniobacter flavus gen. nov., sp. nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia.Sangwan P, Chen X, Hugenholtz P, Janssen PHAppl Environ Microbiol10.1128/AEM.70.10.5875-5881.20042004Bacteria/*classification/genetics/*isolation & purification/metabolism, Base Composition, Base Sequence, DNA, Bacterial/chemistry/genetics, Genes, Bacterial, Microscopy, Electron, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Species SpecificityGenetics
Genetics21460085Genome sequence of Chthoniobacter flavus Ellin428, an aerobic heterotrophic soil bacterium.Kant R, van Passel MW, Palva A, Lucas S, Lapidus A, Glavina del Rio T, Dalin E, Tice H, Bruce D, Goodwin L, Pitluck S, Larimer FW, Land ML, Hauser L, Sangwan P, de Vos WM, Janssen PH, Smidt HJ Bacteriol10.1128/JB.00295-112011Amino Acids/metabolism, Bacteria/*genetics/growth & development/isolation & purification/metabolism, Carboxylic Acids/metabolism, DNA, Bacterial/*chemistry/*genetics, *Genome, Bacterial, Molecular Sequence Data, Polysaccharides/metabolism, *Sequence Analysis, DNA, Soil MicrobiologyMetabolism

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
21325Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-22515Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22515)
43403Parveen Sangwan, Xiaolei Chen, Philip Hugenholtz, Peter H. JanssenChthoniobacter flavus gen. nov., sp. nov., the First Pure-Culture Representative of Subdivision Two, Spartobacteria classis nov., of the Phylum Verrucomicrobia10.1128/AEM.70.10.5875-5881.2004Appl. Environ. Microbiol. 70: 5875-5881 200415466527
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
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