Strain identifier

BacDive ID: 14133

Type strain: Yes

Species: Mucilaginibacter gracilis

Strain Designation: TPT18

Strain history: <- S. N. Dedysh, Winogradski Inst. Microbiol., RAS, Moscow, Russia; TPT18 <- T. A. Pankratov

NCBI tax ID(s): 423350 (species)

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General

@ref: 7616

BacDive-ID: 14133

DSM-Number: 18602

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative, rod-shaped

description: Mucilaginibacter gracilis TPT18 is a microaerophile, mesophilic, Gram-negative bacterium that was isolated from 10–20 cm below the surface of the acidic Sphagnum peat bog Bakchar.

NCBI tax id

  • NCBI tax id: 423350
  • Matching level: species

strain history

  • @ref: 7616
  • history: <- S. N. Dedysh, Winogradski Inst. Microbiol., RAS, Moscow, Russia; TPT18 <- T. A. Pankratov

doi: 10.13145/bacdive14133.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Mucilaginibacter
  • species: Mucilaginibacter gracilis
  • full scientific name: Mucilaginibacter gracilis Pankratov et al. 2007

@ref: 7616

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Mucilaginibacter

species: Mucilaginibacter gracilis

full scientific name: Mucilaginibacter gracilis Pankratov et al. 2007

strain designation: TPT18

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32192negative20.75 µm0.45 µmrod-shapedno
69480no90.691
69480negative99.978

pigmentation

  • @ref: 32192
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7616
  • name: TPT 18 MEDIUM (DSMZ Medium 1127)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1127
  • composition: Name: TPT 18 MEDIUM (DSMZ Medium 1127) Composition: Agar 14.0 g/l Glucose 0.5 g/l Casitone 0.1 g/l Yeast extract 0.1 g/l MgSO4 x 7 H2O 0.05 g/l CaCl2 x 2 H2O 0.02 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7616positivegrowth25mesophilic
32192positivegrowth02-33
32192positiveoptimum17.5psychrophilic

culture pH

@refabilitytypepH
32192positivegrowth4.2-8.2
32192positiveoptimum6.2

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7616microaerophile
32192facultative aerobe

spore formation

@refspore formationconfidence
32192no
69481no100
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
32192NaClpositivegrowth0-1 %
32192NaClpositiveoptimum0.5 %

observation

  • @ref: 32192
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3219222599arabinose+carbon source
3219217057cellobiose+carbon source
3219228757fructose+carbon source
3219228260galactose+carbon source
3219217234glucose+carbon source
3219217716lactose+carbon source
3219217306maltose+carbon source
3219215361pyruvate+carbon source
3219216634raffinose+carbon source
3219226546rhamnose+carbon source
3219217814salicin+carbon source
3219217992sucrose+carbon source
3219227082trehalose+carbon source
3219218222xylose+carbon source

enzymes

@refvalueactivityec
32192catalase+1.11.1.6
32192cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 7616
  • sample type: 10–20 cm below the surface of the acidic Sphagnum peat bog Bakchar
  • host species: Sphagnum
  • geographic location: western Siberia, Tomsk region (56° 51' N 82° 50' E)
  • country: Russia
  • origin.country: RUS
  • continent: Asia
  • latitude: 56.85
  • longitude: 82.8333

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Wetland (Swamp)
#Condition#Acidic

taxonmaps

  • @ref: 69479
  • File name: preview.99_27329.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_1071;97_16491;98_20459;99_27329&stattab=map
  • Last taxonomy: Mucilaginibacter gracilis subclade
  • 16S sequence: AM490403
  • Sequence Identity:
  • Total samples: 125
  • soil counts: 69
  • aquatic counts: 14
  • animal counts: 24
  • plant counts: 18

Safety information

risk assessment

  • @ref: 7616
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7616
  • description: Mucilaginibacter gracilis partial 16S rRNA gene, strain TPT18
  • accession: AM490403
  • length: 1451
  • database: ena
  • NCBI tax ID: 423350

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mucilaginibacter gracilis DSM 18602GCA_003633615contigncbi423350
66792Mucilaginibacter gracilis strain DSM 18602423350.3wgspatric423350
66792Mucilaginibacter gracilis DSM 186022775506711draftimg423350

GC content

  • @ref: 32192
  • GC-content: 42.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.252no
anaerobicno99.18yes
halophileno97.526no
spore-formingno93.517no
glucose-utilyes88.718yes
aerobicyes83.328no
flagellatedno96.949no
thermophileno99.401yes
motileno87.833no
glucose-fermentno90.869no

External links

@ref: 7616

culture collection no.: DSM 18602, ATCC BAA 1391, VKM B-2447

straininfo link

  • @ref: 83298
  • straininfo: 398517

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17911309Mucilaginibacter paludis gen. nov., sp. nov. and Mucilaginibacter gracilis sp. nov., pectin-, xylan- and laminarin-degrading members of the family Sphingobacteriaceae from acidic Sphagnum peat bog.Pankratov TA, Tindall BJ, Liesack W, Dedysh SNInt J Syst Evol Microbiol10.1099/ijs.0.65100-02007Aerobiosis, Bacterial Capsules/ultrastructure, Bacterial Typing Techniques, Bacteroidetes/*classification/cytology/*isolation & purification/physiology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Glucans, Hydrogen-Ion Concentration, Locomotion/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pectins/*metabolism, Phylogeny, Polysaccharides/*metabolism, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Siberia, *Soil Microbiology, Sphagnopsida, Temperature, Wetlands, Xylans/*metabolismMetabolism
Phylogeny19648338Mucilaginibacter rigui sp. nov., isolated from wetland freshwater, and emended description of the genus Mucilaginibacter.Baik KS, Park SC, Kim EM, Lim CH, Seong CNInt J Syst Evol Microbiol10.1099/ijs.0.011130-02009Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Fresh Water/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sphingobacterium/*classification/genetics/*isolation & purification/metabolism, WetlandsMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7616Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18602)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18602
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
32192Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2843428776041
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)
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
83298Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398517.1StrainInfo: A central database for resolving microbial strain identifiers