Strain identifier

BacDive ID: 14134

Type strain: Yes

Species: Mucilaginibacter paludis

Strain Designation: TPT56

Strain history: <- S. N. Dedysh, Winogradski Inst. Microbiol., RAS, Moscow, Russia; TPT56 <- T. A. Pankratov

NCBI tax ID(s): 714943 (strain), 423351 (species)

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General

@ref: 7617

BacDive-ID: 14134

DSM-Number: 18603

keywords: genome sequence, 16S sequence, Bacteria, facultative aerobe, heterotroph, mesophilic, Gram-negative, rod-shaped, colony-forming

description: Mucilaginibacter paludis TPT56 is a facultative aerobe, heterotroph, mesophilic bacterium that forms circular colonies and was isolated from sample collected from 10–20 cm below the surface of the Sphagnum peat bog Bakchar.

NCBI tax id

NCBI tax idMatching level
714943strain
423351species

strain history

  • @ref: 7617
  • history: <- S. N. Dedysh, Winogradski Inst. Microbiol., RAS, Moscow, Russia; TPT56 <- T. A. Pankratov

doi: 10.13145/bacdive14134.20230509.8.1

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 paludis
  • full scientific name: Mucilaginibacter paludis Pankratov et al. 2007

@ref: 7617

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Mucilaginibacter

species: Mucilaginibacter paludis

full scientific name: Mucilaginibacter paludis Pankratov et al. 2007 emend. Hahnke et al. 2016

strain designation: TPT56

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32192negative20.75 µm0.65 µmrod-shapedno
28434negative6-15 µm0.5-0.8 µmrod-shapedno
69480negative99.943

colony morphology

  • @ref: 28434
  • colony size: 3-10 mm
  • colony color: light pink to reddish
  • colony shape: circular
  • medium used: 1:10 R2A agar

pigmentation

@refproductionname
32192yes
28434noFlexirubin-Type

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_18603_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7617R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830; with strain-specific modifications) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
284341:10 R2A agaryes

culture temp

@refgrowthtypetemperaturerange
7617positivegrowth25mesophilic
32192positivegrowth02-33
32192positiveoptimum17.5psychrophilic
28434positiveoptimum20-25

culture pH

@refabilitytypepH
32192positivegrowth4.2-8.2
32192positiveoptimum6.2
28434positiveoptimum6-6.5
28434positivegrowth4.2-8.2

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32192facultative aerobe
28434facultative aerobe

nutrition type

  • @ref: 28434
  • type: heterotroph

spore formation

@refspore formationconfidence
32192no
28434no
69481no100
69480no99.703

halophily

@refsaltgrowthtested relationconcentration
32192NaClpositivegrowth0-1 %
32192NaClpositiveoptimum0.5 %
28434NaClpositivegrowth0-1 %(w/v)

observation

  • @ref: 32192
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3219217057cellobiose+carbon source
3219228757fructose+carbon source
3219228260galactose+carbon source
3219217234glucose+carbon source
3219217716lactose+carbon source
3219217306maltose+carbon source
3219237684mannose+carbon source
3219217268myo-inositol+carbon source
32192506227N-acetylglucosamine+carbon source
3219226546rhamnose+carbon source
3219217992sucrose+carbon source
3219227082trehalose+carbon source
3219218222xylose+carbon source
2843430089acetate-assimilation
2843415963ribitol-assimilation
2843458187alginate-hydrolysis
2843422605arabinitol-assimilation
2843418305arbutin-assimilation
2843417968butyrate-assimilation
2843427689decanoate-assimilation
2843485146carboxymethylcellulose-hydrolysis
2843417057cellobiose+builds acid from
2843462968cellulose-hydrolysis
2843417029chitin-hydrolysis
2843437397chondroitin sulfate+hydrolysis
2843416947citrate-assimilation
2843417108D-arabinose-assimilation
2843417057cellobiose+assimilation
2843415824D-fructose+assimilation
2843412931D-galactonate+assimilation
2843412936D-galactose+assimilation
2843417634D-glucose+assimilation
2843417716lactose+assimilation
2843416024D-mannose+assimilation
284346731melezitose-assimilation
2843428053melibiose-assimilation
2843416634raffinose-assimilation
2843463150D-rhamnose+assimilation
2843465327D-xylose+assimilation
2843416813galactitol-assimilation
284344853esculin-hydrolysis
2843428757fructose+builds acid from
284345181fucoidan-hydrolysis
2843429806fumarate-assimilation
2843428260galactose+builds acid from
2843485248gellan gum+hydrolysis
2843417234glucose+fermentation
2843417234glucose+builds acid from
2843428304heparin-hydrolysis
2843415443inulin-assimilation
2843417716lactose+builds acid from
284346364laminarin+hydrolysis
284346364laminarin+builds acid from
2843479285leucrose+assimilation
284346452lichenin-hydrolysis
2843425115malate-assimilation
2843417306maltose+assimilation
2843417306maltose+builds acid from
2843429864mannitol-assimilation
2843437684mannose+builds acid from
2843417268myo-inositol+assimilation
28434506227N-acetylglucosamine+assimilation
2843417272propionate-assimilation
2843427941pullulan+hydrolysis
2843415361pyruvate-assimilation
2843426546rhamnose+builds acid from
2843417814salicin-assimilation
2843430911sorbitol-assimilation
284349215spectinomycin+hydrolysis
2843428017starch+hydrolysis
2843430031succinate-assimilation
2843417992sucrose+assimilation
2843417992sucrose+fermentation
2843417992sucrose+builds acid from
2843427082trehalose+assimilation
2843431011valerate-assimilation
2843437166xylan+hydrolysis
2843437166xylan+builds acid from
2843418222xylose+builds acid from

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
2843417698chloramphenicolyesyes30 µg
2843417076streptomycinyesyes10 µg
284346104kanamycinyesyes30 µg
2843428971ampicillinyesyes10 µg
2843417833gentamicinyesyes10 µg
284346472lincomycinyesyes10 µg
284347507neomycinyesyes10 µg
2843428368novobiocinyesyes10 µg

enzymes

@refvalueactivityec
32192catalase+1.11.1.6
32192cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitude
7617sample collected from 10–20 cm below the surface of the Sphagnum peat bog BakcharSphagnumwestern Siberia, Tomsk region (56° 51' N 82° 50' E)RussiaRUSAsia56.8582.8333
28434sphagnum peat bog Bakcharwestern siberia in the Tomsk RegionRussiaRUSAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Wetland (Swamp)
#Host#Plants#Moss

taxonmaps

  • @ref: 69479
  • File name: preview.99_1909.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_1071;97_1249;98_1500;99_1909&stattab=map
  • Last taxonomy: Mucilaginibacter paludis subclade
  • 16S sequence: AM490402
  • Sequence Identity:
  • Total samples: 582
  • soil counts: 322
  • aquatic counts: 75
  • animal counts: 130
  • plant counts: 55

Safety information

risk assessment

  • @ref: 7617
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7617
  • description: Mucilaginibacter paludis partial 16S rRNA gene, strain TPT56
  • accession: AM490402
  • length: 1406
  • database: ena
  • NCBI tax ID: 714943

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mucilaginibacter paludis DSM 18603GCA_000166195chromosomencbi714943
66792Mucilaginibacter paludis DSM 18603714943.3wgspatric714943
66792Mucilaginibacter paludis TPT56, DSM 186032506520020draftimg714943

GC content

@refGC-contentmethod
761746.1
2843446.1thermal denaturation, midpoint method (Tm)
761742.9sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.409yes
flagellatedno96.678yes
gram-positiveno96.632no
anaerobicno98.405yes
aerobicyes58.088yes
halophileno96.887no
spore-formingno91.756yes
thermophileno99.641yes
glucose-utilyes89.72yes
glucose-fermentno87.318no

External links

@ref: 7617

culture collection no.: DSM 18603, ATCC BAA 1394, VKM B-2446

straininfo link

  • @ref: 83299
  • straininfo: 402696

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/urltitlepubmedID_cross_referencejournal
7617Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18603)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18603
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
2843410.1099/ijs.0.65100-017911309
32192Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128434
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 life28604660 35: 676-683 2017
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
83299Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402696.1StrainInfo: A central database for resolving microbial strain identifiers