Strain identifier

BacDive ID: 12496

Type strain: Yes

Species: Paludibacter propionicigenes

Strain history: A. Ueki WB4.

NCBI tax ID(s): 694427 (strain), 185300 (species)

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General

@ref: 6835

BacDive-ID: 12496

DSM-Number: 17365

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

description: Paludibacter propionicigenes DSM 17365 is an anaerobe, chemoorganotroph, mesophilic bacterium that was isolated from rice plant residue.

NCBI tax id

NCBI tax idMatching level
185300species
694427strain

strain history

@refhistory
6835<- A. Ueki
67770A. Ueki WB4.

doi: 10.13145/bacdive12496.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Paludibacteraceae
  • genus: Paludibacter
  • species: Paludibacter propionicigenes
  • full scientific name: Paludibacter propionicigenes Ueki et al. 2006

@ref: 6835

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Paludibacteraceae

genus: Paludibacter

species: Paludibacter propionicigenes

full scientific name: Paludibacter propionicigenes Ueki et al. 2006

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31612negative1.3-1.7 µm0.5-0.6 µmrod-shapedno
27900negative1.3-1.7 µm0.5-0.6 µmrod-shapedno

colony morphology

  • @ref: 6835
  • type of hemolysis: gamma
  • incubation period: 3-7 days

pigmentation

  • @ref: 31612
  • production: yes

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_17365_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 6835
  • name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104
  • composition: Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
6835positivegrowth30mesophilic
31612positivegrowth15-35
31612positiveoptimum30mesophilic
27900positiveoptimum30mesophilic
27900positivegrowth15-35
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
31612positivegrowth5-7.6
31612positiveoptimum6.6
27900positivegrowth5.0-7.6
27900positiveoptimum6.6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6835anaerobe
31612anaerobe
27900obligate anaerobe

nutrition type

  • @ref: 27900
  • type: chemoorganotroph

spore formation

@refspore formation
31612no
27900no

halophily

@refsaltgrowthtested relationconcentration
31612NaClpositivegrowth0-0.5 %
31612NaClpositiveoptimum0-0.5 %
27900NaClpositivegrowth0-0.5 %(w/v)

observation

@refobservation
31612aggregates in chains
27900growth in presence of bile salts
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3161222599arabinose+carbon source
3161217057cellobiose+carbon source
3161228757fructose+carbon source
3161228260galactose+carbon source
3161217234glucose+carbon source
3161228087glycogen+carbon source
3161217306maltose+carbon source
3161237684mannose+carbon source
3161228053melibiose+carbon source
3161218222xylose+carbon source
2790022599arabinose+growth
2790022599arabinose+builds acid from
2790017057cellobiose+growth
2790017057cellobiose+builds acid from
2790062968cellulose-growth
2790062968cellulose-degradation
2790016813galactitol-growth
279004853esculin+hydrolysis
2790016236ethanol-growth
2790028757fructose+growth
2790028757fructose+builds acid from
2790029806fumarate-growth
2790028260galactose+growth
2790028260galactose+builds acid from
279005291gelatin-
2790017234glucose+growth
2790017234glucose+builds acid from
2790017754glycerol-growth
2790028087glycogen+growth
2790028087glycogen+builds acid from
2790017268myo-inositol-growth
2790024996lactate-growth
2790017716lactose-growth
2790025115malate-growth
2790017306maltose+growth
2790017306maltose+builds acid from
2790029864mannitol-growth
2790037684mannose+growth
2790037684mannose+builds acid from
279006731melezitose-growth
2790028053melibiose+growth
2790028053melibiose+builds acid from
2790015361pyruvate-growth
2790016634raffinose-growth
2790026546rhamnose-growth
2790033942ribose-growth
2790017814salicin-growth
2790030911sorbitol-growth
2790027922sorbose-growth
2790028017starch+growth
2790028017starch+builds acid from
2790030031succinate-growth
2790017992sucrose-growth
2790027082trehalose-growth
2790037166xylan-growth
2790018222xylose+growth
2790018222xylose+builds acid from
6838016199urea-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
2790030089acetateyes
2790017272propionateyes
2790016136hydrogen sulfideno
2790035581indoleno
6838035581indoleno

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
27900urease-3.5.1.5
68380serine arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase+3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
6835-+/-+++/--++-+------+--+----+----
6835--+++-++-+------+--+----+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
6835rice plant residueYamagataJapanJPNAsia38.25140.34
27900rice plant residue (rice straw) sample collected from irrigated rice field soil in the Shonai Brach of the Yamagata Agricultural Experimental Station (Fujishima-machi, Yamagata)JapanJapanJPNAsia
60057Soil,rice plant residue in anoxic rice fieldJapanJPNAsia
67770Rice plant residue in anoxic rice-field soilJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Environmental#Terrestrial#Wetland (Swamp)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2130.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_297;96_1166;97_1370;98_1664;99_2130&stattab=map
  • Last taxonomy: Paludibacter propionicigenes subclade
  • 16S sequence: AB910740
  • Sequence Identity:
  • Total samples: 22588
  • soil counts: 846
  • aquatic counts: 3218
  • animal counts: 18145
  • plant counts: 379

Safety information

risk assessment

  • @ref: 6835
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paludibacter propionicigenes gene for 16S ribosomal RNA, partial sequenceAB9107401489ena185300
6835Paludibacter propionicigenes gene for 16S ribosomal RNA, partial sequenceAB0788421447ena694427

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paludibacter propionicigenes WB4, DSM 17365649633080completeimg694427
67770Paludibacter propionicigenes WB4GCA_000183135completencbi694427

GC content

@refGC-contentmethod
3161239.3
2790039.3high performance liquid chromatography (HPLC)

External links

@ref: 6835

culture collection no.: DSM 17365, JCM 13257, CCUG 53888, WB 4

straininfo link

  • @ref: 81715
  • straininfo: 289869

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16403864Paludibacter propionicigenes gen. nov., sp. nov., a novel strictly anaerobic, Gram-negative, propionate-producing bacterium isolated from plant residue in irrigated rice-field soil in Japan.Ueki A, Akasaka H, Suzuki D, Ueki KInt J Syst Evol Microbiol10.1099/ijs.0.63896-02006Agriculture, Base Composition, Fatty Acids, Gram-Negative Anaerobic Bacteria/chemistry/*classification/isolation & purification/physiology, Molecular Sequence Data, Propionates/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species Specificity, TemperatureGenetics
Genetics21475585Complete genome sequence of Paludibacter propionicigenes type strain (WB4).Gronow S, Munk C, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Rohde M, Goker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HPStand Genomic Sci10.4056/sigs.15038462011

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6835Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17365)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17365
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
2790010.1099/ijs.0.63896-016403864
31612Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127900
60057Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53888)https://www.ccug.se/strain?id=53888
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 life 35: 676-683 201728604660
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
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
81715Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID289869.1StrainInfo: A central database for resolving microbial strain identifiers