Strain identifier

BacDive ID: 12558

Type strain: Yes

Species: Prevotella paludivivens

Strain Designation: KB7

Strain history: A. Ueki KB7.

NCBI tax ID(s): 185294 (species)

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General

@ref: 7300

BacDive-ID: 12558

DSM-Number: 17968

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

description: Prevotella paludivivens KB7 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from soil, flooded rice field.

NCBI tax id

  • NCBI tax id: 185294
  • Matching level: species

strain history

@refhistory
7300<- A. Ueki; KB7
67770A. Ueki KB7.

doi: 10.13145/bacdive12558.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Prevotellaceae
  • genus: Prevotella
  • species: Prevotella paludivivens
  • full scientific name: Prevotella paludivivens Ueki et al. 2007

  • synonyms

    • @ref: 20215
    • synonym: Segatella paludivivens

@ref: 7300

domain: Bacteria

phylum: Not assigned to order

class: Not assigned to order

order: Not assigned to order

family: Not assigned to family

genus: Segatella

species: Segatella paludivivens

full scientific name: Segatella paludivivens (Ueki et al. 2007) Hitch et al. 2023

strain designation: KB7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32071negative1.7 µm0.75 µmrod-shapedno
125438negative93.859
125439negative99.8

colony morphology

  • @ref: 7300
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7300PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: 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
7300COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

culture temp

@refgrowthtypetemperature
7300positivegrowth30
32071positivegrowth10-40
32071positiveoptimum30
67770positivegrowth30

culture pH

@refabilitytypepH
32071positivegrowth4.7-7.6
32071positiveoptimum6.2

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7300anaerobe
32071anaerobe
125438anaerobe91.732

spore formation

@refspore formationconfidence
32071no
125439no99.6

halophily

@refsaltgrowthtested relationconcentration
32071NaClpositivegrowth0.0-1.0 %
32071NaClpositiveoptimum0.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-11(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3207122599arabinose+carbon source
3207117057cellobiose+carbon source
3207128757fructose+carbon source
3207128260galactose+carbon source
3207117234glucose+carbon source
3207117716lactose+carbon source
3207117306maltose+carbon source
3207137684mannose+carbon source
3207126546rhamnose+carbon source
3207133942ribose+carbon source
3207117814salicin+carbon source
3207117992sucrose+carbon source
3207118222xylose+carbon source
6838027897tryptophan-energy source
6838017632nitrate-reduction
6838016024D-mannose-fermentation
6838016199urea-hydrolysis
6838016634raffinose-fermentation
6838029016arginine-hydrolysis

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
68380serine arylamidase-
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380glutamyl-glutamate 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
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase+3.2.1.55
68380beta-galactosidase+3.2.1.23
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
7300--+++/-+++-+------+--+----+--+-
7300--++-+++-+------+--+----+--+-
7300--++-+++-+------+--+----+--+-
7300---+-+++-+/---+---+--+----+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7300soil, flooded rice fieldYamagataJapanJPNAsia
67770Rice plant residue in flooded rice-field soil

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Aquatic
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3700.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_44;96_1908;97_2295;98_2827;99_3700&stattab=map
  • Last taxonomy: Prevotella paludivivens subclade
  • 16S sequence: AB547704
  • Sequence Identity:
  • Total samples: 20621
  • soil counts: 284
  • aquatic counts: 2106
  • animal counts: 18111
  • plant counts: 120

Safety information

risk assessment

  • @ref: 7300
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Prevotella paludivivens gene for 16S ribosomal RNA, partial sequence, strain: JCM 13650AB5477041491nuccore185294
7300Prevotella paludivivens gene for 16S ribosomal RNA, partial sequence, strain: KB7AB0788271418nuccore185294

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Prevotella paludivivens DSM 179681122990.3wgspatric1122990
66792Prevotella paludivivens JCM 136501236488.3wgspatric1122990
66792Prevotella paludivivens JCM 136502585427906draftimg1122990
66792Prevotella paludivivens DSM 179682515154072draftimg1122990
67770Prevotella paludivivens DSM 17968 = JCM 13650GCA_000373185scaffoldncbi1122990
67770Prevotella paludivivens DSM 17968 = JCM 13650GCA_000613605contigncbi1122990

GC content

@refGC-contentmethod
730039.2
730037.3sequence analysis
6777039.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthfacultative aerobe64.8
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.8
125439BacteriaNetmotilityAbility to perform movementno70.4
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.6
125438gram-positivegram-positivePositive reaction to Gram-stainingno93.859yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes91.732yes
125438spore-formingspore-formingAbility to form endo- or exosporesno89.955yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no96.343yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.996yes
125438motile2+flagellatedAbility to perform flagellated movementno87yes

External links

@ref: 7300

culture collection no.: DSM 17968, JCM 13650, KCTC 15702

straininfo link

  • @ref: 81772
  • straininfo: 309478

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17684261Prevotella paludivivens sp. nov., a novel strictly anaerobic, Gram-negative, hemicellulose-decomposing bacterium isolated from plant residue and rice roots in irrigated rice-field soil.Ueki A, Akasaka H, Satoh A, Suzuki D, Ueki KInt J Syst Evol Microbiol10.1099/ijs.0.64914-02007Anaerobiosis, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Oryza/*microbiology, Phylogeny, Polysaccharides/*metabolism, Prevotella/classification/*isolation & purification/*physiology, RNA, Ribosomal, 16S/genetics, Soil MicrobiologyGenetics
Phylogeny35050847Prevotella herbatica sp. nov., a plant polysaccharide-decomposing anaerobic bacterium isolated from a methanogenic reactor.Ueki A, Tonouchi A, Kaku N, Ueki KInt J Syst Evol Microbiol10.1099/ijsem.0.0052212022Anaerobiosis, Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Phylogeny, Polysaccharides/chemistry, *Prevotella/classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7300Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17968)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17968
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
32071Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128318
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)
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
81772Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309478.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1