Strain identifier

BacDive ID: 1625

Type strain: Yes

Species: Phocaeicola paurosaccharolyticus

Strain Designation: WK042

Strain history: A. Ueki WK042.

NCBI tax ID(s): 1236498 (strain), 732242 (species)

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General

@ref: 9078

BacDive-ID: 1625

DSM-Number: 21004

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

description: Phocaeicola paurosaccharolyticus WK042 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from rice-straw residue from a methanogenic fermenter treating cattle waste.

NCBI tax id

NCBI tax idMatching level
1236498strain
732242species

strain history

@refhistory
9078<- A. Ueki, Yamagata Univ., Tsuruoka, Japan; WK042
67770A. Ueki WK042.

doi: 10.13145/bacdive1625.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Bacteroidaceae
  • genus: Phocaeicola
  • species: Phocaeicola paurosaccharolyticus
  • full scientific name: Phocaeicola paurosaccharolyticus (Ueki et al. 2011) García-López et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacteroides paurosaccharolyticus

@ref: 9078

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Phocaeicola

species: Phocaeicola paurosaccharolyticus

full scientific name: Phocaeicola paurosaccharolyticus (Ueki et al. 2011) García-López et al. 2020

strain designation: WK042

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29851negative3.15 µm0.75 µmrod-shapedno
69480negative91.713

pigmentation

  • @ref: 29851
  • production: no

Culture and growth conditions

culture medium

  • @ref: 9078
  • name: CHOPPED MEAT MEDIUM (DSMZ Medium 78)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/78
  • composition: Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

culture temp

@refgrowthtypetemperature
9078positivegrowth30
29851positivegrowth10-40
29851positiveoptimum35
67770positivegrowth30

culture pH

  • @ref: 29851
  • ability: positive
  • type: optimum
  • pH: 7.7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
9078anaerobe
29851anaerobe
69480anaerobe93.738

spore formation

@refspore formationconfidence
29851no
69480no91.96

halophily

@refsaltgrowthtested relationconcentration
29851NaClpositivegrowth<2 %
29851NaClpositiveoptimum1 %

observation

  • @ref: 67770
  • observation: quinones: MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2985130089acetate+carbon source
2985122599arabinose+carbon source
2985123652dextrin+carbon source
2985117234glucose+carbon source
2985128087glycogen+carbon source
2985117306maltose+carbon source
2985137684mannose+carbon source
2985117272propionate+carbon source
2985115361pyruvate+carbon source
2985126546rhamnose+carbon source
2985130031succinate+carbon source
2985118222xylose+carbon source
298514853esculin+hydrolysis
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

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-
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
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 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
9078--++-+++++++/--+--+--+----+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
9078rice-straw residue from a methanogenic fermenter treating cattle wasteHokkaidoJapanJPNAsia
67770Methanogenic reactor treating waste from cattle farms

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Engineered#Waste
#Host#Mammals#Bovinae (Cow, Cattle)
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5167.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_2514;97_3068;98_3851;99_5167&stattab=map
  • Last taxonomy: Phocaeicola paurosaccharolyticus subclade
  • 16S sequence: AB298727
  • Sequence Identity:
  • Total samples: 23999
  • soil counts: 823
  • aquatic counts: 6726
  • animal counts: 16180
  • plant counts: 270

Safety information

risk assessment

  • @ref: 9078
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacteroides paurosaccharolyticus gene for 16S ribosomal RNA, partial sequenceAB5476451493nuccore1236498
9078Bacteroides paurosaccharolyticus JCM 15092 gene for 16S rRNA, partial sequenceAB2987271472nuccore1236498

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides paurosaccharolyticus JCM 150921236498.4wgspatric1236498
66792Bacteroides paurosaccharolyticus JCM 150922585427865draftimg1236498
67770Phocaeicola paurosaccharolyticus JCM 15092 JCM 15092GCA_000613805contigncbi1236498

GC content

@refGC-contentmethod
907841.0high performance liquid chromatography (HPLC)
2985141
6777037.1genome sequence analysis
6777041high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno91.713no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes93.738no
69480spore-formingspore-formingAbility to form endo- or exosporesno91.96yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no95.009no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.873yes
69480flagellatedmotile2+Ability to perform flagellated movementno88.5yes

External links

@ref: 9078

culture collection no.: DSM 21004, JCM 15092

straininfo link

  • @ref: 71271
  • straininfo: 397244

literature

  • topic: Phylogeny
  • Pubmed-ID: 20348319
  • title: Bacteroides paurosaccharolyticus sp. nov., isolated from a methanogenic reactor treating waste from cattle farms.
  • authors: Ueki A, Abe K, Ohtaki Y, Kaku N, Watanabe K, Ueki K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.022566-0
  • year: 2010
  • mesh: Acids, Acyclic/metabolism, Animals, Bacterial Typing Techniques, Bacteroides/*classification/genetics/isolation & purification/metabolism, Base Composition, Bioreactors/*microbiology, Cattle, DNA, Bacterial/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Japan, Methane/biosynthesis, Molecular Sequence Data, Monosaccharides/metabolism, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature, Vitamin K 2/analysis
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
9078Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21004)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21004
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
29851Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126225
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
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)
71271Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397244.1StrainInfo: A central database for resolving microbial strain identifiers