Strain identifier

BacDive ID: 12548

Type strain: Yes

Species: Leyella stercorea

Strain history: H. Hayashi CB35.

NCBI tax ID(s): 1002367 (strain), 363265 (species)

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General

@ref: 7430

BacDive-ID: 12548

DSM-Number: 18206

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

description: Leyella stercorea CCUG 55595 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces.

NCBI tax id

NCBI tax idMatching level
1002367strain
363265species

strain history

@refhistory
7430<- H. Hayashi; CB35
67770H. Hayashi CB35.

doi: 10.13145/bacdive12548.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Prevotellaceae
  • genus: Leyella
  • species: Leyella stercorea
  • full scientific name: Leyella stercorea (Hayashi et al. 2007) Hitch et al. 2023

  • synonyms

    • @ref: 20215
    • synonym: Prevotella stercorea

@ref: 7430

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Prevotellaceae

genus: Prevotella

species: Prevotella stercorea

full scientific name: Prevotella stercorea Hayashi et al. 2007

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31995negative1.16 µm0.33 µmrod-shapedno
69480negative100

colony morphology

@refincubation period
74303-7 days
606612 days

pigmentation

  • @ref: 31995
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7430FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)yeshttps://mediadive.dsmz.de/medium/1203aName: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water
7430COLUMBIA 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
7430PYG 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

culture temp

@refgrowthtypetemperaturerange
7430positivegrowth37mesophilic
31995positiveoptimum37mesophilic
60661positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7430anaerobe
31995anaerobe
60661anaerobe
69480anaerobe99.688

spore formation

@refspore formationconfidence
31995no
69481no100
69480no99.998

observation

  • @ref: 67770
  • observation: quinones: MK-12, MK-13

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3199517234glucose+carbon source
3199517716lactose+carbon source
3199517306maltose+carbon source
3199537684mannose+carbon source
31995506227N-acetylglucosamine+carbon source
3199516634raffinose+carbon source
3199517992sucrose+carbon source
6838016199urea-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
31995acid phosphatase+3.1.3.2
31995alkaline phosphatase+3.1.3.1
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-
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
7430--++++---+---+--+--+----+----
7430-+++-+---+-+/--+--+--+----+----
7430--++-+---+---+-----+----+--+-
7430--++-+---+---+--+--+----+--+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7430human faecesJapanJPNAsia
60661Human feces,52-yr-old healthy manJapanJPNAsia
67770Human feces

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_11787.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_781;96_3984;97_5649;98_7099;99_11787&stattab=map
  • Last taxonomy: Prevotella stercorea subclade
  • 16S sequence: AB244774
  • Sequence Identity:
  • Total samples: 22313
  • soil counts: 191
  • aquatic counts: 437
  • animal counts: 21622
  • plant counts: 63

Safety information

risk assessment

  • @ref: 7430
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7430
  • description: Prevotella stercorea gene for 16S ribosomal RNA, partial sequence, strain: CB35
  • accession: AB244774
  • length: 1488
  • database: ena
  • NCBI tax ID: 1002367

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Prevotella stercorea DSM 182061002367.3wgspatric1002367
66792Prevotella stercorea DSM 182062513237318draftimg1002367
67770Leyella stercorea DSM 18206GCA_000235885scaffoldncbi1002367

GC content

@refGC-contentmethod
743048.2
6777048.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.735no
flagellatedno96.89yes
gram-positiveno96.906yes
anaerobicyes98.965yes
aerobicno97.731yes
halophileno89.038no
spore-formingno96.871yes
thermophileno97.361yes
glucose-utilyes86.201yes
glucose-fermentyes59.511no

External links

@ref: 7430

culture collection no.: CCUG 55595, CB 35, DSM 18206, JCM 13469, KCTC 15079

straininfo link

  • @ref: 81763
  • straininfo: 293996

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17473237Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces.Hayashi H, Shibata K, Sakamoto M, Tomita S, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.64778-02007Anaerobiosis, Bacterial Typing Techniques, Bacteroidaceae Infections/*microbiology, Base Composition, Carbohydrate Metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Enzymes/analysis, Fatty Acids/analysis, Feces/*microbiology, Genes, rRNA/genetics, Humans, Molecular Sequence Data, Movement, Phylogeny, Pigments, Biological/biosynthesis, Prevotella/chemistry/*classification/*isolation & purification/physiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Spores, Bacterial, Vitamin K 2/analysisEnzymology
Phylogeny36029281Prevotella merdae sp. nov., a new bacterial species isolated from human faeces.Maaloum M, Afouda P, Lo CI, Dubourg G, Nguyen TT, Levasseur A, Saile R, Raoult D, Fournier PEFEMS Microbiol Lett10.1093/femsle/fnac0662022Adult, Bacterial Typing Techniques, DNA, Bacterial/genetics, *Fatty Acids, Feces/microbiology, Humans, Phylogeny, *Prevotella/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7430Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18206)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18206
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
31995Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2824928776041
60661Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55595)https://www.ccug.se/strain?id=55595
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)
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
81763Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID293996.1StrainInfo: A central database for resolving microbial strain identifiers