Strain identifier

BacDive ID: 12547

Type strain: Yes

Species: Segatella copri

Strain history: H. Hayashi CB7.

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7429

BacDive-ID: 12547

DSM-Number: 18205

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

description: Segatella copri DSM 18205 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces.

NCBI tax id

NCBI tax idMatching level
537011strain
165179species

strain history

@refhistory
7429<- H. Hayashi; CB7
67770H. Hayashi CB7.

doi: 10.13145/bacdive12547.20230509.8.1

Name and taxonomic classification

LPSN

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

    • @ref: 20215
    • synonym: Prevotella copri

@ref: 7429

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Prevotellaceae

genus: Prevotella

species: Prevotella copri

full scientific name: Prevotella copri Hayashi et al. 2007 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31995negative0.95 µm0.83 µmrod-shapedno
69480negative99.997

colony morphology

  • @ref: 7429
  • type of hemolysis: gamma
  • incubation period: 2-3 days

pigmentation

  • @ref: 31995
  • production: no

Culture and growth conditions

culture medium

  • @ref: 7429
  • name: SCHAEDLER BROTH (ROTH; 5772) (DSMZ Medium 1669)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1669
  • composition: Name: SCHAEDLER BROTH (Roth; 5772) (DSMZ Medium 1669) Composition: Glucose 5.83 g/l Casein peptone 5.66 g/l Yeast extract 5.0 g/l Peptone mixture 5.0 g/l Tris 3.0 g/l NaCl 1.66 g/l Soy peptone 1.0 g/l K2HPO4 0.83 g/l L-Cysteine HCl x H2O 0.4 g/l Hemin 0.01 g/l Resazurin 0.001 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7429positivegrowth37mesophilic
31995positiveoptimum37mesophilic
61579positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7429anaerobe
31995anaerobe
61579anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
31995no
69481no100
69480no99.999

observation

  • @ref: 67770
  • observation: quinones: MK-10, MK-11, MK-12, MK-13

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3199522599arabinose+carbon source
3199517057cellobiose+carbon source
3199517234glucose+carbon source
3199517716lactose+carbon source
3199517306maltose+carbon source
3199516634raffinose+carbon source
3199526546rhamnose+carbon source
3199517814salicin+carbon source
3199517992sucrose+carbon source
3199518222xylose+carbon source
319954853esculin+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
31995acid phosphatase+3.1.3.2
31995alkaline phosphatase+3.1.3.1
31995alpha-galactosidase+3.2.1.22
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
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
7429--++-+++--------+--+----+--+/--
7429--+++/-+++---+/-----+--+----+----
7429--+++/-+++---+/-----+--+----+----
7429--+++/-+++--------+--+----+--+/--
7429--++++++--------+--+----+----
7429--++-+++--------+--+----+--+/--
7429--+++/-+++--------+--+----+--+-
7429--++++++---+----+--+----+--+/--
7429--++++++---+----+--+----+--+/--
7429--++++++---+----+--+----+--+/--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7429human faecesJapanJPNAsia
61579Human feces,52-yr-old healthy manJapanJPNAsia
67770Human feces

isolation source categories

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

Safety information

risk assessment

  • @ref: 7429
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
31995Prevotella copri gene for 16S rRNA, partial sequence, strain: CB7AB0649231494nuccore537011
7429Prevotella copri gene for 16S ribosomal RNA, partial sequence, strain: JCM 13464AB6492791493ena537011

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Segatella copri DSM 18205 FDAARGOS_1573GCA_020735445completencbi537011
66792Segatella copri DSM 18205GCA_009495405contigncbi537011
66792Prevotella copri DSM 18205 NZ_Prevotella_copri_PS131S11_modGCA_902167755contigncbi537011
66792Prevotella copri DSM 18205537011.5wgspatric537011
66792Prevotella copri DSM 18205 strain NZ_Prevotella_copri_PS131S11_mod537011.429wgspatric537011
66792Prevotella copri pcref165179.299wgspatric165179
66792Prevotella copri CB7, DSM 182052562617166draftimg537011
67770Segatella copri DSM 18205GCA_000157935scaffoldncbi537011
66792Segatella copri DSM 18205GCA_025151535completencbi537011
66792Segatella copri JCM13464GCA_026015395contigncbi165179
66792Prevotella copri DSM 18205 strain FDAARGOS_1573537011.438completepatric537011
66792Prevotella copri DSM 18205 strain FDAARGOS_1573537011.437completepatric537011

GC content

@refGC-contentmethod
742945.3
742944.8sequence analysis
6777045.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.933yes
gram-positiveno97.555yes
anaerobicyes99.524yes
aerobicno99.003no
halophileno92.345no
spore-formingno96.288yes
motileno92.359yes
thermophileno97.793yes
glucose-utilyes84.102yes
glucose-fermentyes65.523no

External links

@ref: 7429

culture collection no.: DSM 18205, JCM 13464, CCUG 58058, CB 7

straininfo link

  • @ref: 81762
  • straininfo: 308623

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
Phylogeny32697186Prevotella hominis sp. nov., isolated from human faeces.Liou JS, Huang CH, Ikeyama N, Lee AY, Chen IC, Blom J, Chen CC, Chen CH, Lin YC, Hsieh SY, Huang L, Ohkuma M, Watanabe K, Sakamoto MInt J Syst Evol Microbiol10.1099/ijsem.0.0043422020Adult, Bacteria, Anaerobic/classification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Humans, Nucleic Acid Hybridization, *Phylogeny, Prevotella/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Taiwan, Vitamin K 2/chemistryPathogenicity
Phylogeny33430782Development of a real-time quantitative PCR method for detection and quantification of Prevotella copri.Verbrugghe P, Van Aken O, Hallenius F, Nilsson ABMC Microbiol10.1186/s12866-020-02063-42021Adult, Animals, Benzothiazoles/chemistry, DNA Primers/genetics, DNA, Bacterial/genetics, Diamines/chemistry, Feces/*microbiology, Female, High-Throughput Nucleotide Sequencing, Humans, Male, Mice, Phylogeny, Prevotella/genetics/*isolation & purification, Quinolines/chemistry, RNA, Ribosomal, 16S/*genetics, Real-Time Polymerase Chain Reaction/*methods, Sensitivity and Specificity, Sequence Analysis, DNA, Young AdultPathogenicity
Metabolism34142143Novel xylan-degrading enzymes from polysaccharide utilizing loci of Prevotella copri DSM18205.Linares-Pasten JA, Hero JS, Pisa JH, Teixeira C, Nyman M, Adlercreutz P, Martinez MA, Karlsson ENGlycobiology10.1093/glycob/cwab0562021Glycoside Hydrolases/chemistry/*metabolism, Kinetics, Models, Molecular, Polysaccharides/chemistry/*metabolism, Prevotella/*chemistry/metabolism, Xylans/chemistry/*metabolismEnzymology
Metabolism34180602Cultivation of the gut bacterium Prevotella copri DSM 18205(T) using glucose and xylose as carbon sources.Huang F, Sardari RRR, Jasilionis A, Book O, Oste R, Rascon A, Heyman-Linden L, Holst O, Karlsson ENMicrobiologyopen10.1002/mbo3.12132021Bioreactors/microbiology, Culture Media/metabolism, Fermentation, Formates/metabolism, Gastrointestinal Microbiome, Glucose/*metabolism, Humans, Prevotella/genetics/*growth & development/isolation & purification/*metabolism, Xylose/*metabolismCultivation

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7429Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18205)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18205
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
61579Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58058)https://www.ccug.se/strain?id=58058
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
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
81762Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID308623.1StrainInfo: A central database for resolving microbial strain identifiers