Strain identifier
BacDive ID: 12547
Type strain:
Species: Segatella copri
Strain history: H. Hayashi CB7.
NCBI tax ID(s): 537011 (strain), 165179 (species)
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 id | Matching level |
---|---|
537011 | strain |
165179 | species |
strain history
@ref | history |
---|---|
7429 | <- H. Hayashi; CB7 |
67770 | H. 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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31995 | negative | 0.95 µm | 0.83 µm | rod-shaped | no | |
69480 | negative | 99.997 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
7429 | positive | growth | 37 | mesophilic |
31995 | positive | optimum | 37 | mesophilic |
61579 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
7429 | anaerobe | |
31995 | anaerobe | |
61579 | anaerobe | |
69480 | anaerobe | 100 |
spore formation
@ref | spore formation | confidence |
---|---|---|
31995 | no | |
69481 | no | 100 |
69480 | no | 99.999 |
observation
- @ref: 67770
- observation: quinones: MK-10, MK-11, MK-12, MK-13
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31995 | 22599 | arabinose | + | carbon source |
31995 | 17057 | cellobiose | + | carbon source |
31995 | 17234 | glucose | + | carbon source |
31995 | 17716 | lactose | + | carbon source |
31995 | 17306 | maltose | + | carbon source |
31995 | 16634 | raffinose | + | carbon source |
31995 | 26546 | rhamnose | + | carbon source |
31995 | 17814 | salicin | + | carbon source |
31995 | 17992 | sucrose | + | carbon source |
31995 | 18222 | xylose | + | carbon source |
31995 | 4853 | esculin | + | hydrolysis |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | 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
@ref | value | activity | ec |
---|---|---|---|
31995 | acid phosphatase | + | 3.1.3.2 |
31995 | alkaline phosphatase | + | 3.1.3.1 |
31995 | alpha-galactosidase | + | 3.2.1.22 |
68380 | serine arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | glycin arylamidase | - | |
68380 | alanine arylamidase | + | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | - | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | + | 3.4.11.1 |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | L-arginine arylamidase | - | |
68380 | alkaline phosphatase | + | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | + | 3.2.1.55 |
68380 | beta-glucosidase | + | 3.2.1.21 |
68380 | alpha-glucosidase | + | 3.2.1.20 |
68380 | beta-galactosidase | + | 3.2.1.23 |
68380 | alpha-galactosidase | + | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7429 | - | - | + | + | - | + | + | + | - | - | - | - | - | - | - | - | + | - | - | + | - | - | - | - | + | - | - | +/- | - |
7429 | - | - | + | + | +/- | + | + | + | - | - | - | +/- | - | - | - | - | + | - | - | + | - | - | - | - | + | - | - | - | - |
7429 | - | - | + | + | +/- | + | + | + | - | - | - | +/- | - | - | - | - | + | - | - | + | - | - | - | - | + | - | - | - | - |
7429 | - | - | + | + | +/- | + | + | + | - | - | - | - | - | - | - | - | + | - | - | + | - | - | - | - | + | - | - | +/- | - |
7429 | - | - | + | + | + | + | + | + | - | - | - | - | - | - | - | - | + | - | - | + | - | - | - | - | + | - | - | - | - |
7429 | - | - | + | + | - | + | + | + | - | - | - | - | - | - | - | - | + | - | - | + | - | - | - | - | + | - | - | +/- | - |
7429 | - | - | + | + | +/- | + | + | + | - | - | - | - | - | - | - | - | + | - | - | + | - | - | - | - | + | - | - | + | - |
7429 | - | - | + | + | + | + | + | + | - | - | - | + | - | - | - | - | + | - | - | + | - | - | - | - | + | - | - | +/- | - |
7429 | - | - | + | + | + | + | + | + | - | - | - | + | - | - | - | - | + | - | - | + | - | - | - | - | + | - | - | +/- | - |
7429 | - | - | + | + | + | + | + | + | - | - | - | + | - | - | - | - | + | - | - | + | - | - | - | - | + | - | - | +/- | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
7429 | human faeces | Japan | JPN | Asia |
61579 | Human feces,52-yr-old healthy man | Japan | JPN | Asia |
67770 | Human feces |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
31995 | Prevotella copri gene for 16S rRNA, partial sequence, strain: CB7 | AB064923 | 1494 | nuccore | 537011 |
7429 | Prevotella copri gene for 16S ribosomal RNA, partial sequence, strain: JCM 13464 | AB649279 | 1493 | ena | 537011 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Segatella copri DSM 18205 FDAARGOS_1573 | GCA_020735445 | complete | ncbi | 537011 |
66792 | Segatella copri DSM 18205 | GCA_009495405 | contig | ncbi | 537011 |
66792 | Prevotella copri DSM 18205 NZ_Prevotella_copri_PS131S11_mod | GCA_902167755 | contig | ncbi | 537011 |
66792 | Prevotella copri DSM 18205 | 537011.5 | wgs | patric | 537011 |
66792 | Prevotella copri DSM 18205 strain NZ_Prevotella_copri_PS131S11_mod | 537011.429 | wgs | patric | 537011 |
66792 | Prevotella copri pcref | 165179.299 | wgs | patric | 165179 |
66792 | Prevotella copri CB7, DSM 18205 | 2562617166 | draft | img | 537011 |
67770 | Segatella copri DSM 18205 | GCA_000157935 | scaffold | ncbi | 537011 |
66792 | Segatella copri DSM 18205 | GCA_025151535 | complete | ncbi | 537011 |
66792 | Segatella copri JCM13464 | GCA_026015395 | contig | ncbi | 165179 |
66792 | Prevotella copri DSM 18205 strain FDAARGOS_1573 | 537011.438 | complete | patric | 537011 |
66792 | Prevotella copri DSM 18205 strain FDAARGOS_1573 | 537011.437 | complete | patric | 537011 |
GC content
@ref | GC-content | method |
---|---|---|
7429 | 45.3 | |
7429 | 44.8 | sequence analysis |
67770 | 45.3 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 96.933 | yes |
gram-positive | no | 97.555 | yes |
anaerobic | yes | 99.524 | yes |
aerobic | no | 99.003 | no |
halophile | no | 92.345 | no |
spore-forming | no | 96.288 | yes |
motile | no | 92.359 | yes |
thermophile | no | 97.793 | yes |
glucose-util | yes | 84.102 | yes |
glucose-ferment | yes | 65.523 | no |
External links
@ref: 7429
culture collection no.: DSM 18205, JCM 13464, CCUG 58058, CB 7
straininfo link
- @ref: 81762
- straininfo: 308623
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17473237 | Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces. | Hayashi H, Shibata K, Sakamoto M, Tomita S, Benno Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.64778-0 | 2007 | Anaerobiosis, 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/analysis | Enzymology |
Phylogeny | 32697186 | Prevotella 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 M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004342 | 2020 | Adult, 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/chemistry | Pathogenicity |
Phylogeny | 33430782 | Development of a real-time quantitative PCR method for detection and quantification of Prevotella copri. | Verbrugghe P, Van Aken O, Hallenius F, Nilsson A | BMC Microbiol | 10.1186/s12866-020-02063-4 | 2021 | Adult, 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 Adult | Pathogenicity |
Metabolism | 34142143 | Novel 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 EN | Glycobiology | 10.1093/glycob/cwab056 | 2021 | Glycoside Hydrolases/chemistry/*metabolism, Kinetics, Models, Molecular, Polysaccharides/chemistry/*metabolism, Prevotella/*chemistry/metabolism, Xylans/chemistry/*metabolism | Enzymology |
Metabolism | 34180602 | Cultivation 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 EN | Microbiologyopen | 10.1002/mbo3.1213 | 2021 | Bioreactors/microbiology, Culture Media/metabolism, Fermentation, Formates/metabolism, Gastrointestinal Microbiome, Glucose/*metabolism, Humans, Prevotella/genetics/*growth & development/isolation & purification/*metabolism, Xylose/*metabolism | Cultivation |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7429 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18205) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18205 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
31995 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28249 | 28776041 | |
61579 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 58058) | https://www.ccug.se/strain?id=58058 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68380 | Automatically annotated from API rID32A | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
81762 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID308623.1 | StrainInfo: A central database for resolving microbial strain identifiers |