Strain identifier
BacDive ID: 1613
Type strain:
Species: Bacteroides coprosuis
Strain Designation: PC 139
Strain history: CCUG 50528 <-- T. R. Whitehead PC 139.
NCBI tax ID(s): 679937 (strain), 151276 (species)
General
@ref: 7330
BacDive-ID: 1613
DSM-Number: 18011
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped
description: Bacteroides coprosuis PC 139 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from pig faeces, swine manure.
NCBI tax id
NCBI tax id | Matching level |
---|---|
679937 | strain |
151276 | species |
strain history
@ref | history |
---|---|
7330 | <- A. P. Rooney <- T. R. Whitehead; PC 139 |
67770 | CCUG 50528 <-- T. R. Whitehead PC 139. |
doi: 10.13145/bacdive1613.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: Bacteroidaceae
- genus: Bacteroides
- species: Bacteroides coprosuis
- full scientific name: Bacteroides coprosuis Whitehead et al. 2005
@ref: 7330
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Bacteroidaceae
genus: Bacteroides
species: Bacteroides coprosuis
full scientific name: Bacteroides coprosuis Whitehead et al. 2005 emend. Hahnke et al. 2016
strain designation: PC 139
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31598 | negative | 1.9 µm | 1 µm | rod-shaped | no | |
69480 | no | 91.259 | ||||
69480 | negative | 99.999 |
colony morphology
- @ref: 7330
- incubation period: 2-3 days
multimedia
- @ref: 66793
- multimedia content: EM_DSM_18011_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 7330
- name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
- growth: yes
- link: https://mediadive.dsmz.de/medium/104
- composition: Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
7330 | positive | growth | 37 | mesophilic |
31598 | positive | growth | 25-37 | mesophilic |
31598 | positive | optimum | 37 | mesophilic |
58893 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
7330 | anaerobe | |
31598 | anaerobe | |
58893 | anaerobe | |
69480 | anaerobe | 98.922 |
spore formation
@ref | spore formation | confidence |
---|---|---|
31598 | no | |
69481 | no | 100 |
69480 | no | 99.996 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31598 | 17234 | glucose | + | carbon source |
31598 | 17306 | maltose | + | carbon source |
31598 | 4853 | esculin | + | hydrolysis |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | 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 |
---|---|---|---|
31598 | acid phosphatase | + | 3.1.3.2 |
31598 | alpha-galactosidase | + | 3.2.1.22 |
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate 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 6-phosphate | - | |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7330 | - | - | - | + | - | + | + | - | - | + | - | - | - | - | - | - | + | - | - | + | - | - | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
7330 | pig faeces, swine manure | near Peoria | USA | USA | North America | |
58893 | Swine manure,storage pit | Illinois,near Peoria | USA | USA | North America | 1998 |
67770 | Swine-manure storage pits |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Suidae (Pig,Swine) |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_411.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15892;96_278;97_307;98_341;99_411&stattab=map
- Last taxonomy: Bacteroides coprosuis subclade
- 16S sequence: AF319778
- Sequence Identity:
- Total samples: 11064
- soil counts: 733
- aquatic counts: 1370
- animal counts: 8819
- plant counts: 142
Safety information
risk assessment
- @ref: 7330
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
31598 | Bacteroides coprosuis strain PC139 16S ribosomal RNA gene, partial sequence | AF319778 | 1523 | nuccore | 679937 |
7330 | Bacteroides coprosuis gene for 16S ribosomal RNA, partial sequence, strain: JCM 13475 | AB510699 | 1490 | ena | 151276 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bacteroides coprosuis DSM 18011 | 679937.3 | wgs | patric | 679937 |
66792 | Bacteroides coprosuis PC 139, DSM 18011 | 2503982039 | draft | img | 679937 |
67770 | Bacteroides coprosuis DSM 18011 | GCA_000212915 | chromosome | ncbi | 679937 |
GC content
@ref | GC-content | method |
---|---|---|
7330 | 36.4 | |
7330 | 35.0 | sequence analysis |
67770 | 36.4 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 93.607 | yes |
flagellated | no | 97.005 | no |
gram-positive | no | 96.843 | no |
anaerobic | yes | 96.167 | no |
aerobic | no | 96.866 | yes |
halophile | no | 73.907 | no |
spore-forming | no | 95.345 | yes |
thermophile | no | 97.354 | yes |
glucose-util | yes | 89.289 | yes |
glucose-ferment | yes | 65.918 | no |
External links
@ref: 7330
culture collection no.: DSM 18011, CCUG 50528, JCM 13475, NRRL B-41113
straininfo link
- @ref: 71258
- straininfo: 281441
literature
- topic: Phylogeny
- Pubmed-ID: 16280519
- title: Bacteroides coprosuis sp. nov., isolated from swine-manure storage pits.
- authors: Whitehead TR, Cotta MA, Collins MD, Falsen E, Lawson PA
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.63869-0
- year: 2005
- mesh: Animals, Bacteroides/classification/genetics/*isolation & purification, DNA, Ribosomal/genetics, Manure/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Swine/*microbiology
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
7330 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18011) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18011 | ||||
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 | ||||
31598 | 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 | 27886 | 28776041 | ||
58893 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 50528) | https://www.ccug.se/strain?id=50528 | ||||
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) | ||||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 28604660 | 35: 676-683 2017 | ||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68380 | Automatically annotated from API rID32A | ||||||
69479 | João 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 | ||||
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 | ||||
71258 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID281441.1 | StrainInfo: A central database for resolving microbial strain identifiers |