Strain identifier
BacDive ID: 12525
Type strain:
Species: Prevotella bivia
Strain Designation: 653C
Strain history: CIP <- 1997, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 10109 <- L.V. Holdeman: strain VPI 6822 <- D. Blazevic: strain 653C
NCBI tax ID(s): 868129 (strain), 28125 (species)
General
@ref: 8886
BacDive-ID: 12525
DSM-Number: 20514
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, human pathogen
description: Prevotella bivia 653C is an anaerobe, mesophilic human pathogen that was isolated from endometrium.
NCBI tax id
NCBI tax id | Matching level |
---|---|
868129 | strain |
28125 | species |
strain history
@ref | history |
---|---|
8886 | <- ATCC; ATCC 29303 <- L. V. Holdeman; VPI 6822 (Bacteroides bivius) <- D. Blazevic; 653C |
67770 | T. Mitsuoka <-- L. V. Holdeman VPI 6822 <-- D. Balzeric. |
116825 | CIP <- 1997, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 10109 <- L.V. Holdeman: strain VPI 6822 <- D. Blazevic: strain 653C |
doi: 10.13145/bacdive12525.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: Prevotellaceae
- genus: Prevotella
- species: Prevotella bivia
- full scientific name: Prevotella bivia (Holdeman and Johnson 1977) Shah and Collins 1990
synonyms
- @ref: 20215
- synonym: Bacteroides bivius
@ref: 8886
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Prevotellaceae
genus: Prevotella
species: Prevotella bivia
full scientific name: Prevotella bivia (Holdeman and Johnson 1977) Shah and Collins 1990
strain designation: 653C
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 95.894 | ||
69480 | 99.993 | negative | ||
116825 | no | negative | rod-shaped |
colony morphology
@ref | type of hemolysis | incubation period |
---|---|---|
8886 | gamma | 2-3 days |
45193 | 1-2 days |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_20514_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_20514_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_20514_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_20514_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_20514_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8886 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
39197 | MEDIUM 20 - for Anaerobic bacteria | yes | Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml) | |
8886 | CHOPPED MEAT MEDIUM (DSMZ Medium 78) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium78.pdf | |
116825 | CIP Medium 20 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8886 | positive | growth | 37 | mesophilic |
39197 | positive | growth | 37 | mesophilic |
45193 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
8886 | anaerobe | |
45193 | anaerobe | |
69480 | anaerobe | 99.501 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.998 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
116825 | 17632 | nitrate | - | reduction |
116825 | 16301 | nitrite | - | reduction |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | energy source |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
116825 | 35581 | indole | no |
68380 | 35581 | indole | no |
metabolite tests
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68380 | serine arylamidase | - | |
68380 | histidine 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 |
116825 | oxidase | - | |
116825 | catalase | - | 1.11.1.6 |
116825 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116825 | - | + | - | - | - | - | - | - | - | - | + | + | - | - | - | + | - | + | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8886 | - | - | - | + | + | + | - | - | - | + | + | - | - | + | - | - | + | - | - | + | - | - | - | - | + | + | - | + | - |
8886 | - | - | - | + | - | + | - | - | - | + | - | - | - | + | - | - | + | - | - | + | - | - | - | - | + | +/- | - | - | - |
8886 | - | - | - | + | + | + | - | - | - | + | - | - | - | + | - | - | + | - | - | + | - | - | - | - | + | + | - | +/- | - |
8886 | - | - | - | + | + | + | - | - | - | + | + | - | - | + | - | - | + | - | - | + | - | - | - | - | + | +/- | - | +/- | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
8886 | endometrium |
45193 | Human endometrium |
67770 | Endometrium |
116825 | Endometrium |
isolation source categories
- Cat1: #Host Body-Site
- Cat2: #Urogenital tract
taxonmaps
- @ref: 69479
- File name: preview.99_379.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_44;96_260;97_284;98_317;99_379&stattab=map
- Last taxonomy: Prevotella bivia subclade
- 16S sequence: AB547673
- Sequence Identity:
- Total samples: 92490
- soil counts: 1096
- aquatic counts: 1913
- animal counts: 88928
- plant counts: 553
Safety information
risk assessment
@ref | pathogenicity human | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|---|
8886 | yes | yes | 2 | Risk group (German classification) |
116825 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
8886 | Prevotella bivia gene for 16S ribosomal RNA, partial sequence, strain: JCM 6331 | AB547673 | 1490 | ena | 28125 |
67770 | Prevotella bivia strain ATCC 29303 16S ribosomal RNA gene, partial sequence | L16475 | 1471 | ena | 28125 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Prevotella bivia DSM 20514 | 868129.3 | wgs | patric | 868129 |
66792 | Prevotella bivia JCVIHMP010 | 553171.3 | wgs | patric | 553171 |
66792 | Prevotella bivia 653C, DSM 20514 | 2509601036 | draft | img | 868129 |
67770 | Prevotella bivia DSM 20514 | GCA_000262545 | scaffold | ncbi | 868129 |
GC content
@ref | GC-content | method |
---|---|---|
8886 | 40.0 | |
67770 | 40 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 93.294 | no |
flagellated | no | 96.389 | no |
gram-positive | no | 96.885 | no |
anaerobic | yes | 97.657 | yes |
halophile | no | 86.236 | no |
spore-forming | no | 96.313 | no |
thermophile | no | 97.955 | no |
glucose-util | yes | 88.594 | no |
aerobic | no | 98.028 | yes |
glucose-ferment | yes | 64.794 | no |
External links
@ref: 8886
culture collection no.: DSM 20514, ATCC 29303, NCTC 11156, CCUG 9557, CIP 105105, JCM 6331, LMG 6452, VPI 6822, AIP 10109
straininfo link
- @ref: 81744
- straininfo: 3862
literature
- topic: Enzymology
- Pubmed-ID: 2324268
- title: Protein banding patterns of the outer membrane-enriched fraction of Bacteroides bivius.
- authors: Dinsmoor MJ, Ebersole JE, Gibbs RS
- journal: J Clin Microbiol
- DOI: 10.1128/jcm.28.3.405-408.1990
- year: 1990
- mesh: Bacterial Outer Membrane Proteins/*analysis/immunology, Bacteroides/*chemistry/immunology, Cross Reactions, Electrophoresis, Polyacrylamide Gel, Enzyme-Linked Immunosorbent Assay, Humans, Immune Sera/immunology, Molecular Weight, Predictive Value of Tests
- topic2: Pathogenicity
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8886 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20514) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20514 | |||
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 | |||
39197 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17086 | ||||
45193 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 9557) | https://www.ccug.se/strain?id=9557 | |||
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 | 35: 676-683 2017 | 28604660 | |
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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68380 | Automatically annotated from API rID32A | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
81744 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID3862.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116825 | Curators of the CIP | Collection of Institut Pasteur (CIP 105105) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105105 |