Strain identifier
BacDive ID: 12520
Type strain:
Species: Odoribacter splanchnicus
Strain Designation: 1651/6
Strain history: CCUG 21054 A <-- CCM 6029 <-- H. Werner 1651/6.
NCBI tax ID(s): 709991 (strain), 28118 (species)
General
@ref: 9023
BacDive-ID: 12520
DSM-Number: 20712
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Odoribacter splanchnicus 1651/6 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from abdominal abscess.
NCBI tax id
NCBI tax id | Matching level |
---|---|
709991 | strain |
28118 | species |
strain history
@ref | history |
---|---|
9023 | <- NCTC {1985} <- H. Werner; 1651/6 |
67770 | CCUG 21054 A <-- CCM 6029 <-- H. Werner 1651/6. |
doi: 10.13145/bacdive12520.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: Odoribacteraceae
- genus: Odoribacter
- species: Odoribacter splanchnicus
- full scientific name: Odoribacter splanchnicus (Werner et al. 1975) Hardham et al. 2008
synonyms
- @ref: 20215
- synonym: Bacteroides splanchnicus
@ref: 9023
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Odoribacteraceae
genus: Odoribacter
species: Odoribacter splanchnicus
full scientific name: Odoribacter splanchnicus (Werner et al. 1975) Hardham et al. 2008 emend. Hahnke et al. 2016
strain designation: 1651/6
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.998
colony morphology
- @ref: 47264
- incubation period: 2-3 days
multimedia
- @ref: 66793
- multimedia content: EM_DSM_20712_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
9023 | 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 |
9023 | CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) | yes | https://mediadive.dsmz.de/medium/110 | Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
9023 | positive | growth | 37 | mesophilic |
47264 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
9023 | anaerobe | |
47264 | anaerobe | |
69480 | anaerobe | 99.999 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.991 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | + | energy source |
metabolite production
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- production: yes
metabolite tests
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- indole test: +
enzymes
@ref | value | activity | ec |
---|---|---|---|
68380 | serine arylamidase | - | |
68380 | glycin arylamidase | - | |
68380 | alanine arylamidase | + | 3.4.11.2 |
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 | 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 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
9023 | - | - | + | + | - | - | - | - | - | + | - | - | - | + | - | + | + | + | - | + | - | + | - | - | + | - | - | - | - |
9023 | - | - | + | + | - | +/- | - | - | - | + | - | - | + | + | - | + | + | + | - | + | - | + | +/- | +/- | + | - | +/- | - | - |
9023 | - | - | + | + | - | - | - | - | - | + | - | - | + | + | - | + | + | + | - | + | - | + | + | - | + | - | - | + | - |
9023 | - | - | + | + | - | - | - | - | - | + | - | - | + | + | - | + | + | + | - | + | - | + | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
9023 | abdominal abscess |
47264 | Human abdominal abscess |
67770 | Abdominal abscess |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host Body-Site | #Other | #Abdomen |
#Host Body-Site | #Other | #Abscess |
taxonmaps
- @ref: 69479
- File name: preview.99_2542.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_332;96_1367;97_1624;98_1975;99_2542&stattab=map
- Last taxonomy: Odoribacter splanchnicus subclade
- 16S sequence: NR_074535
- Sequence Identity:
- Total samples: 218669
- soil counts: 1276
- aquatic counts: 5874
- animal counts: 211105
- plant counts: 414
Safety information
risk assessment
- @ref: 9023
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
9023 | Odoribacter splanchnicus strain DSM 220712 16S ribosomal RNA, partial sequence | NR_074535 | 1512 | nuccore | 28118 |
67770 | Odoribacter splanchnicus gene for 16S ribosomal RNA, partial sequence, strain: JCM 15291 | AB547649 | 1485 | ena | 28118 |
67770 | Odoribacter splanchnicus strain NCTC 10825 16S ribosomal RNA gene, partial sequence | L16496 | 1467 | ena | 28118 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Odoribacter splanchnicus DSM 20712 DSM 220712 | GCA_000190535 | complete | ncbi | 709991 |
66792 | Odoribacter splanchnicus NCTC10825 | GCA_900187175 | complete | ncbi | 28118 |
66792 | Odoribacter splanchnicus DSM 20712 FDAARGOS_1579 | GCA_020736405 | chromosome | ncbi | 709991 |
66792 | Odoribacter splanchnicus DSM 220712 | 709991.3 | complete | patric | 709991 |
66792 | Odoribacter splanchnicus strain NCTC10825 | 28118.6 | complete | patric | 28118 |
66792 | Odoribacter splanchnicus 1651/6, DSM 20712 | 649633078 | complete | img | 709991 |
66792 | Odoribacter splanchnicus NCTC 10825 | 2773857890 | complete | img | 28118 |
66792 | Odoribacter splanchnicus DSM 20712 strain FDAARGOS_1579 | 709991.142 | complete | patric | 709991 |
66792 | Odoribacter splanchnicus DSM 20712 strain FDAARGOS_1579 | 709991.141 | complete | patric | 709991 |
GC content
- @ref: 9023
- GC-content: 43.4
- method: sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 90.248 | no |
flagellated | no | 96.762 | no |
gram-positive | no | 97.035 | no |
anaerobic | yes | 98.102 | yes |
aerobic | no | 97.24 | no |
halophile | no | 79.501 | no |
spore-forming | no | 92.294 | no |
glucose-util | yes | 85.088 | no |
thermophile | no | 98.796 | yes |
glucose-ferment | yes | 52.904 | no |
External links
@ref: 9023
culture collection no.: DSM 20712, ATCC 29572, CCUG 21054, CIP 104287, LMG 8202, NCTC 10825, CCUG 21054 A, CCM 6029, JCM 15291
straininfo link
- @ref: 81739
- straininfo: 1214
literature
topic | Pubmed-ID | title | authors | journal | year | mesh | topic2 | DOI |
---|---|---|---|---|---|---|---|---|
Phylogeny | 168701 | [A new butyric acid-producing bacteroides species: B. splanchnicus n. sp. (author's transl)]. | Werner H, Rintelen G, Kunstek-Santos H | Zentralbl Bakteriol Orig A | 1975 | Acetates/biosynthesis, Aminoglycosides, Anaerobiosis, Bacteria/classification, Bacteroides/*classification/enzymology/metabolism, Butyrates/biosynthesis, Carbohydrate Metabolism, Cephalosporins, Chloramphenicol, Erythromycin, Lincomycin, Penicillin Resistance, Penicillins, Polymyxins, Propionates/biosynthesis, Rifampin, Tetracycline, Valerates/biosynthesis | Metabolism | |
Metabolism | 9236738 | Formation of a dipeptidyl arylamidase by Bacteroides splanchnicus NCTC 10825 with specificities towards glycylprolyl-x and valylalanine-x substrates. | Macfarlane S, Macfarlane GT | J Med Microbiol | 1997 | Aminopeptidases/antagonists & inhibitors/*biosynthesis/isolation & purification/metabolism, Bacteroides/*enzymology/growth & development, Caseins/metabolism, Chromatography, Gel, Colon/microbiology, Culture Media, Dipeptides/*metabolism, Humans, Hydrogen-Ion Concentration, Isoelectric Focusing, Phenylmethylsulfonyl Fluoride/pharmacology, Protease Inhibitors/pharmacology, Substrate Specificity, Thimerosal/pharmacology | Enzymology | 10.1099/00222615-46-7-547 |
Phylogeny | 19542124 | Butyricimonas synergistica gen. nov., sp. nov. and Butyricimonas virosa sp. nov., butyric acid-producing bacteria in the family 'Porphyromonadaceae' isolated from rat faeces. | Sakamoto M, Takagaki A, Matsumoto K, Kato Y, Goto K, Benno Y | Int J Syst Evol Microbiol | 2009 | Animals, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification/physiology, Butyric Acid/*metabolism, DNA, Bacterial/analysis, Fatty Acids/analysis, Feces/*microbiology, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rats, Sequence Analysis, DNA, Species Specificity, Vitamin K 2/analysis | Genetics | 10.1099/ijs.0.007674-0 |
Genetics | 21677857 | Complete genome sequence of Odoribacter splanchnicus type strain (1651/6). | Goker M, Gronow S, Zeytun A, Nolan M, Lucas S, Lapidus A, Hammon N, Deshpande S, Cheng JF, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Ovchinikova G, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Brambilla EM, Rohde M, Detter JC, Woyke T, Bristow J, Markowitz V, Hugenholtz P, Eisen JA, Kyrpides NC, Klenk HP | Stand Genomic Sci | 2011 | 10.4056/sigs.1714269 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9023 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20712) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20712 | |||
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 | |||
47264 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 21054 A) | https://www.ccug.se/strain?id=21054 | |||
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 | |||||
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 | |||
81739 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1214.1 | StrainInfo: A central database for resolving microbial strain identifiers |