Strain identifier
BacDive ID: 1630
Type strain:
Species: Bacteroides oleiciplenus
Strain history: Y. Watanabe B210 (=YIT 12058).
NCBI tax ID(s): 742727 (strain), 626931 (species)
General
@ref: 16383
BacDive-ID: 1630
DSM-Number: 22535
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped
description: Bacteroides oleiciplenus DSM 22535 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces .
NCBI tax id
NCBI tax id | Matching level |
---|---|
742727 | strain |
626931 | species |
strain history
@ref | history |
---|---|
16383 | <- Y. Watanabe, Yakult Central Institute for Microbiological Research <- F. Nagai and M. Morotomi; YIT 12058 |
67770 | Y. Watanabe B210 (=YIT 12058). |
doi: 10.13145/bacdive1630.20230509.8.1
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 oleiciplenus
- full scientific name: Bacteroides oleiciplenus Watanabe et al. 2010
@ref: 16383
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Bacteroidaceae
genus: Bacteroides
species: Bacteroides oleiciplenus
full scientific name: Bacteroides oleiciplenus Watanabe et al. 2010
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29531 | negative | 1.4-55.0 µm | 1-1.9 µm | rod-shaped | no | |
69480 | no | 94.8 | ||||
69480 | negative | 99.998 |
colony morphology
- @ref: 62496
- incubation period: 1 day
pigmentation
- @ref: 29531
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16383 | CHOPPED MEAT MEDIUM (DSMZ Medium 78) | yes | https://mediadive.dsmz.de/medium/78 | Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water |
16383 | 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 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16383 | positive | growth | 37 | mesophilic |
29531 | positive | growth | 37 | mesophilic |
29531 | positive | optimum | 37 | mesophilic |
62496 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
29531 | positive | growth | 7 |
29531 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
16383 | anaerobe | |
29531 | anaerobe | |
62496 | anaerobe | |
69480 | anaerobe | 99.513 |
spore formation
@ref | spore formation | confidence |
---|---|---|
29531 | no | |
69481 | no | 100 |
69480 | no | 99.963 |
observation
@ref | observation |
---|---|
29531 | aggregates in chains |
67770 | quinones: MK-10, MK-11 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29531 | 22599 | arabinose | + | carbon source |
29531 | 17754 | glycerol | + | carbon source |
29531 | 29864 | mannitol | + | carbon source |
29531 | 26546 | rhamnose | + | carbon source |
29531 | 17814 | salicin | + | carbon source |
29531 | 30911 | sorbitol | + | carbon source |
29531 | 27082 | trehalose | + | carbon source |
68367 | 27082 | trehalose | - | builds acid from |
68367 | 62345 | L-rhamnose | + | builds acid from |
68367 | 30911 | sorbitol | - | builds acid from |
68367 | 16634 | raffinose | + | builds acid from |
68367 | 6731 | melezitose | - | builds acid from |
68367 | 16024 | D-mannose | + | builds acid from |
68367 | 17057 | cellobiose | + | builds acid from |
68367 | 17754 | glycerol | - | builds acid from |
68367 | 4853 | esculin | + | hydrolysis |
68367 | 5291 | gelatin | - | hydrolysis |
68367 | 30849 | L-arabinose | + | builds acid from |
68367 | 65327 | D-xylose | + | builds acid from |
68367 | 17814 | salicin | - | builds acid from |
68367 | 17306 | maltose | + | builds acid from |
68367 | 17992 | sucrose | + | builds acid from |
68367 | 17716 | lactose | + | builds acid from |
68367 | 16899 | D-mannitol | - | builds acid from |
68367 | 17634 | D-glucose | + | builds acid from |
68367 | 16199 | urea | - | hydrolysis |
68367 | 27897 | tryptophan | + | energy source |
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 | Chebi-ID | metabolite | production |
---|---|---|---|
68367 | 35581 | indole | yes |
68380 | 35581 | indole | yes |
metabolite tests
@ref | Chebi-ID | metabolite | indole test |
---|---|---|---|
68380 | 35581 | indole | + |
68367 | 35581 | indole | + |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29531 | alpha-galactosidase | + | 3.2.1.22 |
29531 | catalase | + | 1.11.1.6 |
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 |
68367 | beta-glucosidase | + | 3.2.1.21 |
68367 | gelatinase | - | |
68367 | urease | - | 3.5.1.5 |
API 20A
@ref | IND | URE | GLU | MAN | LAC | SAC | MAL | SAL | XYL | ARA | GEL | ESC | GLY | CEL | MNE | MLZ | RAF | SOR | RHA | TRE |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16383 | + | - | + | - | + | + | + | - | + | + | - | + | - | + | + | - | + | - | + | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16383 | - | - | + | + | - | + | + | + | - | + | + | + | + | - | - | + | + | - | - | + | - | - | - | - | + | - | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
16383 | human faeces (healtyh Japanese adult male) | Tokyo | Japan | JPN | Asia | |
62496 | Human feces,healthy adult man | Japan | JPN | Asia | 2009 | |
67770 | Human feces |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | #Male |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_4010.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_1274;97_2457;98_3039;99_4010&stattab=map
- Last taxonomy: Bacteroides
- 16S sequence: AB547644
- Sequence Identity:
- Total samples: 56164
- soil counts: 312
- aquatic counts: 659
- animal counts: 54909
- plant counts: 284
Safety information
risk assessment
- @ref: 16383
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Bacteroides oleiciplenus gene for 16S ribosomal RNA, partial sequence, strain: JCM 16102 | AB547644 | 1485 | ena | 742727 |
16383 | Bacteroides oleiciplenus gene for 16S rRNA, partial sequence, strain: YIT 12058 | AB490803 | 1476 | ena | 742727 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bacteroides oleiciplenus YIT 12058 | GCA_000315485 | scaffold | ncbi | 742727 |
66792 | Bacteroides oleiciplenus YIT 12058 | 742727.4 | wgs | patric | 742727 |
66792 | Bacteroides oleiciplenus YIT 12058 | 2534681837 | draft | img | 742727 |
GC content
@ref | GC-content | method |
---|---|---|
16383 | 43.6 | high performance liquid chromatography (HPLC) |
29531 | 43.6 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 92.12 | yes |
flagellated | no | 97.295 | yes |
gram-positive | no | 97.221 | yes |
anaerobic | yes | 94.661 | no |
aerobic | no | 95.887 | yes |
halophile | no | 91.83 | no |
spore-forming | no | 92.618 | no |
thermophile | no | 99.119 | yes |
glucose-util | yes | 88.434 | no |
glucose-ferment | yes | 70.998 | no |
External links
@ref: 16383
culture collection no.: DSM 22535, JCM 16102, CCUG 60913, YIT 12058, KCTC 15130
straininfo link
- @ref: 71276
- straininfo: 402131
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19767355 | Bacteroides clarus sp. nov., Bacteroides fluxus sp. nov. and Bacteroides oleiciplenus sp. nov., isolated from human faeces. | Watanabe Y, Nagai F, Morotomi M, Sakon H, Tanaka R | Int J Syst Evol Microbiol | 10.1099/ijs.0.015107-0 | 2009 | Bacteroides/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Feces/*microbiology, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics | Pathogenicity |
Phylogeny | 21724955 | Bacteroides stercorirosoris sp. nov. and Bacteroides faecichinchillae sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces. | Kitahara M, Sakamoto M, Tsuchida S, Kawasumi K, Amao H, Benno Y, Ohkuma M | Int J Syst Evol Microbiol | 10.1099/ijs.0.032706-0 | 2011 | Aerobiosis, Animals, Bacterial Typing Techniques, Bacteroides/*classification/genetics/*isolation & purification/physiology, Chinchilla/*microbiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Feces/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
16383 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22535) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22535 | ||||
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 | ||||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
29531 | 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 | 28776041 | 25928 | ||
62496 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 60913) | https://www.ccug.se/strain?id=60913 | ||||
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/ | |||||
68367 | Automatically annotated from API 20A | ||||||
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 | ||||
71276 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402131.1 | StrainInfo: A central database for resolving microbial strain identifiers |