Strain identifier
BacDive ID: 1600
Type strain:
Species: Bacteroides thetaiotaomicron
Strain history: CIP <- 1994, ATCC <- T.D. Wilkins: strain WAL 2926 <- V.L. Sutter
NCBI tax ID(s): 818 (species)
General
@ref: 1004
BacDive-ID: 1600
DSM-Number: 2255
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Bacteroides thetaiotaomicron DSM 2255 is an anaerobe, mesophilic bacterium that was isolated from perforated appendix.
NCBI tax id
- NCBI tax id: 818
- Matching level: species
strain history
@ref | history |
---|---|
1004 | <- ATCC; ATCC 29741 <- T. D. Wilkins; WAL 2926 <- V. L. Sutter; |
123519 | CIP <- 1994, ATCC <- T.D. Wilkins: strain WAL 2926 <- V.L. Sutter |
doi: 10.13145/bacdive1600.20230509.8.1
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 thetaiotaomicron
- full scientific name: Bacteroides thetaiotaomicron (Distaso 1912) Castellani and Chalmers 1919 (Approved Lists 1980)
synonyms
@ref synonym 20215 Bacteroides fragilis subsp. thetaiotaomicron 20215 Bacillus thetaiotaomicron
@ref: 1004
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Bacteroidaceae
genus: Bacteroides
species: Bacteroides thetaiotaomicron
full scientific name: Bacteroides thetaiotaomicron (Distaso 1912) Castellani and Chalmers 1919 emend. Hahnke et al. 2016
type strain: no
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 90.49 | ||
69480 | 99.993 | negative | ||
123519 | no | negative | rod-shaped |
colony morphology
@ref | incubation period |
---|---|
1004 | 1-2 days |
123519 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
1004 | 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 |
1004 | FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) | yes | https://mediadive.dsmz.de/medium/1203a | Name: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water |
1004 | 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 |
123519 | CIP Medium 20 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20 |
culture temp
- @ref: 1004
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
1004 | anaerobe | |
69480 | anaerobe | 98.65 |
123519 | anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.986 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
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 | 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 |
123519 | 4853 | esculin | - | hydrolysis |
123519 | 17632 | nitrate | - | reduction |
123519 | 16301 | nitrite | - | reduction |
123519 | 17632 | nitrate | + | respiration |
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 |
---|---|---|---|
123519 | 35581 | indole | yes |
68380 | 35581 | indole | yes |
metabolite tests
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- indole test: +
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | - | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68380 | serine arylamidase | - | |
68380 | alanine arylamidase | + | 3.4.11.2 |
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 | 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 | 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 | catalase | - | 1.11.1.6 |
68367 | beta-glucosidase | + | 3.2.1.21 |
68367 | gelatinase | - | |
68367 | urease | - | 3.5.1.5 |
123519 | oxidase | - | |
123519 | beta-galactosidase | + | 3.2.1.23 |
123519 | gelatinase | - | |
123519 | amylase | - | |
123519 | caseinase | - | 3.4.21.50 |
123519 | catalase | - | 1.11.1.6 |
123519 | tween esterase | +/- | |
123519 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123519 | - | + | - | + | - | - | - | - | - | - | + | + | - | + | - | + | - | + | - | - |
API 20A
@ref | IND | URE | GLU | MAN | LAC | SAC | MAL | SAL | XYL | ARA | GEL | ESC | GLY | CEL | MNE | MLZ | RAF | SOR | RHA | TRE | CAT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1004 | - | - | + | - | + | + | + | - | + | + | - | + | - | + | + | + | + | - | + | + | - |
1004 | + | - | + | - | + | + | + | - | + | + | - | + | - | + | + | - | + | - | + | + |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1004 | - | - | + | + | - | + | + | + | - | + | + | + | + | + | - | + | + | + | - | + | - | + | - | - | + | - | +/- | + | - |
1004 | - | - | + | + | - | + | + | + | +/- | + | + | + | + | + | - | + | + | + | - | + | - | + | - | - | + | - | - | +/- | - |
1004 | - | - | + | + | - | + | + | + | - | + | + | + | + | + | - | + | + | + | - | + | - | + | - | +/- | + | +/- | +/- | +/- | - |
1004 | - | - | + | + | - | + | + | + | - | + | + | + | + | + | - | + | + | +/- | - | + | - | + | - | - | + | - | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | isolation date |
---|---|---|
1004 | perforated appendix | |
123519 | Human, Perforated appendix | 1973 |
isolation source categories
- Cat1: #Host Body-Site
- Cat2: #Gastrointestinal tract
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
1004 | 2 | Risk group (German classification) |
123519 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Bacteroides thetaiotaomicron 16S-23S ribosomal RNA intergenic spacer, partial sequence | AF385897 | 532 | ena | 818 |
20218 | Bacteroides thetaiotaomicron strain ATCC 29741 clone 1 16S-23S ribosomal RNA intergenic spacer, partial sequence | GQ496397 | 543 | ena | 818 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bacteroides thetaiotaomicron ATCC 29741 | GCA_004349615 | scaffold | ncbi | 818 |
66792 | Bacteroides thetaiotaomicron strain ATCC 29741 | 818.972 | wgs | patric | 818 |
66792 | Bacteroides thetaiotaomicron strain FDAARGOS_935 | 818.1394 | complete | patric | 818 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 92.35 | no |
flagellated | no | 96.536 | no |
gram-positive | no | 97.339 | no |
anaerobic | yes | 95.057 | yes |
halophile | no | 89.395 | no |
spore-forming | no | 94.358 | no |
glucose-util | yes | 88.615 | no |
aerobic | no | 95.295 | yes |
thermophile | no | 99.684 | no |
glucose-ferment | yes | 70.356 | no |
External links
@ref: 1004
culture collection no.: DSM 2255, ATCC 29741, WAL 2926, CIP 104207, CCUG 34778, NCTC 13706
straininfo link
- @ref: 71245
- straininfo: 1215
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Cultivation | 518079 | Collaborative evaluation of a proposed reference dilution method of susceptibility testing of anaerobic bacteria. | Sutter VL, Barry AL, Wilkins TD, Zabransky RJ | Antimicrob Agents Chemother | 10.1128/AAC.16.4.495 | 1979 | Anaerobiosis, Anti-Bacterial Agents/*pharmacology, Bacteria/*drug effects, Culture Media, Evaluation Studies as Topic, Microbial Sensitivity Tests/*methods | Pathogenicity |
Pathogenicity | 2280013 | Quality control criteria for testing the susceptibility of anaerobic bacteria to meropenem. | Zabransky RJ, Bayola-Mueller L, Jenkins SG, Pitkin DR, Schreckenberger PC, Celig DM, Spiegel CA | J Clin Microbiol | 10.1128/jcm.28.12.2804-2805.1990 | 1990 | Bacteria, Anaerobic/*drug effects, Meropenem, Microbial Sensitivity Tests/methods/*standards, Quality Control, Reference Values, Thienamycins/*pharmacology | |
Pathogenicity | 2643621 | Quality control guidelines for testing cefotetan in the reference agar dilution procedure for susceptibility testing of anaerobic bacteria. | Zabransky RJ, Bobey DG, Barry AL, Allen SD, Fuchs PC, Gerlach EH, Thornsberry C, Sheikh W, Jones RN | J Clin Microbiol | 10.1128/jcm.27.1.190-191.1989 | 1989 | Bacteria, Anaerobic/*drug effects, Cefotetan/*pharmacology, Microbial Sensitivity Tests/*standards, Multicenter Studies as Topic, Quality Control, Reference Values | |
Pathogenicity | 2896669 | Evaluation of in vitro methods for testing ceftriaxone against anaerobic bacteria, including quality control guidelines. | Barry AL, Jones RN | J Clin Microbiol | 10.1128/jcm.26.4.776-777.1988 | 1988 | Bacteria, Anaerobic/*drug effects, Bacteroides/drug effects, Ceftriaxone/*pharmacology, Clostridium perfringens/drug effects, Microbial Sensitivity Tests/*standards, Quality Control | |
Pathogenicity | 3343304 | Criteria for disk susceptibility tests and quality control guidelines for the cefoperazone-sulbactam combination. | Barry AL, Jones RN | J Clin Microbiol | 10.1128/jcm.26.1.13-17.1988 | 1988 | Bacteria, Anaerobic/*drug effects, Bacteroides/drug effects, Cefoperazone/*pharmacology, Drug Combinations, Enterobacteriaceae/drug effects, Gram-Negative Bacteria/*drug effects, Microbial Sensitivity Tests/*standards, Pseudomonas/drug effects, Quality Control, Sulbactam/*pharmacology | |
Pathogenicity | 3888103 | Establishment of MICs of moxalactam for control and reference anaerobic organisms in agar dilution and microdilution techniques. | Sutter VL, Emmerman J, Randall E, Zabransky RJ, Birk RJ | Antimicrob Agents Chemother | 10.1128/AAC.27.3.424 | 1985 | Agar, Bacteria, Anaerobic/*drug effects, Microbial Sensitivity Tests, Microbiological Techniques, Moxalactam/*pharmacology | |
Pathogenicity | 3972999 | Evaluation of broth microdilution susceptibility results for anaerobic organisms by use of a rapid direct colony inoculum. | Mangels JI, Lindberg LH | J Clin Microbiol | 10.1128/jcm.21.2.269-272.1985 | 1985 | Bacteria, Anaerobic/*drug effects, Humans, Microbial Sensitivity Tests/*methods, Quality Control, Tetracycline/pharmacology | |
Pathogenicity | 6222065 | Establishment of minimum inhibitory concentrations of cefoperazone for control and reference anaerobic organisms. | Zabransky RJ, Randall E, Sutter VL, Birk RJ, Westenfelder G, Emmerman J, Ghoneim AT | J Clin Microbiol | 10.1128/jcm.17.4.711-714.1983 | 1983 | Anaerobiosis, Bacteria/*drug effects, Cefoperazone, Cephalosporins/*pharmacology, Microbial Sensitivity Tests | |
Pathogenicity | 9578166 | Anti-anaerobic activity of erythromycin, azithromycin and clarithromycin: effect of pH adjustment of media to compensate for pH shift caused by incubation in CO2. | Ednie LM, Jacobs MR, Appelbaum PC | J Antimicrob Chemother | 10.1093/jac/41.3.387 | 1998 | Anti-Bacterial Agents/*pharmacology, Azithromycin/pharmacology, Bacteria, Anaerobic/*drug effects/growth & development, Bacterial Infections/microbiology, Carbon Dioxide/chemistry/metabolism, Clarithromycin/pharmacology, Colony Count, Microbial, Culture Media/chemistry/metabolism, Drug Resistance, Microbial, Drug Resistance, Multiple, Erythromycin/pharmacology, Gram-Negative Bacteria/drug effects/growth & development, Humans, Hydrogen-Ion Concentration, Microbial Sensitivity Tests, Oxygenases/pharmacology | Metabolism |
Metabolism | 11709306 | A MATE family multidrug efflux transporter pumps out fluoroquinolones in Bacteroides thetaiotaomicron. | Miyamae S, Ueda O, Yoshimura F, Hwang J, Tanaka Y, Nikaido H | Antimicrob Agents Chemother | 10.1128/AAC.45.12.3341-3346.2001 | 2001 | *ATP-Binding Cassette Transporters, Amino Acid Sequence, Anti-Infective Agents/antagonists & inhibitors/*metabolism, Bacterial Proteins/antagonists & inhibitors/genetics/*metabolism, Bacteroides/drug effects/genetics/*metabolism, Blotting, Southern, Cloning, Molecular, DNA, Bacterial/chemistry/genetics, Drug Resistance, Microbial, Drug Resistance, Multiple, Genes, Bacterial, Microbial Sensitivity Tests, Molecular Sequence Data, Mutation, Norfloxacin/metabolism | Pathogenicity |
Pathogenicity | 16258869 | Inducible metronidazole resistance in nim-positive and nim-negative bacteroides fragilis group strains after several passages metronidazole containing columbia agar plates. | Schaumann R, Petzold S, Fille M, Rodloff AC | Infection | 10.1007/s15010-005-5061-9 | 2005 | Anti-Infective Agents/*pharmacology, Bacteroides fragilis/*drug effects, *Drug Resistance, Bacterial/genetics, *Gene Expression Regulation, Bacterial, Genes, Bacterial, Metronidazole/*pharmacology, Microbial Sensitivity Tests, Polymerase Chain Reaction | |
Metabolism | 18512954 | Characterization of chondroitin sulfate lyase ABC from Bacteroides thetaiotaomicron WAL2926. | Shaya D, Hahn BS, Park NY, Sim JS, Kim YS, Cygler M | Biochemistry | 10.1021/bi800353g | 2008 | Amino Acid Sequence, Animals, Bacterial Proteins/chemistry/genetics/*metabolism, Bacteroides/*enzymology, Binding Sites/genetics, Calcium/chemistry/pharmacology, Carbohydrate Sequence, Catalysis/drug effects, Catalytic Domain/genetics, Chondroitin ABC Lyase/chemistry/genetics/*metabolism, Chondroitin Sulfates/chemistry/metabolism, Glycosaminoglycans/chemistry/metabolism, Histidine/chemistry/metabolism, Hydrogen-Ion Concentration, Kinetics, Magnesium/chemistry/pharmacology, Models, Molecular, Molecular Sequence Data, Mutation, Osmolar Concentration, Protein Structure, Tertiary, Substrate Specificity, Temperature, Tyrosine/chemistry/metabolism | Enzymology |
Pathogenicity | 23461830 | Determination of disk diffusion and MIC quality control guidelines for GSK2251052: a novel boron-containing antibacterial. | Ross JE, Scangarella-Oman N, Jones RN | Diagn Microbiol Infect Dis | 10.1016/j.diagmicrobio.2013.01.007 | 2013 | Anti-Bacterial Agents/*pharmacology, Gram-Negative Bacteria/*drug effects, Gram-Positive Bacteria/*drug effects, Humans, Microbial Sensitivity Tests/methods/*standards, *Quality Control |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1004 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2255) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2255 | |||
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 | |
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) | |||
68367 | Automatically annotated from API 20A | |||||
68380 | Automatically annotated from API rID32A | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
71245 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1215.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123519 | Curators of the CIP | Collection of Institut Pasteur (CIP 104207) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104207 |