Strain identifier
BacDive ID: 5414
Type strain: 
Species: Eubacterium barkeri
Strain history: ATCC 25849 <-- L. DS. Smith VPI 5359.
NCBI tax ID(s): 1528 (species)
version 8.1 (current version)
General
@ref: 587
BacDive-ID: 5414
DSM-Number: 1223
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive
description: Eubacterium barkeri DSM 1223 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from mud.
NCBI tax id
- NCBI tax id: 1528
- Matching level: species
strain history
| @ref | history |
|---|---|
| 587 | <- ATCC <- L.DS. Smith, VPI 5359 <- I. Pastan |
| 67770 | ATCC 25849 <-- L. DS. Smith VPI 5359. |
doi: 10.13145/bacdive5414.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Eubacteriaceae
- genus: Eubacterium
- species: Eubacterium barkeri
- full scientific name: Eubacterium barkeri (Stadtman et al. 1972) Collins et al. 1994
synonyms
- @ref: 20215
- synonym: Clostridium barkeri
@ref: 587
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Eubacteriaceae
genus: Eubacterium
species: Eubacterium barkeri
full scientific name: Eubacterium barkeri (Stadtman et al. 1972) Collins et al. 1994
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 99.553
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 587 | NICOTINIC ACID MEDIUM (DSMZ Medium 152) | yes | https://mediadive.dsmz.de/medium/152 | Name: NICOTINIC ACID MEDIUM (DSMZ Medium 152) Composition: Yeast extract 10.0 g/l Nicotinic acid 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 CaCl2 x 2 H2O 0.008 g/l MgSO4 x 7 H2O 0.008 g/l Distilled water |
| 587 | 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 |
|---|---|---|---|---|
| 587 | positive | growth | 30-37 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 587 | anaerobe | |
| 69480 | anaerobe | 99.742 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 98.806 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 587 | mud | Potomac river | USA | USA | North America |
| 67770 | Mud | Potomac River | USA | USA | North America |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Mud (Sludge)
Safety information
risk assessment
- @ref: 587
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 587 | Eubacterium barkeri strain ATCC 25849 16S ribosomal RNA gene, partial sequence | M23927 | 1527 | ena | 1528 |
| 67770 | Eubacterium barkeri gene for 16S ribosomal RNA, partial sequence, strain: JCM 1389 | LC036314 | 1486 | ena | 1528 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Eubacterium barkeri strain VPI 5359 | 1528.7 | wgs | patric | 1528 |
| 66792 | Eubacterium barkeri VPI 5359 | 2642422543 | draft | img | 1528 |
| 67770 | Eubacterium barkeri VPI 5359 | GCA_900107125 | scaffold | ncbi | 1528 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 587 | 45.0 | |
| 67770 | 45 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 92.431 | no |
| gram-positive | yes | 81.503 | no |
| anaerobic | yes | 99.591 | yes |
| aerobic | no | 98.255 | yes |
| halophile | no | 79.384 | no |
| spore-forming | no | 78.298 | no |
| glucose-util | yes | 82.609 | no |
| flagellated | no | 96.279 | no |
| glucose-ferment | yes | 61.614 | no |
| thermophile | no | 98.862 | yes |
External links
@ref: 587
culture collection no.: DSM 1223, ATCC 25849, NCIB 10623, VKM B-1775, VPI 5359, JCM 1389, BCRC 14473, BCRC 17243, CGMCC 1.5084, NCIMB 10623
straininfo link
- @ref: 74903
- straininfo: 38696
literature
- topic: Metabolism
- Pubmed-ID: 30285910
- title: Eubacterium maltosivorans sp. nov., a novel human intestinal acetogenic and butyrogenic bacterium with a versatile metabolism.
- authors: Feng Y, Stams AJM, Sanchez-Andrea I, de Vos WM
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.003028
- year: 2018
- topic2: Phylogeny
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 587 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1223) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1223 | |
| 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 | |
| 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/ | ||
| 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 | |
| 74903 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID38696.1 | StrainInfo: A central database for resolving microbial strain identifiers |