Strain identifier
BacDive ID: 2511
Type strain: 
Species: unclassified bacterium
Strain Designation: LD64
Strain history: <- N. O. van Gylswyk, Swedish Univ. Agric. Sci., Uppsala, Sweden; LD64 (Sarcina sp.) <- N. O. van Gylswyk {1991}
NCBI tax ID(s): 1869227 (species)
version 8.1 (current version)
General
@ref: 4155
BacDive-ID: 2511
DSM-Number: 11001
keywords: genome sequence, 16S sequence, anaerobe, mesophilic, Gram-positive
description: unclassified bacterium LD64 is an anaerobe, mesophilic, Gram-positive prokaryote that was isolated from cow rumen, grass-silage diet.
NCBI tax id
- NCBI tax id: 1869227
- Matching level: species
strain history
- @ref: 4155
- history: <- N. O. van Gylswyk, Swedish Univ. Agric. Sci., Uppsala, Sweden; LD64 (Sarcina sp.) <- N. O. van Gylswyk {1991}
doi: 10.13145/bacdive2511.20230509.8.1
Name and taxonomic classification
@ref: 4155
phylum: Not assigned to order
class: Not assigned to order
order: Clostridiales
family: Not assigned to family
genus: unclassified
species: unclassified bacterium
full scientific name: unclassified bacterium
strain designation: LD64
type strain: no
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 99.719
Culture and growth conditions
culture medium
- @ref: 4155
- name: SUCCINICLASTICUM MEDIUM (DSMZ Medium 666)
- growth: yes
- link: https://mediadive.dsmz.de/medium/666
- composition: Name: SUCCINICLASTICUM MEDIUM (DSMZ Medium 666; with strain-specific modifications) Composition: NaHCO3 6.4 g/l NaCl 0.45 g/l (NH4)2SO4 0.45 g/l Na2S x 9 H2O 0.3 g/l L-Cysteine HCl x H2O 0.3 g/l KH2PO4 0.23 g/l K2HPO4 0.23 g/l MgSO4 x 7 H2O 0.09 g/l CaCl2 x 2 H2O 0.06 g/l Indigocarmine 0.005 g/l Rumen fluid Distilled water
culture temp
- @ref: 4155
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 4155 | anaerobe | |
| 69480 | anaerobe | 98.828 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.998 |
Isolation, sampling and environmental information
isolation
- @ref: 4155
- sample type: cow rumen, grass-silage diet
- country: Sweden
- origin.country: SWE
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Mammals | #Bovinae (Cow, Cattle) |
| #Host Body-Site | #Organ | #Rumen |
taxonmaps
- @ref: 69479
- File name: preview.99_42411.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_780;96_4829;97_8047;98_30817;99_42411&stattab=map
- Last taxonomy: Lachnospiraceae
- 16S sequence: MN336244
- Sequence Identity:
- Total samples: 6434
- soil counts: 432
- aquatic counts: 178
- animal counts: 5606
- plant counts: 218
Sequence information
16S sequences
- @ref: 4155
- description: Bacterium strain DSM _11001 16S ribosomal RNA gene, partial sequence
- accession: MN336244
- length: 1518
- database: ena
- NCBI tax ID: 1869227
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sarcina sp. DSM 11001 | GCA_900101015 | scaffold | ncbi | 1798184 |
| 66792 | Sarcina sp. DSM 11001 Rumen_Coassembly_mag_1199 | GCA_905235985 | contig | ncbi | 1798184 |
| 66792 | Sarcina sp. DSM 11001 | 1798184.3 | wgs | patric | 1798184 |
| 66792 | Sarcina sp. DSM 11001 strain Rumen_Coassembly_mag_1199 | 1798184.6 | wgs | patric | 1798184 |
| 66792 | Sarcina sp. DSM 11001 | 2608642105 | draft | img | 1798184 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 90.478 | no |
| flagellated | no | 95.981 | no |
| gram-positive | yes | 82.581 | no |
| anaerobic | yes | 99.242 | yes |
| aerobic | no | 98.324 | yes |
| halophile | no | 86.313 | no |
| spore-forming | no | 69.138 | no |
| glucose-ferment | yes | 74.969 | no |
| thermophile | no | 96.259 | yes |
| glucose-util | yes | 82.654 | no |
External links
@ref: 4155
culture collection no.: DSM 11001
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 4155 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11001) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11001 | |
| 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) | |
| 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 |