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Yorodumi- EMDB-16488: Cryo-electron tomogram of an intact Bacteroides thetaiotaomicron ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16488 | |||||||||
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Title | Cryo-electron tomogram of an intact Bacteroides thetaiotaomicron DSM 2079 cell. | |||||||||
Map data | Cryo-electron tomogram of a Bacteroides thetaiotaomicron DSM 2079 cell. | |||||||||
Sample |
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Keywords | Bacteria / Bacteroides / UNKNOWN FUNCTION | |||||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Wimmer BH / Medalia O | |||||||||
Funding support | 1 items
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Citation | Journal: Microlife / Year: 2023 Title: Phylogenetic diversity of core rumen microbiota as described by cryo-ET. Authors: Benedikt H Wimmer / Sarah Moraïs / Ran Zalk / Itzhak Mizrahi / Ohad Medalia / Abstract: Microbial taxonomy is critical for describing ecosystem composition, yet the link between taxonomy and properties of microbes, such as their cellular architecture, remains poorly defined. We ...Microbial taxonomy is critical for describing ecosystem composition, yet the link between taxonomy and properties of microbes, such as their cellular architecture, remains poorly defined. We hypothesized that the cellular architecture represents microbial niche adaptation. We used cryo-electron microscopy and tomography to analyze microbial morphology in order to associate cellular architecture with phylogeny and genomic contents. As a model system, we chose the core rumen microbiome and imaged a large isolate collection covering 90% of its richness at the order level. Based on quantifications of several morphological features, we found that the visual similarity of microbiota is significantly related to their phylogenetic distance. Up to the level, closely related microbes have similar cellular architectures, which are highly correlated with genome similarity. However, in more distantly related bacteria, the correlation both with taxonomy and genome similarity is lost. This is the first comprehensive study of microbial cellular architecture and our results highlight that structure remains an important parameter in classification of microorganisms, along with functional parameters such as metabolomics. Furthermore, the high-quality images presented in this study represent a reference database for the identification of bacteria in anaerobic ecosystems. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16488.map.gz | 235.4 MB | EMDB map data format | |
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Header (meta data) | emd-16488-v30.xml emd-16488.xml | 10.5 KB 10.5 KB | Display Display | EMDB header |
Images | emd_16488.png | 162.5 KB | ||
Filedesc metadata | emd-16488.cif.gz | 3.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16488 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16488 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16488.map.gz / Format: CCP4 / Size: 720 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||
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Annotation | Cryo-electron tomogram of a Bacteroides thetaiotaomicron DSM 2079 cell. | ||||||||||||||||||||
Voxel size | X=Y=Z: 8.641 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Bacteroides thetaiotaomicron DSM 2079
Entire | Name: Bacteroides thetaiotaomicron DSM 2079 |
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Components |
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-Supramolecule #1: Bacteroides thetaiotaomicron DSM 2079
Supramolecule | Name: Bacteroides thetaiotaomicron DSM 2079 / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Bacteroides thetaiotaomicron (bacteria) / Strain: DSM 2-79 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 / Details: TBS |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Blot 3-4s. |
Details | diluted to OD = 0.150, grown in YCFA + 1% Glucose |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: Aurion / Diameter: 10 nm |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 42000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 41 |
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Details | imod reconstruction |