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- EMDB-15445: Cryo-electron tomogram of Agathobacter ruminis DSM 29029 -

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Basic information

Entry
Database: EMDB / ID: EMD-15445
TitleCryo-electron tomogram of Agathobacter ruminis DSM 29029
Map databinned, CTF-corrected, dose-filtered WBP of a cryo-electron tomogram of Agathobacter ruminis DSM 29029
Sample
  • Cell: Agathobacter ruminis DSM 29029
KeywordsMicrobiome / Bacterium / Rumen / UNKNOWN FUNCTION
Biological speciesAgathobacter ruminis (bacteria)
Methodelectron tomography / cryo EM
AuthorsWimmer BH
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionJul 21, 2022-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateJun 7, 2023-
Current statusJun 7, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15445.png

Downloads & links

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Map

FileDownload / File: emd_15445.map.gz / Format: CCP4 / Size: 637.2 MB / Type: IMAGE STORED AS SIGNED BYTE
Annotationbinned, CTF-corrected, dose-filtered WBP of a cryo-electron tomogram of Agathobacter ruminis DSM 29029
Voxel sizeX=Y=Z: 8.839 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)16.651260000000001 (±9.233053)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin16-17-375
Dimensions928960750
Spacing960928750
CellA: 8485.439 Å / B: 8202.592 Å / C: 6629.25 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Agathobacter ruminis DSM 29029

EntireName: Agathobacter ruminis DSM 29029
Components
  • Cell: Agathobacter ruminis DSM 29029

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Supramolecule #1: Agathobacter ruminis DSM 29029

SupramoleculeName: Agathobacter ruminis DSM 29029 / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Agathobacter ruminis (bacteria) / Strain: DSM 29029

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4 / Details: PBS
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: 5ul bacteria + 3ul gold mixed on grid, blot for 4 seconds.
DetailsCultured to early stationary phase in YCFA-Glucose, diluted to OD 0.15 in PBS.
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3708 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-7 / Average exposure time: 1.4 sec. / Average electron dose: 3.41 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Detailsmovies aligned using alignframes.
Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.1.X) / Number images used: 41

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