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TitlePhylogenetic diversity of core rumen microbiota as described by cryo-ET.
Journal, issue, pagesMicrolife, Vol. 4, Page uqad010, Year 2023
Publish dateMar 23, 2023
AuthorsBenedikt H Wimmer / Sarah Moraïs / Ran Zalk / Itzhak Mizrahi / Ohad Medalia /
PubMed AbstractMicrobial 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.
External linksMicrolife / PubMed:37223726 / PubMed Central
MethodsEM (tomography)
Structure data

EMDB-15445: Cryo-electron tomogram of Agathobacter ruminis DSM 29029
Method: EM (tomography)

EMDB-15447: Cryo-electron tomogram of Butyrivibrio fibrisolvens CF3
Method: EM (tomography)

EMDB-15448: Cryo-electron tomogram of Pseudobutyrivibrio sp. LB2011
Method: EM (tomography)

EMDB-15449: Cryo-electron tomogram of Wolinella sp. ATCC 33567
Method: EM (tomography)

EMDB-16474: Cryo-electron tomogram of an intact Bacteroides caccae DSM 19024 cell.
Method: EM (tomography)

EMDB-16477: Cryo-electron tomogram of an intact Bacteroides cellulosyliticus CRE21 cell (DSM 14838)
Method: EM (tomography)

EMDB-16478: Cryo-electron tomogram of an intact Lachnospira multipara G6 (ATCC 19207) cell.
Method: EM (tomography)

EMDB-16479: Cryo-electron tomogram of a Roseburia intestinalis DSM 14610 cell.
Method: EM (tomography)

EMDB-16488: Cryo-electron tomogram of an intact Bacteroides thetaiotaomicron DSM 2079 cell.
Method: EM (tomography)

Source
  • Agathobacter ruminis (bacteria)
  • Butyrivibrio fibrisolvens (bacteria)
  • Pseudobutyrivibrio sp. (bacteria)
  • Wolinella succinogenes (bacteria)
  • Bacteroides caccae (bacteria)
  • Bacteroides cellulosilyticus DSM 14838 (bacteria)
  • Lachnospira multipara ATCC 19207 (bacteria)
  • Roseburia intestinalis L1-82 (bacteria)
  • Bacteroides thetaiotaomicron (bacteria)

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