Phylogenetic diversity of core rumen microbiota as described by cryo-ET

Benedikt H Wimmer; Sarah Moraïs; Ran Zalk; Itzhak Mizrahi; Ohad Medalia

doi:10.1093/femsml/uqad010

Phylogenetic diversity of core rumen microbiota as described by cryo-ET

Microlife. 2023 Mar 23:4:uqad010. doi: 10.1093/femsml/uqad010. eCollection 2023.

Authors

Benedikt H Wimmer¹, Sarah Moraïs^{2

3}, Ran Zalk⁴, Itzhak Mizrahi^{2

3}, Ohad Medalia¹

Affiliations

¹ Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
² National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
³ Department of Life Sciences, Ben-Gurion-University of the Negev, Beer-Sheva 84105, Israel.
⁴ Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.

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 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 Family 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.

Keywords: anaerobic microorganisms; cellular architecture; cryo-electron microscopy; cryo-electron tomography; gut microbiome; rumen microbiome; taxonomy.