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

Microbial taxonomy is critical for describing ecosystem composition, yet the link between taxonomy and properties ofmicrobes, such as their cellular architecture, remains poorly defined.We hypothesized that the cellular architecture representsmicrobial niche adaptation. We used cryo-electronmicroscopy and tomography to analyzemicrobial morphology in order to associate cellular architecture with phylogeny and genomic contents. As amodel 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.