Phylogeny and metabolism ofEndomicrobiaceae and ElusimicrobiaceaeExploring reductive genome evolution in two hostassociated lineages of Elusimicrobiota

The tree of life has many deep-branching lineages which remain unexplored. One of them, the phylum Elusimicrobiota, belongs to the PVC superphylum and comprises at least four class-level lineages but only two cultured representatives. Like their uncultured relatives in the families Elusimicrobiaceae and Endomicrobiaceae, they colonize the intestinal tracts of various invertebrate and vertebrate hosts. In my doctoral thesis, I analyzed the diversity, evolutionary history, and metabolic potential of host-associated Elusimicrobiota in termites and their closest relatives, cockroaches, through a combination of cultivation and comparative genomics. New isolates from cockroach guts revealed that these new species, like their closest relative Elusimicrobium minutum, are small, Gram-negative pleomorphic ultramicrobacteria with a distinct growth cycle. Using physiological characterization, I could document that the three species are obligate anaerobic fermenters, restricted to a few hexoses, which are fermented to mainly acetate, ethanol, lactate, and hydrogen. Using more than 100 metagenome-assembled genomes (MAGs) of uncultured Elusimicrobiaceae, I uncovered underlying metabolic pathways and outlined a new phylogenomic framework for the family. Based on phylogenomic, physiological, and morphological evidence, I could describe these isolates as three more species of the phylum (Parelusimicrobium proximum gen. nov., sp. nov., Elusimicrobium posterum sp. nov., and Elusimicrobium simillimum sp. nov.) and proposed a comprehensive taxonomy for all lineages in the family under the rules of SeqCode. The second host-associated family, Endomicrobiaceae, is an excellent model for studying the evolution of intracellular endosymbionts, as the family comprises both freeliving representatives and endosymbionts of termite gut flagellates. Metagenomic analysis of the gut microbiota of a wide range of termites allowed us to reconstruct more than 1700 MAGs. Using phylogenomic analysis, I corroborated the sister position of termite Endomicrobiaceae to representatives from ruminants, leading to the proposal of eight new genera. I documented a progressive genome erosion in the new genus Endomicrobiellum, which contains all characterized flagellate endosymbionts to date. The loss of nearly all biosynthetic capacities in some Endomicrobiellum lineages indicates a decline in their originally mutualistic relationship with their flagellate host, shedding new light on the symbiotic range of endosymbiont-flagellate relationships. Massive gene losses in their catabolic and anabolic functions were compensated with the acquisition of new functions through horizontal gene transfer from other gut bacteria. Putative donors of the new functions, including new uptake systems for sugar phosphates and ATP, are primarily other flagellate endosymbionts, including previously unknown lineages. My results document the overall importance of horizontal gene transfer in the convergent evolution of intracellular symbioses. Overall, the results of my research provide new insights into the two families Elusimicrobiaceae and Endomicrobiaceae. My finding revealed parallels in their adaptations to nutrient-rich environments, such as the hindguts of cockroaches and termites or the cytoplasm of termite flagellates. My results also provided evidence for the convergent evolution of unrelated endosymbionts and highlighted the genomic adaptations that enable them to thrive in the intracellular environment of termite gut flagellates.