Comprehensive analysis of the microbial consortium in the culture of flagellate Monocercomonoides exilis

Monocercomonoides exilis is the only known amitochondriate eukaryote, making it an excellent model for studying the implications of mitochondrial reduction from a cellular and evolutionary point of view. Although M. exilis is an endobiotic heterotroph, it can grow in vitro, albeit with an uncharacterized and complex prokaryotic community. All attempts to grow M. exilis axenically have been unsuccessful. Here, we use metagenomic sequencing at different time points during culture growth to describe the composition and dynamics of this community. We assembled genomes of 24 from at least the 30 different bacterial species within. Based on DNA read abundances, M. exilis represents less than 1.5%, and the representation of dominant bacterial members changes over time. Genome-scale metabolic reconstruction, differential expression analysis and measurements of metabolites in the media showed that the community depends on organic carbon oxidation, fermentation, and hydrogen production without methanogenesis. This is consistent with the rapid decline of amino acids, nucleotides, glyceraldehyde, lactate, fatty acids, and alcohols in the media. The community depends on recycling the external supply of amino acids since it has a limited capacity to fix nitrogen gas and lacks ammonia oxidizers to close the nitrogen cycle. With the senescence of the culture, we observe changes in the expression of several metabolic pathways in M. exilis, particularly those adapting to starvation. We do not reveal any clear metabolic link to explain the dependence of M. exilis on prokaryotes.