Since the beginning of the project, several tasks from the work packages described within the proposal were successfully completed.
We collected 450,000 rRNA gene sequences related to the TM6 phylum, originating from publicly available metagenomes. Using this dataset along with associated environmental metadata, we showed that TM6 is distributed in a wide range of environments, although it occurred at highest frequencies in soil, fresh and marine water, as well as sediments. Interestingly, these environments represent hotspots for protists such as amoebae, which could serve as hosts for supporting TM6 growth. By extracting all TM6 sequences covering the variable region V4 of the 16S rRNA gene, we then showed that TM6 is a moderately diversified phylum, comprised of 1,390 operational taxonomic units at 97% similarity.
In parallel, TM6 whole genomes were recovered from publicly available metagenomes, and the TM6 isolate available was sequenced in house. In total, 22 (near)complete TM6 genomes were collected for further investigations. By means of comparative genomics, we determined that all TM6 genomes analyzed were extremely reduced in their metabolic capabilities. In line with these observations, a wide array of transporters involved in aminoacid and energy import were identified, allowing the bacteria to efficiently subvert host resources for replication. These features clearly indicate that TM6 are extremely dependent on other (micro)organisms for thriving, and are thus adopting a parasitic lifestyle.
In parallel, using the TM6 model Vermiphilus pyriformis that we were able to grow and maintain in laboratory conditions, we described in details the bacterium lifecycle within its natural host, the amoeba Vermamoeba vermiformis. Using fluorescence in situ hybridization along with confocal microscopy, a detailed analysis of the infection process was performed, allowing to characterize and better understand the replication cycle of TM6 bacteria. Using this approach, we showed that V. pyriformis completes its replication cycle 48 hours, and efficiently colonizes the whole amoebal population. V. pyriformis also showed dramatic morphological changes during its replication, transiting from a small infection stage (400 nm), to a filamentous replication phase (up to 5µm), before switching back to an infectious phase, preceding the bacterial excretion from the amoeba host. These features highlight an unusual cell division process.
The progress achieved during the project were presented in form of a poster at the 16th International Symposium of Microbial Ecology (ISME), held at Montréal in 2016. An oral presentation of this work was also done during the “Let’s talk about Symbiosis” workshop organized by the University of Vienna and the Medical University of Vienna, in 2016. Actions for outreach were also undertaken, notably a participation to the 2017 edition of KinderUni (
https://kinderuni.at(s’ouvre dans une nouvelle fenêtre)).
Ultimately, this MSCA funded project allowed me to integrate a new and stimulating laboratory. This experience greatly expanded my professional network, as well as the array of techniques used in my field of expertise. Thanks to this, I successfully passed the selection, and was appointed to a permanent position of Assistant Professor at the University of Poitiers, hence the anticipated termination of the present project.
The MSCA support greatly helped me to become an independent researcher, by obtaining a position in full adequation with my career goals.
