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Biography |
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Dr. Mizuno is a biologist and holds a master’s degree in Biotechnology and Bioinformatics. In her PhD she has described new genomes of uncultured microbes and their viruses using metagenomics. She is interested in microbial ecology as a whole and has recently joined the Institute Pasteur to study the evolutionary relationships of mobile elements in Archaea. https://www.researchgate.net/profile/Carolina_Megumi_Mizuno2 — https://research.pasteur.fr/en/member/carolina-mizuno/
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Abstract |
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Marine Metagenomics: widening horizons for uncultured microbes and their viruses |
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Microbiology has undergone a profound revolution in the last decades by the development of next-generation sequencing (NGS). Apart from revolutionizing genome sequencing of cultured microbes, these new technologies have had an important role in shaping the emerging field of metagenomics, which deals largely with the genomic information of those microbes that have remained uncultured. These microbes are the vast majority and it has been estimated that only ~1% of all the microbial species available on earth have been cultured so far. In the last years, metagenomics studies have immensely contributed to reveal new insights into the fascinating microbial marine world and its importance in the maintenance of life on our planet.
Marine microbes are thought to be the only form of life on Earth for billions of years and responsible for the development of life as it is today. They are responsible for the maintenance of the planet’s biogeochemical cycles and it is estimated that photosynthetic marine cyanobacteria are responsible for the production of more than 50% of all the oxygen in the atmosphere. Most marine microbes are known to be exceptionally difficult to grow in the laboratory, and according to some estimates, 99% still remain uncultured. Even the most abundant of the marine microbes, Pelagibacter ubique, has been only successfully cultured in the laboratory after more than 10 years of work.
Using metagenomics, we described novel groups of low GC Actinobacteria from marine environments expanding the knowledge of these uncultured microbes. We also described a new sub-class of marine low GC Actinobacteria, estimated to be the smallest (both in cell-size and in genome) free living bacteria described so far. Both works contributed to the perception of marine actinobacterial groups as important players in the marine environment with distinct and important contributions to nutrient cycling in the oceans.
The use of metagenomics has also acquired a central role in the studies of viruses. Viruses are the most abundant entities on Earth and contain a largely unexplored wealth of genomic diversity. They play a critical role in the biology of their hosts and in ecosystem functioning at large. The critical bottleneck of studying viruses is the need to obtain their hosts in axenic cultures before they themselves can be cultured. Moreover, the application of metagenomics has been also hampered by the difficult of obtaining sufficient amount of DNA for sequencing. As an alternative to the classical methods, we have used cellular metagenomics fosmids to recover complete genomes of uncultured viruses, effectively bypassing several longstanding bottlenecks. Using this approach, we have described more than thousand large genomic fragments of viruses, of which 208 represented complete viral genomes. With a single study we tripled the number of marine viral genomes available in the public databases. These new approaches provided a glimpse into the vast and diverse marine viral groups and have opened a route towards viral population genomics.
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