Photo by Esther Molina-Menor: J. M. Martí (left) and C. Peña-Garay.

This doctoral thesis, directed by Carlos Peña-Garay, proposes new methods of analysis of the dynamics of microorganism communities. The results of the thesis have been published in journals such as "Methods in Molecular Biology" or "Biofilms and Microbiomes". The thesis was defended on March 29, 2019 and received the grade of Outstanding.

Culture-independent microbiome analysis methods are revolutionizing biology. Whether in a clinical or environmental sample, metagenomics can reveal which microorganisms exist and what they actually do. Metagenomics is a powerful tool for the study of microbial communities, but it requires equally powerful analysis methods. Current challenges in the analysis of metagenomic data include accurately comparing samples, estimating the uncertainty of results, and effectively removing contamination. The rarer the microbes are in an environment, the more essential it is to have solutions to these problems. Examples of niches with few microbes are not only oligotrophic habitats but also many tissues and body fluids.

José Manuel Martí's doctoral research implements a novel approach to the dynamics of microbial communities studied by metagenomics. This has been achieved through the development of new techniques in the field of computational microbiology, supported by statistical, mathematical and parallel computing methods. This strategy was used to analyze longitudinal metagenomic clinical and environmental data. By eliminating multiple types of contamination and providing confidence levels for the results, J. M. Martí was finally able to reveal the dynamics of microbial communities in an efficient and robust way.

J. M. Martí is fluent in different "languages" of science and engineering, as his previous education ranges from a bachelor's degree in electronics to a master's degree in astrophysics. Coinciding with the creation of the Institute of Integrative Systems Biology I²SysBio (joint center Universitat de València-CSIC), he moved from the doctoral program in Theoretical Physics to the Biodiversity and Evolutionary Biology program of the Universitat de València. His doctoral research has been supervised by C. Peña-Garay (CSIC scientist in the Theoretical and Computational Biology Program of I²SysBio), current director of the Canfranc Underground Laboratory.

The panel, which rated the thesis as "Outstanding", was composed of José Luis García (CSIC research professor and director of I²SysBio), Fátima Al-Shahrour (CNIO National Cancer Research Center in Madrid) and José C. Nacher (Faculty of Sciences, Toho University, Japan).