Cristina Vilanova, Adriel Latorre, Manuel Porcar

This doctoral thesis, directed by Cristina Vilanova and Manuel Porcar, analyzes various strategies for nanopore sequencing analysis of microbial communities of biotechnological interest. The results of this research have been published in the journals Bioresource Technology, Renewable Energy, Systematic and Applied Microbiology, Frontiers in Microbiology, Scientific Reports and Biology Methods and Protocols. The thesis was defended on April 29, 2022.

Microbiomes, understood as microecosystems that change over time and space, refer to microbial communities and their ecological interactions.  Modern sequencing technologies allow global analysis of the genomes present in microbiomes, including metataxonomic analysis, metagenomics or metatranscriptomics. One of the most recent technologies is nanopore-based sequencing, which has advantages from both a scientific and business point of view. The main objective of this thesis, "Optimizing Nanopore-based microbiome sequencing for characterizing biotechnologically-relevant ecosystems", is the validation of experimental methods and computational tools for the use of nanopore-based metagenomics and metatranscriptomics to address industrial or biotechnological problems. The first proof of concept was the use of these third-generation sequencing methods focused on the analysis of the bacterial and archaeal communities involved in biogas production. On the other hand, the potential of in situ metataxonomic sequencing was tested in a bioprospecting expedition aimed at studying the microbial communities of some biolayers of the Tabernas desert. Finally, the performance of various methods for nanopore-based metagenomics assembly was evaluated to define the advantages and limitations of this technology compared to the state of the art of metagenomic assembly. It is the first time that a global comparison of all the available tools has been carried out, paving the way towards the standardization of bioinformatics procedures applied to metagenomic sequencing based on nanopores.

Adriel Latorre's thesis was carried out at the spin-off of the Universitat de València Darwin Bioprospecting Excellence SL in collaboration with the Biotechnology and Synthetic Biology research group of I2SysBio under the supervision of Cristina Vilanova (Scientific Director of Darwin Bioprospecting Excellence) and Manuel Porcar (UV researcher at I2SysBio and General Director of Darwin Bioprospecting Excellence). During the development of his thesis Adriel Latorre has enjoyed a contract within the Industrial Doctorate Program (Ministry of Science and Innovation, FEDER). The qualifying panel was made up of Alex Mira (Oral Microbiome Laboratory, FISABIO), Olga Francino (Department of Animal and Food Science, UAB) and Juli Peretó (Department of Biochemistry and Molecular Biology, UV and I2SysBio), who have rated the thesis as outstanding.