Innovative bioinformatics approaches in microbial research

Bioinformatics has become integral to modern biological research, offering critical tools for data analysis and developing innovative methodologies across diverse scientific disciplines. This thesis explores the application of bioinformatics in microbial research, with a particular focus on bacterial genomics, evolution, and structural biology. The work is divided into two main sections: the development of bioinformatics tools and methods, and their application to epidemiological studies using real-world datasets. The first section includes the description of P-DOR, a novel pipeline designed to facilitate outbreak reconstruction and characterization by integrating genomic data with epidemiological metadata. The subsequent chapter discusses the development of a novel index to assess bacterial genomic plasticity, capturing the temporal dynamics of gene acquisition and loss, which are crucial for understanding pathogen adaptation. In the third chapter of the first main section, the thesis delves into in silico structural biology, as a new tool to investigate host-microbe interactions. In particular, I developed an AlphaFold-Multimer wrapper, aimed to enhance protein-protein interaction predictions, significantly improving the efficiency of large-scale screenings. The second section applies these and other bioinformatics tools to microbial datasets of biomedical interest, the first being an epidemiological reconstruction of a multidrug-resistant Acinetobacter baumannii outbreak during the COVID-19 pandemic in Italy. The study underscores the importance of genomic surveillance and robust infection control measures in outbreak management. The final chapter presents a global genomic analysis of the zoonotic parasite Cryptosporidium parvum, revealing the evolutionary dynamics and genetic exchanges that have shaped its population structure across Europe and North America. Overall, this thesis wants to underline the importance of bioinformatics in addressing critical questions in microbial research, providing insights into pathogen evolution, outbreak management, and host-microbe interactions.