Combinazione di approcci omici con analisi di equilibri di flusso per esplorare le dinamiche di popolazione in microbiomi anaerobici

Microbial methanogenic metabolism is one of the oldest bio-activities on Earth. This process is one of the main determinants of the fluxes in the global carbon cycle. In fact, in natural ecosystems, around one billion tons of methane is formed through microbial activity. Methanogenic process, mediated by complex microbial communities in anaerobic and microaerophilic environments, has raised great attention due to its energy generation potential. Constraint-based genome-scale metabolic modelling and metabolic flux balance analysis are pioneeristic tools for the investigation of large-scale relationships between genotype, phenotype and environment. Metabolic flux balance allows the integration of genomic data in the individual species-level metabolic models, feedstock information in the form of import flux bounds, and abundance data derived from metagenomic shotgun sequencing. The research reported in this PhD thesis focused on the establishment of a robust pipeline of flux balance analysis to unravel dynamics behind microbial communities involved in anaerobic digestion through two different cases of study: the investigation of a bioengineering process and the analysis of health-related microbial dynamics. The first case of study has been the analysis of the global microbial community behind the Anaerobic Digestion process in engineered systems. Anaerobic Digestion is the process leading to the generation of energy from biogas. Deciphering the anaerobic digestion “black box” is essential to optimise the biogas production and can allow the development of strategies to improve the process efficiency. The microbial community responsible for biogas generation is extremely complex and modifications of the environmental and operational parameters of the reactors deeply influence the abundance of the community members. This investigation helped decipher the correlation existing between species abundance and operational parameters of the biogas reactors. Understanding the required conditions for natural enhancement of desired endogenous consortia under anaerobic conditions paved the way to improve the yield of methane produced. The use of reactors enables a fine tuning of the anaerobic digestion, a dissection and a magnification of each step and component of the process. Therefore, the second case of study involved the application of the anaerobic digestion system as an ecosystem in a vessel for the analysis of metagenomic data from Crohn’s disease patients. In this model an additional complexity was considered: the integration of microbial and host metabolisms. Crohn’s disease is an inflammatory bowel disease affecting the digestive tract, it can lead to abdominal pain, severe diarrhea, weight loss and malnutrition. The inflammation often spreads deep into layers of affected bowel tissues and can be both painful and debilitating, and sometimes may lead to life-threatening complications. Although there is not widespread agreement on the aetiology of Crohn’s disease, microorganisms are recognized as the leading cause of the characteristic severe inflammatory response. The second case of study aimed to analyze metagenomic data of a Crohn’s disease patient with flux balance analysis to inspect the major modifications occurring in his gut microbiota during each stage of the disease development. The core of the project was the integration of longitudinal metagenomic data with flux balance analysis. In particular the development of the gut microbiome during acute and relapsing phases was studied to inspect the main microbe-microbe and microbe-host interplays responsible for the inflammation. The analysis shed light on the most altered metabolites during the disease onset.