The human gut virome: the dark matter of the human gut universe

The gut is home to trillions of microbes, with bacteria and viruses being its most abundant members, forming a dynamic ecosystem that profoundly influences human health. While gut bacterial communities have been linked to various health conditions, the viral component, known as the virome, has remained largely unexplored. This research sheds light on the human gut virome, examining its interactions with bacteria and humans from infancy to adulthood and its role in health and disease. This research reveals how the gut microbiome begins to form at birth, shaped by factors like delivery mode, feeding practices, and colonization by microbes from the maternal gut. The infant gut undergoes rapid development, with interactions between viruses and bacteria playing a crucial role in the maturation of the infant gut ecosystem. In adulthood, the gut microbiome stabilizes and is characterized by individual-specific bacterial and viral communities. The findings of this thesis show how these communities respond to changes like diet and link shifts in gut viruses to conditions such as inflammatory bowel disease (IBD) and obesity. For example, a reduction in specific viral populations, such as Crassvirales phages, was associated with IBD, proposing their importance in maintaining gut health. By developing advanced methods to study gut viruses, this work has expanded knowledge of their diversity, dynamics, and stability. It underscores the importance of viewing the gut microbiome as an interconnected ecosystem where bacteria and viruses work together, offering new perspectives for understanding and improving human health.