The human gut virome is highly diverse, stable and individual-specific.

The human gut contains a vast array of viruses, mostly bacteriophages. The majority remain uncharacterised and their roles in shaping the gut microbiome and in impacting on human health remain poorly understood. We performed longitudinal metagenomic analysis of faecal viruses in healthy adults which reveal high temporal stability, individual specificity and correlation with the bacterial microbiome. Using a database independent approach which uses most of the sequencing data we report the existence of a stable, numerically predominant individual-specific persistent personal virome. Clustering of viral genomes and de novo taxonomic annotation identified several groups of crAss-like and <i>Microviridae</i> bacteriophages as the most stable colonizers of the human gut. CRISPR-based host prediction highlighted connections between these stable viral communities and highly predominant gut bacterial taxa such as <i>Bacteroides</i>, <i>Prevotella</i> and <i>Faecalibacterium</i>. This study provides insights into the structure of the human gut virome and serves as an important baseline for hypothesis-driven research.