IV Jornadas Latinoamericanas de Bacteriófagos

Knowledge of the human gut virome is largely derived from cohorts in Europe, North America, and Asia, while Latin American populations remain underrepresented. This limits our understanding of how gut phage diversity and community structure vary across geographic and socio-demographic contexts. Here, we characterize the virome across Latin America using 606 fecal samples collected from 33 cities in eight countries, spanning a continuous rural–urban gradient.
From this regional dataset, 47,882 viral sequences longer than 10 kb were recovered using metagenomic assembly and multiple independent viral detection approaches, and integrated with the Gut Phage Database (GPD). After dereplication and prevalence- and abundance-based filtering, a final set of 6,183 viral operational taxonomic units (vOTUs) was retained for downstream ecological analyses. Using this vOTU set, community structure was assessed through beta-diversity analyses, revealing consistent differentiation across the rural–urban gradient and geographic origin. Rural samples showed greater dispersion and higher viral diversity, whereas urban samples clustered more tightly, with Mexico and Ecuador contributing strongly to the observed variation, suggesting an interplay between geography and population-level factors.
To further explore the organization underlying these community-level patterns, the 6,183 vOTUs were grouped using shared gene network analyses with vConTACT3, enabling the inference of putative viral taxonomic clusters. This approach identified 155 orders, 853 families, and 3,865 genera, the majority lacking prior classification, highlighting extensive taxonomic novelty in the Latin American gut virome. Family-level composition, summarized through correlation heatmaps, revealed groups of viral families with contrasting associations to rural and urban contexts and country of origin.
Overall, this study establishes a regional reference framework for the diversity and ecological organization of human-associated bacteriophages in Latin America, revealing variation in gut virome composition associated with demographic factors such as lifestyle and highlighting the need for broader, well-characterized population studies.