The human gut virome is dominated by double-stranded DNA bacteriophages, among which crAss-like phages represent one of the most abundant yet least characterized lineages. However, most metagenomic studies have focused on populations from high-income countries, leaving regions such as Latin America underrepresented. In this study, we characterized the diversity, phylogenetic structure, and distribution of crAss-like phages in the Latin American gut microbiome using 606 fecal metagenomes from eight countries. Through metagenomic assembly and a lineage-specific workflow based on hidden Markov models (HMMs), we identified 81 complete crAss-like phage genomes and 38 Gubaphage genomes. Phylogenomic and average nucleotide identity analyses revealed that Latin American phages are distributed across all major crAss-like clades, with a significant contribution of unique lineages not represented in global catalogs. Notably, we identified a subclade within the epsilon lineage that is enriched in Latin American samples, suggesting a region-specific expansion. Gene content analyses revealed a highly conserved structural core and clade-specific accessory repertoires, including genes associated with lysogeny regulation in epsilon. Together, our results expand the global landscape of crAss-like phage diversity and highlight the importance of incorporating underrepresented regions to better understand the evolution and ecology of the human gut virome.
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