Geography and Intestinal Parasites are Associated with Human Gut Microbiome Variation, with Exploratory Ascaris-Associated Functional Signals in Colombian Children

Abstract Geography and intestinal parasites may jointly shape the gut microbiome, yet their relative contributions remain unclear, especially in underrepresented areas, such as Latin America. Using molecular detection for nine intestinal parasites, we sampled Colombian children from urban Medellín (n = 48) and rural Unguía (n = 32), who were classified as parasite-negative, monoparasitized, or polyparasitized. MetaPhlAn 4 and HUMAnN were used for species-level taxonomic and functional profiling. Medellín participants had higher Shannon diversity than Unguía participants (P = 0.0046). Geography was the strongest determinant of community structure (PERMANOVA pseudo-F = 4.998, P = 0.001), although regional dispersion also differed (PERMDISP P = 0.0002). Ascaris lumbricoides and Trichuris trichiura detection were associated with community composition (P = 0.010 and P = 0.013, respectively). Whereas Giardia duodenalis , Blastocystis species, and polyparasitism were not. Dispersion differed by Trichuris status (P = 0.030). Neither individual parasite presence nor polyparasitism significantly altered alpha diversity, and parasite loads were not correlated with diversity indices. Differential taxonomic signatures included both characterized and unclassified species-level genome bins. Functional profiling identified Ascaris as the only parasite associated with metabolic differences after false-discovery-rate correction, involving lipid and sulfur metabolism. These findings indicate that geography is the dominant ecological correlate of gut microbiome variation in this cohort, while parasite-associated effects are agent-specific.