Integrating Metagenomics for Helminth Detection

Soil-transmitted helminths (STH) are prevalent in (sub)tropical regions and pose significant public health challenges, particularly in low-resource settings. These gut-dwelling parasites interact with the microbiota and host immunity, yet their impact on microbial communities remains poorly understood. Traditional STH detection methods, such as microscopy and qPCR, are labor-intensive and rarely integrated into microbiome studies, limiting insights into these interactions. This project explores metagenomic sequencing as a non-invasive tool for STH detection while assessing microbiome alterations linked to infection. We generated 310 fecal metagenomes from mother-child pairs in rural and semi-urban Gabon, enabling a comprehensive analysis of microbial and parasitic communities. By comparing metagenomic detection with conventional diagnostics, we evaluated sequencing accuracy and examined STH-associated microbiome shifts. Note: (1) Metagenomes with the same study ID correspond to samples sequenced across multiple runs/lanes, which were aggregated before analysis. (2) The read counts in the manuscript are lower than those in ENA metadata because the former represent post-QC read counts, while the latter reflect raw sequencing reads