Helminth parasites have been shown to have systemic effects in the host. Using shotgun metagenomic sequencing, we characterise the gut microbiome and resistome of 113 Zimbabwean preschool-aged children (1–5 years). We test the hypothesis that infection with the human helminth parasite, Schistosoma haematobium, is associated with changes in gut microbial and antimicrobial resistance gene abundance/diversity. Here, we show that bacteria phyla Bacteroidetes, Firmicutes, Proteobacteria, and fungi phyla Ascomycota, Microsporidia, Zoopagomycota dominate the microbiome. The abundance of Proteobacteria, Ascomycota, and Basidiomycota differ between schistosome-infected versus uninfected children. Specifically, infection is associated with increases in Pseudomonas, Stenotrophomonas, Derxia, Thalassospira, Aspergillus, Tricholoma, and Periglandula, with a decrease in Azospirillum. We find 262 AMR genes, from 12 functional drug classes, but no association with individual-specific data. To our knowledge, we describe a novel metagenomic dataset of Zimbabwean preschool-aged children, indicating an association between urogenital schistosome infection and changes in the gut microbiome.

蠕虫寄生虫已被证明对宿主具有系统性影响。使用鸟枪法宏基因组测序，我们对 113 名津巴布韦学龄前儿童（1-5 岁）的肠道微生物组和耐药组进行了表征。我们检验了这样的假设：人类蠕虫寄生虫埃及血吸虫的感染与肠道微生物和抗菌素耐药性基因丰度/多样性的变化有关。在这里，我们表明细菌门拟杆菌门、厚壁菌门、变形菌门和真菌门子囊菌门、微孢子虫门、动物菌门在微生物组中占主导地位。血吸虫感染儿童与未感染儿童之间变形菌门、子囊菌门和担子菌门的丰度不同。具体而言，感染与假单胞菌属、寡养单胞菌属、德克夏菌属、海螺菌属、曲霉属、口蘑属和周缘菌属的增加有关，而固氮螺菌属的减少有关。我们从 12 类功能药物中发现了 262 个 AMR 基因，但与个体特异性数据没有关联。据我们所知，我们描述了津巴布韦学龄前儿童的一个新的宏基因组数据集，表明泌尿生殖道血吸虫感染与肠道微生物组变化之间的关联。