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Large intestine-dwelling helminths affect microbiome composition. In sub-Saharan Africa, where helminth infections are endemic, the use of chemotherapeutic drugs is the primary strategy for controlling soil-transmitted helminthiases (STHs). However, the emergence of anthelmintic resistance necessitates the urgent exploration of alternative and complementary treatments to achieve the World Health Organization’s goal of eliminating STHs. One promising avenue involves the manipulation of gut microbiota in at-risk populations. This study aimed to enhance the understanding of the interplay between Trichuris trichiura and the gut microbiome. In this study, we used the Mini-FLOTAC technique for parasitological analyses and a shotgun metagenomic sequencing approach to investigate the effect of T. trichiura on the gut microbiome by comparing infected and non-infected women of reproductive age (WRA) from Pemba. Structural and functional analyses of the gut microbiome revealed that T. trichiura infection shaped the host gut microbiome in WRA. Some taxa vary according to infection status. Prevotella genus was more abundant in healthy participants, whereas species such as Weissella cibaria, Leuconostoc citreum (new emergent probiotics), and Leuconostoc lactis (starter) decreased in infected individuals, suggesting the use of potential probiotic treatments to mitigate dysbiosis induced by STHs. Furthermore, the overall number of common fungi, irrespective of species, was significantly higher in the mycobiome of Trichuris infected participants. Functional analysis revealed significant differences in metabolic pathways (p < 0.05), with cholesterol metabolism and pathogenic infections being more abundant in the infected samples than in the non-infected samples. In conclusion, this study sheds light on the intricate interactions between helminth infections and the gut microbiome in the WRA, particularly in STH-endemic regions. The identified associations between specific gut microbial changes and T. trichiura infection may pave the way for innovative complementary treatments to effectively combat STHs.

Modulating the gut microbiota is recognised as one strategy for preventing and fighting diseases. While the significant impact of diet on the gut microbiota’s composition and function has been extensively researched, there is a notable lack of studies on the interactions between diet, microbiota, and helminth infections. Here, we used a combination of self-reported food intake and a 16S rDNA sequencing approach to analyse the composition of the gut microbiota in women of reproductive age from the two main islands of the Zanzibar archipelago, where helminth infections are endemic. We also applied a Spearman correlation analysis to food/nutrients and gut microbiota. Our results reveal that, despite close ethnic and cultural ties, the participants’ gut microbiota differs depending on their location. A nutrient intake analysis revealed deficiencies in minerals and vitamins, indicating an imbalanced diet. A correlation analysis identified bacterial taxa consistently correlated with specific food or nutrients in healthy women from both locations, and in two types of helminth infections. Escherichia/Shigella abundances, usually associated with Trichuris trichiura infection, consistently correlated with insufficient levels of vitamins B2 and B12. In conclusion, our findings suggest that the increased consumption of specific food like cassava and fish, as well as essential nutrients such as calcium, B vitamins, and vitamin A, may modulate the gut microbiota of populations residing in regions where helminth infections are endemic.