Abstract
Background: Intestinal parasitic infections, caused by helminths and protozoa, are globally distributed and major causes of worldwide morbidity. The gut microbiota may modulate parasite virulence and host response upon infection. The complex interplay between parasites and the gut microbiota is poorly understood, partly due to sampling difficulties in remote areas with high parasite prevalence and burden. Results: In a large study of children in Bissau, Guinea-Bissau, we found high prevalence of intestinal parasites, including hookworms, Entamoeba spp. and Giardia lamblia. By high-quality sequencing of the 16S rRNA gene of fecal samples stored on filter paper from a total of 1,204 children, we demonstrate that the bacterial microbiota is more or less unaltered by helminth infections, whereas it is shaped by the presence of both pathogenic and non-pathogenic protozoa, including Entamoeba spp. and Giardia lamblia. Within-sample (alpha) diversity remains largely unaffected, whereas overall community composition (beta diversity) is significantly affected by infection with both nonpathogenic Entamoeba coli (R2=0.0131, P= 0.0001) and Endolimax nana (R2=0.00902, P= 0.0001), and by pathogenic Entamoeba histolytica (R2=0.0164, P= 0.0001) and Giardia lamblia (R2=0.00676, P= 0.0001). Heavy infection load with multiple parasite species induces more pronounced shifts in microbiota community than mild ones. A total of 31 bacterial genera across all four major gut bacterial phyla associates with protozoan infection, including increased abundance of Prevotella, Campylobacter and two Clostridium clades (IV and WIVb), and decreased abundance of Collinsella (associated with irritable bowel syndrome), Lactobacillus, Ruminococcus, Veillonella and one Clostridium clade (XVIII). Further, we demonstrate that filter papers are usable for storage of samples at room temperature in large-scale studies where immediate freezing is not possible with minor alterations of microbiota composition. Conclusion: In the present largest-to-date study, we demonstrate that the fecal bacterial microbiota is shaped by intestinal parasitic infection, with most pronounced associations for protozoan species. Our results provide insights into the interplay between the microbiota and intestinal parasites, which are useful to understand infection outcome and design further studies aimed at optimizing treatment strategies.