Identification of biomarkers predictive of Ascaris infection and anthelmintics mediated worm clearance using a swine model

In this study, we attempt to understand how the gut microbiota shapes up host-parasite relationships using an integrated multi-omics analysis in a swine-Ascaris model. Thirty 6- to 8-month-old female pigs were randomly divided into three groups (N=10 per group). One group served as normal uninfected controls (NU); the remaining 20 pigs were inoculated per os with ~10,000 infective A. suum eggs; and the infection was allowed to progress for 35 days post-infection (dpi). At 21 dpi, one of the infected groups (IP) was treated with a single daily dose of the anthelmintic drug Panacur for three consecutive days while the other infected pigs remained untreated (IU). At necropsy, intestine pathology was scored; and serum and fecal samples were collected for untargeted metabolome analysis. The fecal microbiota was characterized using full-length 16S rRNA gene-based sequencing and the DADA2 algorithm. Fecal and serum metabolites were categorized for their origin using MetOrigin. The integrated multi-omics analysis was performed using DIABLO algorithms and NetCoMi networking tools. Our results show that A. suum worms were well developed in the infected group, which had a significantly reduced alpha diversity (Simpson, P <0.005) compared to uninfected controls. The infection also altered the abundance of at least 17 bacterial species or strains, including butyrate-producing Clostridium, such as C. butyricum, altering the abundance of 51 fecal metabolites, including microbiota-derived metabolites such as glutaric acid and p-Cresol sulfate, and succinate of mixed origin. Moreover, the anthelmintic treatment was efficacious and eliminated all worms from the gut. Nevertheless, 11 pathways of both host and microbiota origin were significantly enriched in the gut of successfully treated pigs, including peptidoglycan biosynthesis, histidine metabolism (in both feces and serum), and primary bile acid biosynthesis, suggesting the infection-induced alterations may not be transient. In conclusion, the host microbiota modified swine-Ascaris interactions via three different mechanisms. First, microbiota-derived metabolites directly regulate host gene expression, which in turn affects host physiology and immune responses. Second, plasticity of the gut microbiota allows the exploitation of the niche differentiated upon infection, resulting in blossom of certain species or strains in the gut of post-treated animals. Lastly, the host microbiota is likely one of the key determinants of parasite gut microbiota, indirectly exerting its effect on parasite physiology and nutrition. Further studies aiming to understand reciprocal yet complex relations between the gut microbiota, the host, and parasites (including parasite gut microbiota) will be conducive to the design of next-generation functional anthelmintics.