Fig. 1

Infection reduces microbiome richness at the site of infection, and the Ascaris microbiome is less rich than its environment. A Experimental design. German Landrace pigs were infected with either two inoculums of 1000 Ascaris eggs (exp. 1) 2 days apart or a single inoculum of 4000 eggs (exp. 2). Four noninfected controls were also included in this study. Infection was allowed to develop to nematode patency at 56 dpi; controls were kept until 57 dpi. Porcine intestinal contents and Ascaris intestines were harvested for 16S microbiome sequencing. This experiment was performed in two batches. B Lower richness in the jejunum of infected hosts in contrast to noninfected hosts. Bacterial amplicon sequence variant (ASV) richness in the different intestinal compartments, as represented in the scheme, of infected and noninfected hosts. Each point in the box plot represents an individual pig, and the color relates to the infection status. CAscaris microbiome has significantly lower bacterial richness than both noninfected and infected host jejunum microbiome. ASV richness in the intestines of Ascaris worms is lower than at the site of infection (jejunum) in infected and noninfected hosts (data from B). Significance values: *** = p adjusted < 0.001, * = p adjusted < 0.05, Mann–Whitney U-(MWU) tests with Bonferroni correction for multiple testing. DAscaris share specific taxa with infected pigs at the site of infection. ASVs with relative abundance higher than 0.01% in at least 50% of the individuals were determined. Despite the significant difference in richness between jejunum and Ascaris microbiomes, they shared 12 highly abundant and prevalent ASVs. Ascaris shared three ASVs exclusively with infected pigs but none just with noninfected pigs. Jejunum microbiomes from infected and noninfected pigs shared 27 highly abundant and prevalent ASVs, and each had nine unique and specific highly abundant and prevalent ASVs