All statistical analyses on community structure were performed in R v4.0.2 [31]. Species richness was calculated by summing up the number of helminth species per individual. To investigate helminth community diversity and whether it was dominated by a few species, the inverse Simpson’s diversity index was calculated using Vegan package [32]. The value of Simpson's D ranges from 0 to 1, with 0 representing infinite diversity and 1 representing no diversity, so the larger the value of D, the lower the diversity. For this reason, Simpson's index is expressed as its inverse (1/D). We used linear models (LM) for Figs. Figs.22 and and3,3, and generalized mixed models (GLMM), with a repeated measure design, was used to assess the effects on the nemabiome composition after anthelmintic treatment (Fig. (Fig.4g–l),4g–l), using respective diversity indices as the response variable, treatment as a fixed factor and farm as a random structure. GLMM was calculated using the MCMCglmm package [33]. Using a Bayesian framework is robust for analyzing data with unbalanced sample size groups. Run parameters are presented in Table Table2.2. Post-treatment larval culture samples for two IVM farms were omitted because of successful treatment (Fig. (Fig.4j);4j); hence, no nematode DNA was to be analyzed. Data were visualized with ggplot2 [34].

a Nemabiome composition for adults (n = 74) and lambs (n = 84). A difference in nematode species richness (b), and adults were dominated by a few species compared to lambs (c). Boxplots inside the violin plots display the median

a Nemabiome composition for lambs for two periods (2007 n = 35, 2013–2016 n = 49), b Species richness and c Inverse Simpson's diversity index for each period. Boxplots inside the violin plots display the median

Nemabiome composition (ac), EPG (df) and diversity indices: species richness (gi). The shape of the violin plots in panel G indicate that anthelmintic treatment will have a larger effect for individuals with higher species richness prior to treatment. Inverse Simpson's index (jl) prior to and after anthelmintic treatment for ivermectin (n = 25) in the left column, albendazole (n = 14) in the middle column and levamisole (n = 5) in the right column. Boxplots inside the violin plots display the median

Output from MCMCglmm testing of the impact of each of the three anthelmintic drug treatments (IVM = ivermectin, ABZ = albendazole, LEV = levamisole) on species richness and inverse Simpson’s diversity index (see also Fig. Fig.4g–l)4g–l) for farms sampled before and after anthelmintic treatment

1Statistically significant fixed effects are marked with * (P < 0.05)

Prior settings: R (V = 2, nu = 0.2); G (V = 2, nu = 0.02)

Run settings: burn-in  =  50,000; iterations  =  100,000; thinning interval  =  10

As an example, untreated sheep were infected with on average 0.66 fewer species compared to IVM treated sheep. No such effect was found in species richness for LEV, nor for any of the inverse Simpsons’ indices

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