Fig. 3.

Composition at the phylum level of the ovine microbiome (abomasal lumen contents and faeces) and nematode microbiome (larval and adult nematodes). Each ‘Nematode Larvae’ sample contains ~10,000 pooled larvae, five of which are pre-infection larvae and ten of which are post-infection larvae; each ‘Adult Nematode’ sample contains 100 pooled adult nematodes (five H. contortus (four males, one mixed sex) and seven T. circumcincta (five females, one male, one mixed sex) samples); each ‘Abomasum’ sample is derived from the abomasal washings of one of four lambs; and each ‘Faeces’ sample is derived from one of four lambs across ten time points. Phyla constituting less than 1% of the total phylum distribution were labelled ‘Other’. ‘Nematode Larvae’ were omitted from statistical testing due to their obvious distinctiveness from the other sample groups. The other three samples were compared for proportions of the different phyla identified—initially with a Kruskal–Wallis test, and then a Mann–Whitney U test, making individual comparisons if warranted. Critical values were adjusted using the Bonferroni method