Supplementary Information

S1: Rarefaction plot showing relationships between sampling depth and number of bacterial ASVs detected
S2: Most abundant phyla, orders and genera (> 1% of all sequences) acrossF0 adults.BP_Gr1 = F0adults emerging from C. grandis and ovidepositing on S. melongena from Bassin Plat (BP), BP_Gr2 = on C. grandisfrom BP, BP_Gr3 = on C. sativus from BP, M_Gr1 = on S. melongena from Manapany (M), M_Gr2 = on C. grandis from M, M_Gr3 = on C. sativus from M.
S3: ANOVA on α diversity metrics. (Abundance coverage estimator, Inverse Simpson index, Faith’s phylogenetic diversity) calculated from F0 adult microbiomes from different host plants (C. grandis, C. sativus, S. melongena ) and sites (BP: Basin Plat, M: Manapany). n.s.: not significant; ∗: P < 0.05, ∗∗: P < 0.01, *** P < 0.001. C: Cochran’s C.
S4: PERMANOVA and a posteriori comparisons on A) Unweighted Unifrac and B) Generalized Unifrac distances calculated from parental F0 adult microbiomes from two sites (BP: Basin Plat, M: Manapany) and three parental groups for each site. n.s.: not significant; ∗: P < 0.05, ∗∗: P < 0.01, *** P < 0.001.
S5: Principal Coordinates Analysis (PCoA) of microbial communities of F0 adults of Z. cucurbitae. BP_Gr1 = F0 adults emerging from C. grandis and ovidepositing on S. melongena from Bassin Plat (BP), BP_Gr2 = on C. grandis from BP, BP_Gr3 = on C. sativusfrom BP, M_Gr1 = on S. melongena from Manapany (M), M_Gr2 = onC. grandis from M, M_Gr3 = on C. sativus from M. 95% confidence ellipses are shown for each group.
S6: Barplot showing the relative abundance of the most abundant Phyla, orders and genera (> 1% of all sequences) acrossF1 larvae from 2 sites (BP: Basin Plat, M: Manapany) and three host plants ( Co: C. grandis , Cu: C. sativus , So: S. melongena ).
S7: a posterioricomparisons between α diversity metrics. (Abundance coverage estimator, Inverse Simpson index, Faith’s phylogenetic diversity) calculated from F1 larvae from different host plants (Co: C. grandis , Cu: C. sativus , So: S. melongena ) and sites (BP: Basin Plat, M: Manapany). n.s.: not significant; ∗: P < 0.05, ∗∗: P < 0.01, *** P < 0.001.
S8: α diversity metrics. (Abundance coverage estimator, Inverse Simpson index, Faith’s phylogenetic diversity) calculated from F1larvae from different host plants (Co: C. grandis , Cu: C. sativus , So:S. melongena ) and sites (BP: Basin Plat, M: Manapany)
S9: a posteriori comparisons between A) Unweighted Unifrac and B) Generalized Unifrac distances calculated from F1larvae from different host plants (Co: C. grandis, Cu: C. sativus, So: S. melongena) and sites (BP: Basin Plat, M: Manapany). n.s.: not significant; ∗: P < 0.05, ∗∗: P < 0.01, *** P < 0.001.
S10: ALDEx2 analysis of bacterial genera between larval microbiomes from larvae between different host plants and between different sites using ALDEx2. rab.win. = median centered log ratio (clr). Co: C. grandis , Cu: C. sativus , So: S. melongena . BP: Basin Plat, M: Manapany.