Supplementary Table 1. Butterfly sample sizes, taxonomy and feeding guilds Number of individuals retained per host species after rarefaction of the bacterial and fungal sequencing datasets, host species taxonomy, and feeding guilds. Bacteria Fungi Host Species Code Family Subfamily Tribe Genus Species Diet Samples Samples Ade_cytherea 6 3 Nymphalidae Limenitidinae Limenitidini Adelpha cytherea nectar Aer_eurimedia 11 2 Nymphalidae Danainae Ithomiini Aeria eurimedia nectar Ana_fatima 10 1 Nymphalidae Nymphalinae Victorinini Anartia fatima nectar Ant_miltiades 3 3 Nymphalidae Morphinae Morphini Antirrhea miltiades fruit Aph_boisduvalii 5 5 Pieridae Coliadinae NA Aphrissa boisduvalii nectar Ara_togarna 6 5 Lycaenidae Theclinae Eumaeini Arawacus togarna nectar Arc_demophon 8 6 Nymphalidae Charaxinae Preponini Archaeoprepona demophon fruit Cal_atreus 15 12 Nymphalidae Morphinae Brassolini Caligo atreus fruit Cal_brasiliensis 10 8 Nymphalidae Morphinae Brassolini Caligo brasiliensis fruit Cal_illioneus 6 6 Nymphalidae Morphinae Brassolini Caligo illioneus fruit Cat_orgetorix 1 NA Nymphalidae Morphinae Brassolini Catoblepia orgetorix fruit Chl_gaudealis 16 9 Nymphalidae Nymphalinae Melitaeini Chlosyne gaudealis nectar Cis_sp1 2 NA Nymphalidae Satyrinae Satyrini Cissia sp1 fruit Cis_terrestris 20 5 Nymphalidae Satyrinae Satyrini Cissia terrestris fruit Cit_pireta 12 11 Nymphalidae Satyrinae Haeterini Cithaerias pireta fruit Col_sp 2 NA Nymphalidae Nymphalinae Coeini Colobura sp fruit Dry_iulia 4 2 Nymphalidae Heliconiinae Heliconiini Dryas iulia nectar Dul_polita 6 6 Nymphalidae Satyrinae Haeterini Dulcedo polita fruit Eup_westwoodi 4 1 Nymphalidae Satyrinae Satyrini Euptychia westwoodi fruit Eur_albula 4 5 Pieridae Coliadinae NA Eurema albula nectar Eur_nise 5 5 Pieridae Coliadinae NA Eurema nise nectar Ham_feronia 1 NA Nymphalidae Biblidinae Biblidini Hamadryas feronia fruit Hel_cydno 11 2 Nymphalidae Heliconiinae Heliconiini Heliconius cydno nectar Hel_erato 4 2 Nymphalidae Heliconiinae Heliconiini Heliconius erato nectar Hel_sara 9 1 Nymphalidae Heliconiinae Heliconiini Heliconius sara nectar Hes_sp2 1 NA Hesperiidae Hesperiinae NA Hesperiinae sp2 nectar Hes_sp3 1 NA Hesperiidae Hesperiinae NA Hesperiinae sp3 nectar Hyp_cassotis 2 NA Nymphalidae Danainae Ithomiini Hypoleria cassotis nectar pseudognetu Jem_pseudognetus 1 NA Hesperiidae Pyrginae Pyrrhopygini Jemadia nectar s Mar_chiron 4 2 Nymphalidae Cyrestinae Cyrestini Marpesia chiron nectar Mar_merops 4 3 Nymphalidae Cyrestinae Cyrestini Marpesia merops nectar Mar_petreus 7 5 Nymphalidae Cyrestinae Cyrestini Marpesia petreus nectar Mec_lysimnia 1 NA Nymphalidae Danainae Ithomiini Mechanitis lysimnia nectar Mec_polymnia 9 3 Nymphalidae Danainae Ithomiini Mechanitis polymnia nectar Nes_aglaura 2 NA Nymphalidae Biblidinae Epicaliini Nessaea aglaura fruit Ops_bogotanus 1 1 Nymphalidae Morphinae Brassolini Opsiphanes bogotanus fruit Ops_cassina 3 3 Nymphalidae Morphinae Brassolini Opsiphanes cassina fruit Ops_sp1 3 3 NA NA NA NA NA NA Par_ocirrhoe 5 NA Nymphalidae Satyrinae Satyrini Pareuptychia ocirrhoe fruit Par_sp 1 1 Papilionidae Papilioninae Troidini Parides sp nectar Pho_argante 8 10 Pieridae Coliadinae Coliadini Phoebis argante nectar Pie_helvina 13 11 Nymphalidae Satyrinae Haeterini Pierella helvina fruit Pie_luna 1 NA Nymphalidae Satyrinae Haeterini Pierella luna fruit pie_sp1 1 NA Pieridae NA NA pieridae sp1 nectar pie_sp2 1 NA Pieridae NA NA pieridae sp2 nectar Pre_sp 1 NA Nymphalidae Charaxinae Preponini Prepona sp fruit rio_sp1 1 NA Riodinidae NA NA riodinidae sp1 nectar Sip_epaphus 1 NA Nymphalidae Nymphalinae Victorinini Siproeta epaphus nectar Tay_laches 17 11 Nymphalidae Satyrinae Satyrini Taygetis laches fruit Tay_zimri 11 5 Nymphalidae Satyrinae Satyrini Taygetis zimri fruit Tig_acesta 1 NA Nymphalidae Nymphalinae Nymphalini Tigridia acesta fruit Urb_teleus 8 3 Hesperiidae Eudaminae NA Urbanus teleus nectar Supplementary Table 2. Food sample sizes. Number of individual samples retained per flower or fruit species rafter rarefaction of the bacterial and fungal sequencing datasets. Bacteria Fungi Plant Species Food type Samples Samples Dipteryx oleifera 12 13 wild fruit Hamelia patens 8 7 nectar Odontonema cuspidatum 4 3 nectar Psiguria trifila 8 7 nectar Psychotria elata 4 3 nectar Psychotria suerrensis 5 5 nectar Ruellia terminalis 6 4 nectar Stachytarpheta frantzii 8 8 nectar Warszewiczia coccinea 3 2 nectar trap bait 25 14 trap bait Supplementary Table 3. Taxonomic identities of the removed bacterial contaminants. These OTUs were classified as contaminants and removed from the dataset because they were present at higher relatively abundances in the negative controls than in the butterfly samples. OTU ID Phylum Class Order Family Genus Species Notes OTU_165 Actinobacteria Actinobacteria Actinomycetales Corynebacteriaceae Corynebacterium OTU_385 Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Commensalibacter intestini OTU_1532 Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acetobacter a OTU_1614 Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acetobacter OTU_99 Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae b OTU_55 Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Delftia OTU_62 Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Stenotrophomonas OTU_76 Bacteroidetes Bacteroidia Bacteroidales Porphyromonadaceae Dysgonomonas OTU_1344 Bacteroidetes Bacteroidia Bacteroidales Porphyromonadaceae Dysgonomonas OTU_1499 Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus OTU_116 Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus OTU_1846 Firmicutes Bacilli Lactobacillales Enterococcaceae Tetragenococcus halophilus OTU_334 Firmicutes Bacilli Lactobacillales Enterococcaceae OTU_128 Firmicutes Clostridia Clostridiales [Tissierellaceae] Finegoldia a. RDP classified as Swaminathania with low confidence; closest NCBI match was Acetobacter. b. Closest NCBI genus match was Ottowia. Supplementary Table 4. Taxonomic identities of the removed fungal contaminants. 792 fungal OTUs were classified as contaminants and removed from the dataset. OTU ID Phylum Pconf Class Cconf Order Oconf Family Fconf Genus Gconf Species Sconf OTU_1193 Ascomycota 100% Leotiomycetes 79% Helotiales 79% Helotiaceae 45% Hymenoscyphus 32% Articulospora tetracladia 32% OTU_2710 Ascomycota 100% Leotiomycetes 100% Helotiales 100% Helotiaceae 100% Hymenoscyphus 100% Hymenoscyphus caudatus 73% OTU_591 Ascomycota 97% Leotiomycetes 65% Helotiales 52% Helotiaceae 25% Hymenoscyphus 18% Hymenoscyphus fucatus 15% OTU_2358 Ascomycota 94% Leotiomycetes 61% Helotiales 52% Helotiaceae 26% Hymenoscyphus 25% Hymenoscyphus fucatus 21% OTU_1239 Ascomycota 94% Leotiomycetes 51% Helotiales 50% Helotiaceae 19% Hymenoscyphus 15% Hymenoscyphus serotinus 5% OTU_2121 Ascomycota 70% Leotiomycetes 38% Helotiales 32% Helotiaceae 6% Hymenoscyphus 6% Hymenoscyphus sp KUS_F51352 4% OTU_1456 Ascomycota 52% Leotiomycetes 8% Helotiales 7% Helotiaceae 6% Hymenoscyphus 6% Hymenoscyphus sp KUS_F51352 6% OTU_897 Ascomycota 100% Leotiomycetes 100% Helotiales 85% Helotiaceae 46% Hymenoscyphus 43% uncultured Hymenoscyphus ericae complex 43% OTU_660 Ascomycota 99% Leotiomycetes 97% Helotiales 84% [Helotiales] 22% Cadophora 22% Cadophora finlandica 22% OTU_2075 Ascomycota 98% Leotiomycetes 96% Helotiales 62% [Helotiales] 40% Cadophora 38% Cadophora finlandica 38% OTU_1001 Ascomycota 98% Leotiomycetes 97% Helotiales 55% [Helotiales] 48% Cadophora 48% Cadophora finlandica 48% OTU_561 Ascomycota 100% Leotiomycetes 100% Helotiales 98% [Helotiales] 96% Cadophora 96% Cadophora finlandica 96% OTU_2528 Ascomycota 99% Leotiomycetes 93% Helotiales 75% [Helotiales] 42% Cadophora 29% Cadophora finlandica 29% OTU_2548 Ascomycota 100% Leotiomycetes 98% Helotiales 62% [Helotiales] 41% Cadophora 39% Cadophora finlandica 39% OTU_2671 Ascomycota 100% Leotiomycetes 100% Helotiales 100% Vibrisseaceae 100% Phialocephala 98% Phialocephala cf fortinii TV_2003 87% OTU_2114 Ascomycota 100% Leotiomycetes 100% Helotiales 100% Vibrisseaceae 100% Phialocephala 100% Phialocephala scopiformis 99% OTU_1448 Ascomycota 67% Leotiomycetes 10% Helotiales 10% Vibrisseaceae 9% Phialocephala 9% Phialocephala trigonospora 9% OTU_1197 Ascomycota 100% Leotiomycetes 100% Helotiales 100% Vibrisseaceae 100% Phialocephala 100% Phialocephala turiciensis 70% OTU_834 Ascomycota 85% Leotiomycetes 36% Helotiales 29% Vibrisseaceae 9% Phialocephala 9% Phialocephala virens 9% OTU_498 Ascomycota 96% Leotiomycetes 91% Helotiales 75% Vibrisseaceae 22% Phialocephala 21% Phialocephala virens 21% OTU_190 Ascomycota 99% Leotiomycetes 93% Helotiales 72% Vibrisseaceae 22% Phialocephala 22% Phialocephala virens 22% OTU_2084 Ascomycota 100% Leotiomycetes 88% Helotiales 55% Vibrisseaceae 9% Phialocephala 9% Phialocephala virens 9% OTU_398 Ascomycota 100% Leotiomycetes 82% Helotiales 78% Vibrisseaceae 51% Phialocephala 51% Phialocephala virens 51% OTU_868 Ascomycota 100% Leotiomycetes 100% Helotiales 100% Vibrisseaceae 48% Phialocephala 48% Phialocephala virens 48% OTU_626 Ascomycota 100% Leotiomycetes 85% Helotiales 83% Vibrisseaceae 15% Phialocephala 15% Phialocephala virens 15% OTU_1988 Ascomycota 95% Leotiomycetes 56% Helotiales 34% Vibrisseaceae 10% Phialocephala 10% Phialocephala virens 10% OTU_320 Ascomycota 100% Leotiomycetes 100% [Leotiomycetes] 55% [Leotiomycetes] 55% Meliniomyces 55% Meliniomyces bicolor 39% OTU_298 Ascomycota 100% Leotiomycetes 100% [Leotiomycetes]