Legends for Supplementary Material
Supplementary Figure S1 Principal components analysis of bacterial communities in Drosophila determined from 16S rRNA reads with Wolbachia excluded (white square) and included (gray triangle). (a) set-1, (b) set-2, (c) set-3. The data for Wolbachia excluded are displayed in Figure 2 of the main text.
Supplementary Figure S2 PCR products of five bacterial taxa in dissected guts of D. melanogaster strains (a) ZH26, (b) Canton-S. Abbreviations: Ap: Acetobacter pomorum, At: Acetobacter tropicalis; Lb: Lactobacillus brevis; Lf: Lactobacillus fructivorans; Lp: Lactobacillus plantarum.
Supplementary Figure S3 Rarefaction curves of 16S rRNA gene pyrosequences, with OTUs clustered at pair-wise sequence similarity threshold of 97%. The samples contributing to sets 1, 2 and 3 are shown in Supplementary Table S3b-d, and the two technical replicates of D. melanogaster and D. quinaria are indicated.
Supplementary Figure S4 Number of 454 reads per OTU in two technical replicates of V2 region of 16S rRNA gene amplicons for (a) Drosophila melanogaster and (b) Drosophila quinaria.
Supplementary Table S1 Drosophila used for taxon-specific PCR analysis of Acetobacter and Lactobacillus species, and frequency of flies containing each bacterial species Supplementary Table S2 Primer sequences. (a) Taxon-specific primers for PCR amplification of 16S rRNA gene of bacteria. (b) Primers used in the pyrosequencing experiment. The multiplex identifiers (MID) sequences are highlighted in bold.
Supplementary Table S3 454 sequence reads and OTUs of bacteria. (a) Whole bodies of D. melanogaster strain ZH26. (b) Dissected guts of Drosophila set-1, including two technical replicates of D. melanogaster. (c) Dissected guts of Drosophila set-2, including two technical replicates of D. quinaria. (d) Whole bodies of field-collected D. melanogaster. (e) Combined datasets of dissected guts of Drosophila set-1 and set-2. (f) Wild D. melanogaster (AZ, NY1, NY2) and laboratory D. melanogaster (CS1-4: strain Canton-S - CS1: all adult samples of Wong et al., (2011) combined; CS2: sample in set-1 of this study; CS3: dataset of Ridley et al. (2012); 4: dataset of Ridley (2011); and strain ZH26 of this study.
Supplementary Table S4 Comparison of Pyrotagger and QIIME outputs of 454 sequencing
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