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