16s Seq of Ceratitis capitata
For sequencing, each biological replicate was a pool of five adult flies. Flies were surface sterilized for 30 seconds in 0.5% sodium hypochlorite (bleach) (Sigma-Aldrich, Cat. No.7681529) and then washed for 30 seconds in sterile 1M PBS (pH 7.4) three times before being homogenized. We used sterilised pestles to homogenise the samples inside 2-mL microcentrifuge tubes and used three freeze/thaw cycles in liquid nitrogen. 100 L of the third PBS washes were plated on media plates and incubated for up to 48h at 35C to test the efficiency of our protocol; there was no microbial growth in any of the tests. All procedures were performed under a sterilised Biosafety Cabinet We extracted DNA with the DNeasy Blood and Tissue Kit (Qiagen) and quality checked using a NanoDrop (REF). Approximately 100 ng of DNA per sample was used as the template for PCR amplification with bacterial universal primers 515F (5-GTG CCA GCM GCC GCG GTA A-3) and 806R (5-GGA CTA CHV GGG TWT CTA AT-3). Amplicon sequencing was performed using paired end 250 bp V2 chemistry on an Illumina MiSeq platform (provided by the Earlham Institute).