Cloaca microbiota for an adult common waxbill
Total DNA was extracted using the PowerSoil DNA Isolation kit (QIAGEN) following the manufacturers protocol and including negative controls. DNA quantity and quality were estimated using a NanoDropTM 2000 Spectrophotometer (ThermoFisher Scientific, U.S.A.) Amplification of the bacteria V4 hyper-variable region of the 16S rRNA gene was performed (Kozich et al. 2013, Seekatz et al. 2015). Amplicon libraries were pooled and sequenced in two runs in an Illumina MiSeq sequencing platform. PCR and sequencing water negatives were also included. Cloacae samples collected in 2018 were run separately in run one, and all the other samples were in run two.