The choice of DNA extraction protocol affects the quantification of gut microbiomes in two passerines

There is ever increasing need for the robust characterization of the microbial communities of wild animals. DNA extraction from bird feces is challenging and to date, no protocol has proven to be efficient with all bird feces samples. Thus, there is a need to test different extraction protocols for a variety of bird species. We compared five commercial kits and four protocols to extract DNA from black-capped chickadee and blue tit feces. We found that all kits and methods allowed the study of the bacterial microbiota of black-capped chickadee feces, but the choice of kit influenced the measured diversity and composition of microbiota communities. Only two kits out of five allowed the recovery of DNA from blue tit feces. We recommend using PowerSoil by Qiagen or QuickDNA by Zymo Research with black-capped chickadee feces, and MagMAX by Fisher for blue tit feces. Our study highlights the difficulty of extracting microbial DNA from bird feces, points out the limits of comparing bacterial communities across studies using different methods, and proposes optimized efficient protocols to extract microbial DNA from feces of two commonly studied bird species for the study of bacterial microbiota.