Core Microbiome
We defined the community core microbiome as ASVs present in at least 50% of all individuals in each of the three sampling periods (Astudillo-GarcĂ­a et al. 2017, Grond et al. 2017). We studied the community core at multiple taxonomic levels usingPhylocore (Ren and Wu 2016). We also identified a temporal core in birds sampled in triplicate, defined as ASVs found at all three sampling periods within the same bird (Shade et al. 2012). We calculated the proportion of temporal core ASVs to those that are transient and not found at all three sampling periods to identify the average proportion of ASVs that are retained over time.