Sample collection
We banded nestlings at 6-8 days old with a unique color band combination
and a numbered metal band (National Band and Tag, Kentucky, USA). We
collected fecal samples from nestlings opportunistically at this time.
To collect fecal samples, we removed nestlings from the nest and held
them over a sterile weigh boat until they defecated. We then moved the
fecal sample from the tray to a sterile tube, placed it on ice in the
field for up to 6 hours, and then stored it in a -20 °C freezer until
the bacterial DNA was extracted. We transported the samples to the
University of Connecticut and stored them in a -80 °C freezer for
downstream 16S sequencing. Although studies show that the bacterial
community in avian feces does not always represent the entire digesta of
the host (e.g., in the cecum; Wilkinson et al., 2017), fecal samples are
generally representative of the bacterial community in the large
intestines (Videvall et al., 2018; Wilkinson et al., 2017) and are used
when hosts cannot be euthanized. When nests were empty, they were
collected and examined for P. downsi ; the full data set was
reported in Knutie et al., (2023).