2. DNA Extractions
We removed approximately 0.15 g feces from each sample, taking care to
avoid collecting any of the white uric acid. After pouring any ethanol
off the fecal sample, we placed the sample in a weigh boat in a fume
hood for about one minute to allow the evaporation of excess ethanol. We
then transferred the dried fecal sample into a 2 mL
Fisherbrand™ Free-Standing Microcentrifuge Tube with Screw Cap that had
been filled with approximately 100 µL of 460 nm acid-washed glass beads
(Sigma-Aldrich, Inc., St. Louis, Missouri, USA) and 200 µL of PrepMan™
Ultra Sample Preparation Reagent (Thermo Fisher Scientific, Waltham,
Massachusetts, USA). For preen oil samples, we placed the entire
capillary tube tip (containing the preen oil sample) into a 2 mL
microcentrifuge tube containing the same volumes of acid-washed glass
beads and PrepMan™ Ultra Sample Preparation Reagent as used with the
fecal samples. Both types of sample mixtures were homogenized using a
Mini-Beadbeater (BioSpec Products, Bartlesville, Oklahoma, USA) for 1
minute on high, and then placed in a water bath for 10 minutes at 100°C.
For preen oil samples, we removed the capillary tube tip after this
water bath step, at which point the oil sample was no longer observable
in the tip of the capillary tube. For both sample types, we then
centrifuged samples at 14,000 rpm and pipetted off the supernatant. This
supernatant was then used as the DNA extract for PCR. The volume of the
final DNA extract samples was ~75µL, depending on how
much could be pipetted off without collecting the acid-washed beads. To
create a negative control, we followed this protocol using 100 uL of
water instead of a dried fecal sample.
3. PCR Amplification of microbial 16S rRNA
To assess the success of our microbial DNA extraction method, we
performed PCR amplification of hypervariable regions of the 16S rRNA
gene (V3-V4 regions) using our DNA extracts from both fecal and preen
oil samples. The 16S rRNA gene is commonly used to identify bacterial
taxa and quantify microbial diversity. The function of this gene itself
has not changed over time, which indicates that the random changes that
do exist can be a good measure of evolution and variation. This gene is
present in nearly all bacteria and its highly conserved nature coupled
with species-specific regions of variation allows for identification of
different clades of bacteria.
For most of our DNA extractions from fecal samples, we first diluted 1
µL of the concentrated fecal DNA sample in 99 µL of nuclease free water.
If the fecal sample used for microbial extraction was less than 0.1 g,
we used a non-diluted DNA extract sample. Since all collected preen
samples were ~1uL, no dilution of the preen oil DNA
extracts was needed.
We used a total PCR volume of 20 uL, containing master mix, GC enhancer,
forward and reverse primers, DNA, and water. Specifically, each reaction
included 10 uL
Platinum™
II Hot-Start Green PCR Master Mix (2X) from Invitrogen (Waltham,
Massachusetts), 4uL of the Platinum GC Enhancer included with this
master mix, 2uL of nuclease free H20, and 2uL of a
diluted DNA sample. To amplify the V3-V4 region of the 16S rRNA gene, we
also included 1uL of 25uM 341F (CCTACGGGNGGCWGCAG) and 806R
(GACTCHVGGGTATCTAATCC) 16S rRNA primers.
Optimized PCR conditions included an initial denaturation step at 95°C
for 2 min, followed by 30 cycles of denaturation at 95°C for 30 seconds,
annealing at 55°C for 30 seconds, extension at 68°C for 1 min, and a
final elongation at 68°C for 2 min. To confirm successful PCR
amplification, we ran each sample on a 2% agarose gel at 140 V for 50
minutes and verified the presence of bands visually. The expected
product size was ~430 bp.