Discussion
Our new microbial DNA extraction method is effective for avian fecal
samples (Figure 1), which have been traditionally challenging materials
for use in DNA extractions. Our method is also effective for preen gland
oil samples (Figure 1), which likely harbor lower bacterial abundance
due to antimicrobial characteristics of preen oil. Both sample types
were collected across a broad range of avian species. Further, our
method successfully extracted DNA from both gram-positive and
gram-negative bacteria (Table 4). Other studies have found both gram
positive and negative bacteria, supporting the efficacy of this method.
The ease and relative cost effectiveness of our method (Table 1) makes
it particularly advantageous. We hope that our method will facilitate
advances in our understanding of microbiomes from multiple reservoirs
across a wide range of avian species.
While an organism’s host microbiome is a crucial determinant of its
overall health, the full extent of the coevolutionary relationships
between a host and its symbiotic microbes is not known. Recent
discoveries have shown hosts rely on microbes for health and protection
against viruses and pathogens, providing enzymes that break down
molecules. Additionally hosts, rely on microbes for digestion, cognitive
function, growth, development, and more. Gut microbiomes are
particularly important in many taxa. To sample the gut microbiome of
birds, cloacal swabs have been shown to be nonrepresentative of
microbial diversity, only accounting for one component of the digestive
tract, whereas fecal samples contain inputs from the whole
gastrointestinal tract and are thus a more accurate representations of
the entire gut microbiome. However, existing DNA extraction methods have
not been consistently successful when working with avian fecal samples.
Birds and reptiles combine their uric waste with their fecal waste, thus
creating added difficulty in extracting DNA from fecal samples. Our
method is not only reliable with such samples but is considerably
cheaper than most commercial kits used to extract avian microbiome DNA
(Table 1). The low cost and high reliability of our method will improve
the feasibility and accessibility of research on avian host microbiomes.
As microbiome studies have increased in popularity over the last decade,
the range of host reservoirs scientists are studying has expanded as
well. Beyond the abundant and diverse gut microbiome, a potentially
functionally important reservoir in avian species is the microbiome that
exists within the uropygial or preen gland. The preen gland and the oils
produced there are known to affect communication, species recognition,
mate choice, and feather maintenance. The chemical composition of preen
oil is at least partially dependent on the microbes present in this
gland. The bacterial communities present in the uropygial oil are
thought to be less abundant than those within the gut microbiome; yet,
they are predicted to play direct roles in the odor of avian hosts as
well as potentially in feather and body health. Some preliminary studies
in this field of research have observed that disease may not be directly
linked to differences in preen oil microbiomes. Additionally,
differences in microbial communities may correspond with population
differences, and in some species, sex differences have been observed.
The consistent success of our method in extracting microbial DNA from
avian preen oil samples will facilitate new research on this currently
understudied microbiome reservoir.
Because we have established the consistent success of our method in
extracting microbial DNA from two avian sample types that are quite
chemically different, it is likely that our method will be useful across
additional avian microbiome reservoirs. Current variation in the
approaches used for microbial DNA extraction and subsequent
amplification means there is also sometimes variation in the bacteria
that are detected. Using the same extraction methodology across samples
from different reservoirs will allow more consistent and confident
comparisons of microbiomes from different reservoirs for future research
efforts. With increased interest in the relationship between hosts and
their bacterial community composition and abundance across different
microbiome reservoirs, the accurate identification of microbial taxa is
critical. With an enhanced potential to identify and quantify the
symbiotic microbes, the investigation of their impact on host health and
conservation can involve deeper questions. Widespread adoption of our
method would therefore increase the validity of future cross-study and
cross-reservoir comparisons.
To conclude, we have developed and tested a highly efficient microbial
extraction method and verified its efficacy across multiple avian
species. Our method was successful in extracting microbial DNA on the
first attempt from 25 of 25 fecal samples collected from 15 avian
species, and from 11 of 12 preen oil samples collected from 12 avian
species (Figure 1, Tables 2-3). It is also relatively inexpensive
compared with commercial fecal DNA extraction kits (Table 1). We are
confident that our method will be effective and efficient across many
additional avian species globally. Future work should explore the
effectiveness of this method in extracting microbial DNA from reservoirs
in other taxa, including reptile fecal samples as well.