Discussion
The present study is among the first to compare the gut microbiome of
coexisting insular mesocarnivores within the context of fine-scale niche
differentiation. More specifically, we examined gut microbial diversity
and composition between island foxes and island spotted skunks
inhabiting Santa Cruz Island and Santa Rosa Island off the coast of
southern California. We found that both island foxes and island spotted
skunks harbor the core mammalian microbiome, while also exhibiting
species-specific microbial communities. Within species, island of origin
significantly influenced gut microbial communities, with more pronounced
differences observed in island spotted skunks compared to island foxes.
This distinction may reflect the more specialized nature of island
spotted skunk ecology, in contrast to the more generalist nature of
island fox ecology. It may further reflect evolutionary processes
operating during a longer period of separation between island spotted
skunk populations, which diverged roughly 10,000 years ago, compared to
island foxes, which colonized the islands roughly 7,000 years ago .
Regarding their similarities, the shared phylogenetic history of island
foxes and island spotted skunks within the class Mammalia, order
Carnivora, and suborder Caniformia contributes to both host species
harboring phyla that comprise the core mammalian microbiome. These phyla
include Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria,
with the additional phylum Fusobacteria often reported in mammalian
carnivores . Interestingly, we observed higher levels of Fusobacteria in
island foxes, which is consistent with other studies characterizing the
microbiome of species within Canidae . These results reflect the
importance of evolutionary history in shaping the core features of
mammalian microbiomes at higher taxonomic levels .
Yet amid these high-level similarities, we also observed significant
differentiation between island foxes and island spotted skunks. In fact,
species identity explained the largest percentage of variation in our
dataset by a significant margin, with 24% of microbial abundance and
19.1% of microbial presence attributed to host species. This result may
reflect the evolutionary divergence between ancestral lineages of the
Canidae and Mephitidae families roughly 49 million years ago, as well as
ecological differences between these species that likely recur
throughout their range. We posit that the reported patterns of diversity
likely reflect both of these eco-evolutionary processes, and in
particular, the breadth of each species’ ecological niche.
For example, examination of alpha diversity revealed a wider range of
bacterial ASVs detected in island foxes compared to island spotted
skunks, likely resulting from their more generalist resource utilization
. Island foxes encounter a wider variety of food sources and
environments that may contribute to their higher bacterial richness, as
microbiomes are known to reflect an organism’s diet and environmental
setting . Conversely, as island spotted skunks are more specialized in
resource use, they likely experience reduced exposure to these external
sources of microbial variation, thus contributing to their lower
bacterial richness. Their diet provides a likely candidate underlying
this result. Compared to more omnivorous island foxes, island spotted
skunk diets are mostly carnivorous and may therefore require fewer
microbes to digest their smaller range of food sources . Previous
research further showed that carnivore microbiomes tend to exhibit lower
richness than omnivore microbiomes, as meat proteins are easier to
digest than plant compounds . We therefore concluded that species
identity exerted a strong influence on gut microbial communities, likely
due to their dietary differences.
These interspecific differences were further reflected in the relative
abundance of bacterial taxa, as numerous classes significantly differed
between island foxes and island spotted skunks. On both Santa Cruz and
Santa Rosa Islands, island foxes harbored higher relative abundances of
Gammaproteobacteria and Deltaproteobacteria than their island spotted
skunks counterparts. Gammaproteobacteria have been linked to coastal
amphipod species similar to those preyed upon by island foxes . They
have also been associated with soil invertebrates such as earthworms ,
which were recently introduced to the Channel Islands . These results
potentially reflect a dietary preference towards these food sources
among island foxes. It may also reflect evolutionary history, as
Gammaproteobacteria has been isolated from other species within Canidae
. The other class consistently more abundant in island foxes,
Deltaproteobacteria, has been linked to marine environments , and may
further reflect island fox foraging behavior on beaches .
We also noted interspecific differences unique to each island. On Santa
Rosa Island, island spotted skunks exhibit higher abundances of
Epsilonproteobacteria. The genus largely driving this result wasCampylobacter , which is often associated with enteritis in humans
that come into contact with soil, untreated water sources, or animals .
In island spotted skunks, this may derive from their local environment
or prey items, as Campylobacter has previously been isolated from
wild mice . On Santa Cruz Island, Actinobacteria proved to be more
abundant in island spotted skunks. As Actinobacteria is one of the most
abundant bacterial taxa in soils , this may reflect habitat use by
island spotted skunks, which spend more time in ravines or covered
places while foraging for soil-dwelling prey . We therefore posit that
the increased presence of certain bacterial classes in island foxes and
island spotted skunks may derive from eco-evolutionary differences in
their population histories, diets, and preferred habitat types.
While species identity was the strongest predictor of bacterial
composition, we also observed intraspecific differences between island
populations. This pattern was more pronounced in island spotted skunks,
where 15.9% of bacterial abundance and 14.6% of species presence were
attributed to island of origin, compared to 6.3% of bacterial abundance
and 5.6% of species presence in island foxes. We again attribute this
near three-fold difference to two likely factors: the longer separation
time and more specialist ecology of island spotted skunks, as subtle
differences between island habitats may have a stronger effect on their
gut microbial communities. This contrasts with the more recent
colonization events and more generalist ecology of island foxes, which
harbor a greater diversity of microbes that may reflect their
interactions with numerous dietary items and microhabitats across both
islands. This likely has a homogenizing effect on their gut microbial
communities, although we do still find evidence of intraspecific
variation, as previously reported in island fox gut microbial
communities .
Differential abundance testing supported these overarching patterns, as
intraspecific comparisons only revealed one bacterial class
significantly differing between island spotted skunk populations amid no
significant differences between island fox populations. Within skunks,
the Santa Cruz Island population harbored significantly more
Coriobacteriia, which has been linked with the addition of crickets to
the diet of domestic dogs as it helps break down chitin in insect
exoskeletons . These results suggest that Santa Cruz Island spotted
skunks may be eating larger proportions of native arthropod species than
their Santa Rosa counterparts. This link between Coriobacteriia and
crickets is particularly compelling, as previous research reported
Jerusalem crickets (Stenopelmatus fuscus ) as the most frequently
consumed arthropod by Santa Cruz Island spotted skunks . Considered
alongside interspecific results, this finding further underscores the
importance of dietary preference as a driver of gut microbial
composition within and between host populations and species.
In summary, the present study characterized the gut microbiomes of
island foxes and island spotted skunks across two of California’s
Channel Islands: Santa Cruz Island and Santa Rosa Island. We identified
the core mammalian microbiome present in both species likely due to
their shared evolutionary history, and reported evidence of niche
differentiation likely due to differences in diet and habitat use
between these coexisting mesocarnivores. We found that host species was
the primary driver of microbial differentiation within our dataset, and
additionally reported intraspecific variation between island
populations. These intraspecific differences were more pronounced in the
longer separated and more specialist island spotted skunks compared to
the more recently colonized and more generalist island foxes. These
results therefore support the claim that host evolutionary history and
contemporary ecology (i.e. , diet, habitat use, and local
environmental context) all play a role in shaping the gut microbiome.
Commensal bacteria likely reflect – and perhaps even contribute to –
the fine-scale niche differentiation that allows these insular
terrestrial carnivores to coexist. To better understand this ecological
rarity, we recommend further study of the diet, behavior, and bacteria
colonizing these known competitors. This will shed additional light on
the eco-evolutionary processes that have enabled their coexistence since
initial colonization millennia ago, and will hopefully facilitate future
coexistence for many millennia to come.
Acknowledgments: We would like to thank Bridget Parrino,
Heather Alford, Victor Zhang, and Mason London for collecting rectal
swabs from island foxes and island spotted skunks. We thank Robert
Fleischer and Nancy McInerney from the Center for Conservation Genomics
at Smithsonian’s National Zoo and Conservation Biology Institute (NZCBI)
for their support of this project. This work was funded by the
Smithsonian Institution Fellowship Program, Friends of the Island Fox
Research Grant, Georgetown University Annual Research Grant, and
Georgetown University Summer Salary Supplement. Further support was
provided by the NZCBI Center for Conservation Genomics and Center for
Species Survival.