INTRODUCTION
A healthy gut microbiome is thought to be both diverse and relatively
stable (García-García et al. 2019; Rinninella et al. 2019)
but may be heavily affected by a variety of extrinsic and intrinsic
factors, including host genetics, habitat, and diet (Hird et al.2015; Rothschild et al. 2018). The composition and stability of a
healthy microbiome may change as animals undergo recurrent physiological
stressors, such as migration or changing climates across seasons (Sommeret al. 2016; Carey and Assadi-Porter 2017). Increased
understanding of both variation and stability of gut microbial ecologies
related to recurrent physiological stressors can further elucidate host
adaptation to repetitive stress. Here, we ask what changes and what
remains consistent within the gut microbiome of a migratory bird species
across multiple time points and locations within the annual cycle.
Species experiencing seasonal variation in habitat, diet, or
physiological stressors often exhibit correlated changes in their
microbiome (Maurice et al. 2015; Sommer et al. 2016; Renet al. 2017; Smits et al. 2017; Drovetski et al.2019). Migratory animals may undergo seasonal fluctuations in metabolic
needs that, in combination with changing habitats and diets, result in
variable microbiota composition across their annual cycles, but the
extent to which this occurs remains unclear (Jenni and Jenni-Eiermann
1998; Grond et al. 2018).
Gut microbiota of some migratory bird species have been characterized at
discrete portions of the annual cycle, revealing substantial bacterial
diversity (Lewis et al. 2016; Risely et al. 2017; Wuet al. 2018; Cao et al. 2020). Different environments,
such as breeding grounds, wintering grounds, and stopover sites during
migration, have been shown to impact the overall composition of gut
microbiota, likely through exposure from local microbial communities or
food sources (Lewis et al. 2017; Wu et al. 2018).
Additionally, physiological adaptations of migratory birds, such as
intestinal atrophication during active migration, may further affect gut
microbiota (Grond et al. 2018). Given the variability of gut
microbiota and strong environmental effect, it may be difficult to
directly correlate variation in gut microbiota to ongoing biological
processes, specific host traits, or environmental factors without
temporal sampling across different time points of the annual cycle.
(Hird et al. 2014; Capunitan et al. 2020; Song et
al. 2020). Here we recaptured individuals multiple times on their
tropical wintering and temperate breeding grounds to better understand
local and temporal variability in gut microbiota thus reducing sources
of variability known to be associated with sampling different
individuals and different populations (Flores et al. 2014; Hirdet al. 2014; Baxter et al. 2015).
Until now, no migratory songbird has been sampled at multiple time
points and locations across their annual cycles. Migratory birds have
complicated annual cycles that involve twice-annual movements often
spanning thousands of kilometers between stationary breeding and
wintering periods. Once captured, researchers typically have no way to
relocate or recapture the same individuals outside of the original
capture site, especially for species with expansive wintering and
breeding ranges and with populations that may number in the millions.
This inhibits sampling from the same population, let alone the same
individual, at multiple points in the annual cycle. As a result, one
must attempt to measure and control for confounding factors, such as
between population differences, and account for high inter-individual
variability (Flores et al. 2014; Hird et al. 2014; Baxteret al. 2015). Thus, our inability to study the same individuals
across the annual cycle has impeded identification and understanding of
variation within birds associated with seasonal movement.
The Kirtland’s Warbler (Setophaga kirtlandii) provides an unusual
opportunity for studying changes across the annual cycle in a migratory
species. Their small population size as well as restricted breeding and
wintering ranges (Cooper et al. 2019) make it feasible to
relocate individuals across seasons (Cooper et al. 2018; Cooper
and Marra 2020). Following substantial population declines, only 167
singing males were recorded in 1974 and again in 1987, based on breeding
surveys (Kepler et al. 1996). Through extensive conservation
management efforts, the population has increased to approximately 2,300
singing males of which 97% breed across a relatively small area in
Michigan’s Lower Peninsula. This species winters primarily in the scrub
forests of The Bahamas (Cooper et al. 2019), more than 2,000 km
from the breeding grounds. For this study, we radio-tagged individuals
on the wintering grounds and then relocated and recaptured the same
birds on the breeding grounds in Michigan through the use of automated
telemetry towers. We used 16S rRNA next generation sequencing
technologies to catalogue the bacterial communities of individuals. Our
goals were to: (1) characterize the bacterial diversity of Kirtland’s
Warblers at three unique periods of the annual cycle at the population
and individual level; (2) evaluate host sex, age, period of annual
cycle, and location effect on abundance and diversity of gut microbiota;
and (3) determine if a core bacterial profile for Kirtland’s Warblers
exists and if so, establish a species-specific pattern.