Introduction
The gut microbiota is a community of microorganisms inhabiting an organism’s digestive tract that can affect host physiology and health (Gomaa, 2020; Grond et al., 2018). For example, specific gut bacterial taxa, such as Ruminococcus , can aid in host digestion by breaking down indigestible food compounds, such as cellulose, and increase digestive efficiency in humans (Arumugam et al., 2011; Thursby & Juge, 2017). Furthermore, variation in diet, such as a plant-based diet versus a meat-based diet, can shape host gut microbiota as it shifts in response to nutrient availability (Gomaa, 2020; Zhu et al., 2015). Additionally, the host’s immune system can interact with the gut microbiota, specifically by shaping its community composition (Hooper et al., 2012). For example, Kato et al., (2014) found that knockout mice who are deficient in B-cell production have lower gut bacterial diversity compared to non-knockout mice. The gut microbiota can also initiate the production of immune cells to help maintain or develop an effective immune response (Zhang et al., 2017). Studying the dynamic relationships between physiological processes and gut microbiota will be continually important, especially in light of increasing anthropogenic change which can directly and indirectly affect these factors.
Parasites and pathogens, which also affect host health, can directly and indirectly affect microbial communities in the gut (Stensvold & Van Der Giezen, 2018). Within the gut, parasites can directly affect the microbiota by competing with or consuming commensal bacteria (Abt & Pamer, 2014). Parasites might also indirectly affect the gut microbiota via the host’s immune system. For example, gut parasites (e.g.,Heligmosomoides polygyrus ) can activate a non-specific mucosal immune response (e.g., T and Th2 cells), which can select for or against bacterial taxa, such as an increase in gram negative Enterobacteriaceae and a decrease in Enterococcus faecium (Rausch et al., 2018). However, parasites located outside of the gut might also elicit a systemic immune response that could affect the bacterial community in the gut. For example, fish with ectoparasitic fluke (Dactylogyrus lamellatus ) infections have lower gut bacterial diversity compared to uninfected fish, which was likely mediated by elevated expression of immune genes related to the IgM antibody, toll-like receptor 3, and Major histocompatibility factor II responses (Wang et al., 2023). Knutie, (2020) found that parasitic nest fly abundance is negatively correlated with gut bacterial diversity and positively correlated with IgY antibody levels, in eastern bluebirds (Sialia sialis ). Overall, most of these non-model organism studies are correlational and thus the causal effects of parasitism on gut microbiota are not well understood.
Factors related to urbanization, such as changes in food availability, can also influence the gut microbiota of wild hosts (Berlow et al., 2021; Phillips et al., 2018; Teyssier et al., 2020). Studies have found that urban hosts have a larger diet breadth, which can result in greater diversity of the gut bacterial community (Littleford-Colquhoun et al., 2017). For example, non-urban water dragons (Intellagama lesueurii ) feed primarily on invertebrates but urban water dragons feed on invertebrates and plant material, which results in higher gut bacterial diversity. These effects are either because plants introduce additional bacterial taxa or a larger diet breadth selects for different bacteria to aid in digestion. If the latter is supported, a more diverse gut microbial community could help hosts be more equipped to deal with environmental change (Littleford-Colquhoun et al., 2017). In contrast, the gut of house sparrows (Passer domesticus ) consuming a non-urban diet, which is rich in protein, is correlated with higher bacterial diversity compared to urban sparrows whose diet is poor in protein (Teyssier et al., 2020). While increased gut bacterial diversity is generally assumed to be beneficial to hosts, in some cases, such as in organisms with highly specialized diets, lower bacterial diversity can be associated with better health outcomes (Shade et al., 2017). For example, urban coyotes consume carbohydrate-rich anthropogenic food items and have higher bacterial diversity compared to their rural counterparts, but are in poorer body condition and have increased prevalence of the parasite Echinococcus multilocularis(Sugden et al., 2020). Ultimately, these effects of urbanization and other stressors related to human activity (e.g., invasive parasites) are complex and could result in positive or negative implications for host health.
Given the complex effects of human activity on hosts, few studies have examined the influence of multiple synergistic anthropogenic factors, such as urbanization and invasive parasitism, on host gut microbiota. The Galápagos Islands of Ecuador provide an ideal study system to investigate these complex effects. Since 1979, the number of residents and tourists have increased, leading to changes in the natural habitat. These changes include the introduction of non-native species, including parasites (Kerr et al., 2004; Wikelski et al., 2004). For example, the avian vampire fly (Philornis downsi ; hereon, vampire fly) was introduced to the Galápagos in the past several decades and is found on nearly all islands, including human-inhabited islands such as San Cristóbal. Adult flies are non-parasitic but lay their eggs in birds’ nests where the hematophagous larvae feed on nestling hosts and brooding mothers (Fessl et al., 2001; Fessl & Tebbich, 2002). Several studies have found that the vampire fly can have detrimental effects on the survival of nestling Darwin’s finches (Fessl et al., 2010; Kleindorfer & Dudaniec, 2016; Knutie et al., 2016; Koop et al., 2011, 2013; McNew & Clayton, 2018; O’Connor et al., 2010). However, a recent study found that urban finches on San Cristóbal Island are less affected by and more resistant to the vampire fly than non-urban finches (Knutie et al., 2023) who suffer up to 100% mortality due to the fly (Koop et al., 2013; O’Connor et al., 2014). For non-urban finches, the vampire fly does not affect the gut microbiota (Addesso et al., 2020; Knutie, 2018; Knutie et al., 2019). However, because urban finches are more resistant to the fly, and immunological resistance can interact with gut microbiota, parasitism may cause a greater change on the microbiota of urban finches compared to non-urban finches. To date, no studies have causally explored whether parasitism and urbanization interact to affect the gut microbiota of hosts.
The goal of this study is to compare the effects of avian vampire flies and urbanization on the gut microbiota of nestling small ground finches (Geospiza fulignosa ) in 2018 and 2019. Specifically, we experimentally manipulated parasite abundance in urban and non-urban finch nests and then characterized the gut microbiota (i.e., alpha and beta diversity, community composition, relative abundance of taxa). Because diet can influence the gut microbiota (Davidson et al., 2020) and urban finches have a more diverse diet compared to non-urban finches (De León et al., 2019), we hypothesize that urban nestlings will have a different gut microbiota than non-urban nestlings (Loo et al., 2019). Because immunological resistance can be linked to the gut microbiota (Hooper et al., 2012), we predict parasitism will affect and ultimately change the gut microbiota of urban nestlings. Past studies have found that parasitism by vampire flies does not affect the gut microbiota of finch nestlings in non-urban areas (Addesso et al., 2020; Knutie, 2018; Knutie et al., 2019), but their diet is not supplemented. Therefore, we predict that parasitism will not affect the gut microbiota of non-urban nestlings. Further investigation will allow for a more thorough understanding of environmental change on the gut microbiota of small ground finch nestlings.