Effects of Urbanization and Landscape on Gut Microbiomes in White-Crowned Sparrows

Urbanisation Affects Millipede Gut Microbiota Communities by Impeding Host Gene Flow

Urbanisation leads to the alteration of the living environment of soil fauna and isolates them, significantly influencing the evolutionary processes of soil fauna. Faunal gut microbiota serves to bridge hosts with changing environments; thus, they are viable indicators of host adaptation. For this study, we investigated how urbanisation affects the gut microbiota and population genetics of Spirobolus bungii. The results revealed that urbanisation did not affect the genetic diversity of S. bungii populations but acted as a barrier, which hindered its gene flow. Genetic differentiation was associated with the compositional similarity of gut microbiota among populations; however, environmental distinctions had no impact. Our findings highlighted that gene flow between populations was a critical factor, which supported the premise that urbanisation influences the gut microbiota compositions of species. This study contributes to a deeper understanding of the mechanisms that underlie changes in faunal gut microbiota driven by gene flow in the context of urbanisation.

Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices

Comparative approaches in animal gut microbiome research have revealed patterns of phylosymbiosis, dietary and physiological convergences, and environment-host interactions. However, most large-scale comparative studies, especially those that are highly cited, have focused on mammals, and efforts to integrate comparative approaches with existing ecological frameworks are lacking. While mammals serve as useful model organisms, developing generalised principles of how animal gut microbiomes are shaped and how these microbiomes interact bidirectionally with host ecology and evolution requires a more complete sampling of the animal kingdom. Here, we provide an overview of what past comparative studies have taught us about the gut microbiome, and how community ecology theory may help resolve certain contradictions in comparative gut microbiome research. We explore whether certain hypotheses are supported across clades, and how the disproportionate focus on mammals has introduced potential bias into gut microbiome theory. We then introduce a methodological solution by which public gut microbiome data of understudied hosts can be compiled and analysed in a comparative context. Our aggregation and analysis of 179 studies shows that generating data sets with rich host diversity is possible with public data and that key gut microbes associated with mammals are widespread across the animal kingdom. We also show the effects that sample size and taxonomic rank have on comparative gut microbiome studies and that results of multivariate analyses can vary significantly with these two parameters. While challenges remain in developing a universal model of the animal gut microbiome, we show that existing ecological frameworks can help bring us one step closer to integrating the gut microbiome into animal ecology and evolution.

Comparative Study of Gut Microbiome in Urban and Rural Eurasian Tree Sparrows

Gut microbiota play a significant role in various physiological functions, including digestion, nutritional metabolism, and host immune function. The composition of these gut microbes is largely influenced by habitats. This study examines the gut microbiota of the Eurasian tree sparrow (Passer montanus) inhabiting rural and urban environments to understand the effects of habitat variation on microbial composition. We captured 36 rural and 29 urban adult tree sparrows and observed minor differences in body mass but substantial differences in foraging microhabitats between the two groups. Fecal samples from adult males with similar body mass were selected for a gut microbiome analysis to mitigate potential confounding effects, resulting in 20 successfully sequenced samples. The analysis disclosed disparities in gut microbiota diversity and composition between rural and urban sparrows. The urban group demonstrated slightly higher alpha diversity and distinct dominant phyla and genera compared to the rural group. Additionally, differences in the relative abundance of potentially pathogenic bacteria were observed between the groups. Several potentially pathogenic bacteria (e.g., TM7, Staphylococcus, Helicobacter, and Shigella) were more abundant in the urban group, suggesting that tree sparrows may act as transmission vectors and develop stronger immune systems. This could potentially facilitate pathogen dissemination while also contributing to the natural cycling of nutrients and maintaining ecosystem health in urban environments. The beta diversity analysis confirmed structural differences in microbial communities, implicating habitat variation as a contributing factor. Furthermore, the LEfSe analysis emphasized significant differences in gut bacteria abundance (across two phyla, three classes, six orders, seven families, and eight genera) between urban and rural sparrows, with predicted functional differences in metabolic pathways. Notably, lipid metabolism was enriched in urban sparrows, indicating enhanced lipid synthesis and metabolism in urban habitats. In conclusion, this study underscores the profound influence of habitat on the gut microbiota composition and functional potential in tree sparrows. Our findings highlight that urbanization alters the gut microbes and, consequently, the physiological functions of bird species.

The Influence of Microbiota on Wild Birds' Parental Coprophagy Behavior: Current Advances and Future Research Directions

This comprehensive review provides an in-depth exploration of the intriguing phenomenon of parental coprophagy in wild birds and its profound implications on the influence of adult avian parents' health. This review investigates the composition and dynamics of avian feces' microbiota, casting light on the various dietary, environmental, and genetic factors that influence its diversity. Furthermore, it emphasizes parental coprophagy, a behavior observed in numerous bird species, particularly among herbivorous and passerine birds. The review investigates multiple hypotheses proposed to explain the occurrence of coprophagy. It delves into its function as a potential mechanism for transmitting microorganisms, particularly feces bacteria, from nestlings to their parents. This microbial transfer may affect the health and well-being of adult avian parents. In addition, the review highlights the current research deficits and debates surrounding coprophagy. These gaps include crucial aspects such as the onset of coprophagy, its long-term effects on both parents and offspring, the nutritional implications of consuming nestling feces, the potential risks of pathogen transmission, and the ecological and evolutionary factors that drive this behavior. As the review synthesizes existing knowledge and identifies areas requiring additional research, it emphasizes the significance of future studies that comprehensively address these gaps. By doing so, we can understand coprophagy's ecological and evolutionary significance in wild birds, advancing our knowledge on avian biology. This information can improve conservation efforts to protect migratory bird populations and their complex ecosystems.

Urbanization impoverishes taxonomic but not functional diversity of the gut microbiota in a forest specialist ground beetle, Carabus convexus

Symbiotic microorganisms living in the digestive tracts of invertebrates can be crucial in host-symbiont interactions, as they play fundamental roles in important biological processes. Urbanization-related habitat alteration and disturbance, however, considerably affect the environment of host insects, from which their gut microbiota is derived. Still, relatively few studies, all on flying insects, have assessed the impact of urbanization on the gut microbiota of insects. Here, we compared the gut bacterial microbiota in rural and urban individuals of a flightless ground beetle, Carabus convexus, using next generation sequencing. Across the 48 gut samples we identified 1163 different bacterial operational taxonomic units (OTUs), forming significantly different gut bacterial communities in rural versus urban beetles. The taxonomic diversity of the gut bacterial microbiota expressed by the Hill numbers was significantly higher in rural than urban individuals, as well as in rural males vs. females. Smaller differences were found in functional diversity, assessed by the Rao's quadratic entropy which was marginally significantly higher in urban than rural beetles.

Intersecting planetary health: Exploring the impacts of environmental stressors on wildlife and human health

This comprehensive review articulates critical insights into the nexus of environmental stressors and their health impacts across diverse species, underscoring significant findings that reveal profound effects on both wildlife and human health systems. Central to our examination is the role of pollutants, climate variables, and pathogens in contributing to complex disease dynamics and physiological disruptions, with particular emphasis on immune and endocrine functions. This research brings to light emerging evidence on the severe implications of environmental pressures on a variety of taxa, including predatory mammals, raptorial birds, seabirds, fish, and humans, which are pivotal as indicators of broader ecosystem health and stability. We delve into the nuanced interplay between environmental degradation and zoonotic diseases, highlighting novel intersections that pose significant risks to biodiversity and human populations. The review critically evaluates current methodologies and advances in understanding the morphological, histopathological, and biochemical responses of these organisms to environmental stressors. We discuss the implications of our findings for conservation strategies, advocating for a more integrated approach that incorporates the dynamics of zoonoses and pollution control. This synthesis not only contributes to the academic discourse but also aims to influence policy by aligning with the Global Goals for Sustainable Development. It underscores the urgent need for sustainable interactions between humans and their environments, which are critical for preserving biodiversity and ensuring global health security. By presenting a detailed analysis of the interdependencies between environmental stressors and biological health, this review highlights significant gaps in current research and provides a foundation for future studies aimed at mitigating these pressing issues. Our study is significant as it proposes integrative and actionable strategies to address the challenges at the intersection of environmental change and public health, marking a crucial step forward in planetary health science.

Gut Microbiota Profiling as a Promising Tool to Detect Equine Inflammatory Bowel Disease (IBD)

Gastrointestinal disorders are common and debilitating in horses, but their diagnosis is often difficult and invasive. Fecal samples offer a non-invasive alternative to assessing the gastrointestinal health of horses by providing information about the gut microbiota and inflammation. In this study, we used 16S sequencing to compare the fecal bacterial diversity and composition of 27 healthy horses and 49 horses diagnosed with inflammatory bowel disease (IBD). We also measured fecal calprotectin concentration, a marker of intestinal inflammation, in healthy horses and horses with IBD. We found that microbiota composition differed between healthy horses and horses with IBD, although less than five percent of the variation in microbiota composition was explained by individual health status and age. Several differentially abundant bacterial taxa associated with IBD, age, or body condition were depleted from the most dominant Firmicutes phylum and enriched with the Bacteroidota phylum. An artificial neural network model predicted the probability of IBD among the test samples with 100% accuracy. Our study is the first to demonstrate the association between gut microbiota composition and chronic forms of IBD in horses and highlights the potential of using fecal samples as a non-invasive source of biomarkers for equine IBD.

Impacts of coprophagic foraging behaviour on the avian gut microbiome

Avian gut microbial communities are complex and play a fundamental role in regulating biological functions within an individual. Although it is well established that diet can influence the structure and composition of the gut microbiota, foraging behaviour may also play a critical, yet unexplored role in shaping the composition, dynamics, and adaptive potential of avian gut microbiota. In this review, we examine the potential influence of coprophagic foraging behaviour on the establishment and adaptability of wild avian gut microbiomes. Coprophagy involves the ingestion of faeces, sourced from either self (autocoprophagy), conspecific animals (allocoprophagy), or heterospecific animals. Much like faecal transplant therapy, coprophagy may (i) support the establishment of the gut microbiota of young precocial species, (ii) directly and indirectly provide nutritional and energetic requirements, and (iii) represent a mechanism by which birds can rapidly adapt the microbiota to changing environments and diets. However, in certain contexts, coprophagy may also pose risks to wild birds, and their microbiomes, through increased exposure to chemical pollutants, pathogenic microbes, and antibiotic-resistant microbes, with deleterious effects on host health and performance. Given the potentially far-reaching consequences of coprophagy for avian microbiomes, and the dearth of literature directly investigating these links, we have developed a predictive framework for directing future research to understand better when and why wild birds engage in distinct types of coprophagy, and the consequences of this foraging behaviour. There is a need for comprehensive investigation into the influence of coprophagy on avian gut microbiotas and its effects on host health and performance throughout ontogeny and across a range of environmental perturbations. Future behavioural studies combined with metagenomic approaches are needed to provide insights into the function of this poorly understood behaviour.

The effects of urban life on animal immunity: Adaptations and constraints

Land transformation, including urbanization, is a dominant form of anthropogenic change to the global environment at the dawn of the Anthropocene epoch. More and more species are brought into direct contact with humans, being either required to develop broad-scale adaptations to urban environment or filtered out from urbanized areas. While behavioural or physiological adaptations are at the forefront of urban biology research, there is accumulating evidence for divergent pathogen pressure across urbanization gradients, requiring adjustments in host immune function. At the same time, host immunity may be constrained by unfavourable components of an urban environment, such as poor-quality food resources, disturbance, or pollution. Here, I reviewed existing evidence for adaptations and constrains in the immune system of urban animals, focusing on the recent implementation of metabarcoding, genomic, transcriptomic, and epigenomic approaches in urban biology research. I show that spatial variation in pathogen pressure across urban and non-urban landscapes is highly complex and may be context-dependent, but there is solid evidence for pathogen-driven immunostimulation in urban-dwelling animals. I also show that genes coding for molecules directly involved in interactions with pathogens are the prime candidates for immunogenetic adaptations to urban life. Evidence emerging from landscape genomics and transcriptomics show that immune adaptations to urban life may have a polygenic nature, but immune traits may not be among the key biological functions experiencing broad-scale microevolutionary changes in response to urbanization. Finally, I provided recommendations for future research, including i) a better integration of different 'omic' approaches to obtain a more complete picture of immune adaptations to urban life in non-model animal taxa, ii) quantification of fitness landscapes for immune phenotypes and genotypes across urbanization gradient, and iii) much broader taxonomic coverage (including invertebrates) necessary to draw more robust conclusions on how general (or taxa-specific) are immune responses of animals to urbanization.

Comparative Analyses of the Fecal Microbiome of Five Wild Black-Billed Capercaillie (Tetrao parvirostris) Flocks

Black-billed capercaillie (Tetrao parvirostris) was listed as a first-class state-protected animal because it was endangered in China (Category I). This study is the first to examine the diversity and composition of T. parvirostris gut microbiome in the wild. We collected fecal samples from five black-billed capercaillie flock roosting sites (each 20 km apart) in one day. Thirty fecal samples were sequenced with 16S rRNA gene amplicons on the Illumina HiSeq platform. This study is the first to analyze the fecal microbiome composition and diversity of black-billed capercaillie in the wild. At the phylum level, Camplyobacterota, Bacillota, Cyanobacteria, Actinomycetota, and Bacteroidota were the most abundant in the fecal microbiome of black-billed capercaillie. At the genus level, unidentified Chloroplast, Escherichia-Shigella, Faecalitalea, Bifidobacterium, and Halomonas were the dominant genera. Based on alpha and beta diversity analyses, we found no significant differences in the fecal microbiome between five flocks of black-billed capercaillie. Protein families: genetic information processing; protein families: signaling and cellular processes, carbohydrate metabolism; protein families: metabolism and energy metabolism are the main predicted functions of the black-billed capercaillie gut microbiome through the PICRUSt2 method. This study reveals the composition and structure of the fecal microbiome of the black-billed capercaillie under wild survival conditions, and this study provides scientific data for the comprehensive conservation of the black-billed capercaillie.

Past and future: Urbanization and the avian endocrine system

Urban environments are evolutionarily novel and differ from natural environments in many respects including food and/or water availability, predation, noise, light, air quality, pathogens, biodiversity, and temperature. The success of organisms in urban environments requires physiological plasticity and adjustments that have been described extensively, including in birds residing in geographically and climatically diverse regions. These studies have revealed a few relatively consistent differences between urban and non-urban conspecifics. For example, seasonally breeding urban birds often develop their reproductive system earlier than non-urban birds, perhaps in response to more abundant trophic resources. In most instances, however, analyses of existing data indicate no general pattern distinguishing urban and non-urban birds. It is, for instance, often hypothesized that urban environments are stressful, yet the activity of the hypothalamus-pituitary-adrenal axis does not differ consistently between urban and non-urban birds. A similar conclusion is reached by comparing blood indices of metabolism. The origin of these disparities remains poorly understood, partly because many studies are correlative rather than aiming at establishing causality, which effectively limits our ability to formulate specific hypotheses regarding the impacts of urbanization on wildlife. We suggest that future research will benefit from prioritizing mechanistic approaches to identify environmental factors that shape the phenotypic responses of organisms to urbanization and the neuroendocrine and metabolic bases of these responses. Further, it will be critical to elucidate whether factors affect these responses (a) cumulatively or synergistically; and (b) differentially as a function of age, sex, reproductive status, season, and mobility within the urban environment. Research to date has used various taxa that differ greatly not only phylogenetically, but also with regard to ecological requirements, social systems, propensity to consume anthropogenic food, and behavioral responses to human presence. Researchers may instead benefit from standardizing approaches to examine a small number of representative models with wide geographic distribution and that occupy diverse urban ecosystems.

Experimental Exposure to Noise Alters Gut Microbiota in a Captive Songbird

Noise pollution is an unprecedented evolutionary pressure on wild animals that can lead to alteration of stress hormone levels and changes in foraging behavior. Both corticosterone and feeding behavior can have direct effects on gut bacteria, as well as indirect effects through changes in gut physiology. Therefore, we hypothesized that exposure to noise will alter gut microbial communities via indirect effects on glucocorticoids and foraging behaviors. We exposed captive white-crowned sparrows to city-like noise and measured each individuals' corticosterone level, food intake, and gut microbial diversity at the end of four treatments (acclimation, noise, recovery, and control) using a balanced repeated measures design. We found evidence that noise acts to increase corticosterone and decrease food intake, adding to a growing body of research indicating noise exposure affects stress hormone levels and foraging behaviors. We also found evidence to support our prediction for a causal, positive relationship between noise exposure and gut microbial diversity, such that birds had higher measures of alpha diversity during noise exposure. These results help to explain previous findings that urban, free-living white-crowned sparrows have higher bacterial richness than rural sparrows. However, noise appeared to act directly on the gut microbiome or, more likely, through an unmeasured variable, rather than through indirect effects via corticosterone and food intake. Altogether, our study indicates that noise affects plasma corticosterone, feeding behavior, and the gut microbiome in a songbird and raises new questions as to the mechanism linking noise exposure to gut microbial diversity.

An urban diet differentially alters the gut microbiome and metabolomic profiles compared with a seed diet in mourning doves

Urbanization influences food quality and availability for many avian species, with increased access to human refuse and food subsidies in built environments. In relation to such nutritional intakes and their presumed impact on microbes harbored in the intestinal tract and metabolic profiles of host physiological systems, our overall knowledge of the role of gut microbiome (GM) and metabolomic expression in the avian host lags far behind our understanding of mammals. Therefore, the objective of this investigation was to examine the potential differential effect of an urban modeled versus control (i.e., bird seed) diet on the GM, the metabolic profiles of plasma, liver, adipose, kidney, and muscle tissues, and circulating endotoxin and inflammatory factors in urban-caught mourning doves (Zenaida macroura). We hypothesized that the urban diet would differently impact the profiles of the GM and tissue metabolomes and increase plasma lipopolysaccharide (LPS) and proinflammatory factors compared with animals fed a seed diet. After a 4-wk-diet period, contents of the large intestine were sequenced to profile the microbiome, metabolomic analyses were performed on plasma and tissue homogenates, and circulating LPS and inflammatory markers were assessed. The composition of the GM was significantly dissimilar between diets, with greater abundance of Erysipelatoclostridiaceae, Sanguibacteraceae, Oribacterium, and Sanguibacter and decreased circulating LPS in the urban-fed birds. These differences were largely not reflected in the surveyed metabolomes and plasma inflammatory markers. This research supports the notion that the microbial composition in urban doves is impacted by diet, though may only weakly associate with host physiology.

Humanization of wildlife gut microbiota in urban environments

Urbanization is rapidly altering Earth's environments, demanding investigation of the impacts on resident wildlife. Here, we show that urban populations of coyotes (Canis latrans), crested anole lizards (Anolis cristatellus), and white-crowned sparrows (Zonotrichia leucophrys) acquire gut microbiota constituents found in humans, including gut bacterial lineages associated with urbanization in humans. Comparisons of urban and rural wildlife and human populations revealed significant convergence of gut microbiota among urban populations relative to rural populations. All bacterial lineages overrepresented in urban wildlife relative to rural wildlife and differentially abundant between urban and rural humans were also overrepresented in urban humans relative to rural humans. Remarkably, the bacterial lineage most overrepresented in urban anoles was a Bacteroides sequence variant that was also the most significantly overrepresented in urban human populations. These results indicate parallel effects of urbanization on human and wildlife gut microbiota and suggest spillover of bacteria from humans into wildlife in cities.

Changes to the gut microbiota of a wild juvenile passerine in a multidimensional urban mosaic

Urbanisation is a major anthropogenic perturbation presenting novel ecological and evolutionary challenges to wild populations. Symbiotic microorganisms residing in the gastrointestinal tracts (gut) of vertebrates have mutual connections with host physiology and respond quickly to environmental alterations. However, the impact of anthropogenic changes and urbanisation on the gut microbiota remains poorly understood, especially in early development. To address this knowledge gap, we characterised the gut microbiota of juvenile great tits (Parus major) reared in artificial nestboxes and in natural cavities in an urban mosaic, employing two distinct frameworks characterising the urban space. Microbial diversity was influenced by cavity type. Alpha diversity was affected by the amount of impervious surface surrounding the breeding location, and positively correlated with tree cover density. Community composition differed between urban and rural sites: these alterations covaried with sound pollution and distance to the city centre. Overall, the microbial communities reflect and are possibly influenced by the heterogeneous environmental modifications that are typical of the urban space. Strikingly, the choice of framework and environmental variables characterising the urban space can influence the outcomes of such ecological studies. Our results open new perspectives to investigate the impact of microbial symbionts on the adaptive capacity of their hosts.

A Theory of City Biogeography and the Origin of Urban Species

Many of the choices humans make with regard to infrastructure, urban planning and other phenomena have impacts that will last thousands of years. This can readily be seen in modern cities in which contemporary streets run along street grids that were laid out thousands of years prior or even in which ancient viaducts still play a role. However, rarely do evolutionary biologists explicitly consider the future of life likely to be associated with the decisions we are making today. Here, we consider the evolutionary future of species in cities with a focus on the origin of lineages and species. We do so by adjusting evolutionary predictions from the theory of island biogeography so as to correspond to the unique features of cities as islands. Specifically, the species endemic to cities tend to be associated with the gray habitats in cities. Those habitats tend to be dominated by human bodies, pet bodies and stored food. It is among such species where the origin of new lineages is most likely, although most research on evolution in cities has focused on green habitats. We conclude by considering a range of scenarios for the far future and their implications for the origin of lineages and species.

Avian gut microbiomes taking flight

Birds harbor complex gut bacterial communities that may sustain their ecologies and facilitate their biological roles, distribution, and diversity. Research on gut microbiomes in wild birds is surging and it is clear that they are diverse and important - but strongly influenced by a series of environmental factors. To continue expanding our understanding of how the internal ecosystems of birds work in their natural settings, we believe the most pressing needs involve studies on the functional and evolutionary aspects of these symbioses. Here we summarize the state of the field and provide a roadmap for future studies on aspects that are pivotal to understanding the biology of avian gut microbiomes, emphasizing prospects for integrating gut microbiome work in avian conservation and host health monitoring.

Drivers of change and stability in the gut microbiota of an omnivorous avian migrant exposed to artificial food supplementation

Human activities shape resources available to wild animals, impacting diet and probably altering their microbiota and overall health. We examined drivers shaping microbiota profiles of common cranes (Grus grus) in agricultural habitats by comparing gut microbiota and crane movement patterns (GPS-tracking) over three periods of their migratory cycle, and by analysing the effect of artificially supplemented food provided as part of a crane-agriculture management programme. We sampled faecal droppings in Russia (nonsupplemented, premigration) and in Israel in late autumn (nonsupplemented, postmigration) and winter (supplemented and nonsupplemented, wintering). As supplemented food is typically homogenous, we predicted lower microbiota diversity and different composition in birds relying on supplementary feeding. We did not observe changes in microbial diversity with food supplementation, as diversity differed only in samples from nonsupplemented wintering sites. However, both food supplementation and season affected bacterial community composition and led to increased abundance of specific genera (mostly Firmicutes). Cranes from the nonsupplemented groups spent most of their time in agricultural fields, probably feeding on residual grain when available, while food-supplemented cranes spent most of their time at the feeding station. Thus, nonsupplemented and food-supplemented diets probably diverge only in winter, when crop rotation and depletion of anthropogenic resources may lead to a more variable diet in nonsupplemented sites. Our results support the role of diet in structuring bacterial communities and show that they undergo both seasonal and human-induced shifts. Movement analyses provide important clues regarding host diet and behaviour towards understanding how human-induced changes shape the gut microbiota in wild animals.

Shades of grey: host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal

BACKGROUND

Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization (across three cities) on the microbiome of eastern grey squirrels (Sciurus carolinensis). Grey squirrels are ubiquitous in rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate).

RESULTS

Grey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). The bacterial genera characterizing the microbiomes of built-environment squirrels are thought to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built-environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic expectations.

CONCLUSIONS

Squirrel microbiomes differed between city and rural environments, but differences of comparable magnitude were observed between land classes at a within-city scale. We did not observe strong evidence that inter-environmental differences were the result of disparate selective pressures. Rather, our results suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. However, these processes were partly mediated by squirrel coat colour phenotype. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide a useful free-living system with which to study how host genetics mediate environment x microbiome interactions.