A comparison of the nutritional physiology and gut microbiome of urban and rural house sparrows (Passer domesticus)

Using point-of-care devices to examine covariation among blood nutritional-physiological parameters and their relationships with poxvirus infection, habitat urbanization, and male plumage coloration in house finches (Haemorhous mexicanus)

The development of inexpensive and portable point-of-care devices for measuring nutritional physiological parameters from blood (e.g., glucose, ketones) has accelerated our understanding and assessment of real-time variation in human health, but these have infrequently been tested or implemented in wild animals, especially in relation to other key biological or fitness-related traits. Here we used point-of-care devices to measure blood levels of glucose, ketones, uric acid, and triglycerides in free-ranging house finches (Haemorhous mexicanus)-a common songbird in North America that has been well-studied in the context of urbanization, nutrition, health, and sexual selection-during winter and examined (1) repeatability of these methods for evaluating blood levels in these wild passerines, (2) intercorrelations among these measurements within individuals, (3) how blood nutritional-physiology metrics related to a bird's body condition, habitat of origin (urban vs. suburban), poxvirus infection, and sex; and (4) if the expression of male sexually selected plumage coloration was linked to any of the nutritional-physiological metrics. All blood-nutritional parameters were repeatable. Also, there was significant positive covariation between concentrations of circulating triglycerides and glucose and triglycerides and uric acid. Urban finches had higher blood glucose concentrations than suburban finches, and pox-infected individuals had lower blood triglyceride concentrations than uninfected ones. Last, redder males had higher blood glucose, but lower uric acid levels. These results demonstrate that point-of-care devices can be useful, inexpensive ways of measuring real-time variation in the nutritional physiology of wild birds.

Seasonal dynamics in the mammalian microbiome between disparate environments

Host-associated bacterial microbiomes can facilitate host acclimation to seasonal environmental change and are hypothesized to help hosts cope with recent anthropogenic environmental perturbations (e.g., landscape modification). However, it is unclear how recurrent and recent forms of environmental change interact to shape variation in the microbiome. The majority of wildlife microbiome research occurs within a single seasonal context. Meanwhile, the few studies of seasonal variation in the microbiome often restrict focus to a single environmental context. By sampling urban and exurban eastern grey squirrel populations in the spring, summer, autumn, and winter, we explored whether seasonal rhythms in the grey squirrel gut microbiome differed across environments using a 16S amplicon sequencing approach. Differences in the microbiome between urban and exurban squirrels persisted across most of the year, which we hypothesize is linked to anthropogenic food consumption, but we also observed similarities in the urban and exurban grey squirrel microbiome during the autumn, which we attribute to engrained seed caching instincts in preparation for the winter. Host behaviour and diet selection may therefore be capable of maintaining similarities in microbiome structure between disparate environments. However, the depletion of an obligate host mucin glycan specialist (Akkermansia) during the winter in both urban and exurban squirrels was among the strongest differential abundance patterns we observed. In summary, urban grey squirrels showed different seasonal patterns in their microbiome than squirrels from exurban forests; however, in some instances, host behaviour and physiological responses might be capable of maintaining similar microbiome responses across seasons.

Eating in the city: Experimental effect of anthropogenic food resources on the body condition, nutritional status, and oxidative stress of an urban bioindicator passerine

Urban areas provide a constant and predictable supply of anthropogenic processed food. The House Sparrow (Passer domesticus Linnaeus, 1758), a declining urban bioindicator species, has recently been reported to have a high level of oxidative stress, with urban diet or pollutants proposed as the potential cause. In this study, we aimed to experimentally determine the effects of two urban trophic resource types (bar snack food leftovers and pet food) on sparrows' physical condition, plasma biochemical nutritional parameters, and blood oxidative status in captivity. To exclude the potential previous effect of urban pollutants, 75 House Sparrows were captured from a rural area in SE Spain and kept in outdoor aviaries. Individuals were exposed to one of three diet treatments: control diet (fruit, vegetables, poultry grain mixture), bar snack diet (ultra-processed snacks), or cat food diet (dry pellets) for 20 days. Blood samples were collected before and after diet treatments to analyze the relative change rates of 12 variables, including physical condition, nutritional status, and oxidant-antioxidant status. A principal component analysis was run to identify gradients of variables covariation, and Generalized Linear Mixed Models were used to determine the effect of diets on each selected PC and on raw variables. The bar snack diet led to signs of anemia and malnutrition, and females tended to lose body condition. The cat food diet increased oxidative stress indicators and protein catabolism. Unbalanced urban diets can affect the body condition and nutritional physiology of House Sparrows and may also induce oxidative stress despite the absence of environmental pollution.

Effect of urbanization and parasitism on the gut microbiota of Darwin's finch nestlings

Host-associated microbiota can be affected by factors related to environmental change, such as urbanization and invasive species. For example, urban areas often affect food availability for animals, which can change their gut microbiota. Invasive parasites can also influence microbiota through competition or indirectly through a change in the host immune response. These interacting factors can have complex effects on host fitness, but few studies have disentangled the relationship between urbanization and parasitism on an organism's gut microbiota. To address this gap in knowledge, we investigated the effects of urbanization and parasitism by the invasive avian vampire fly (Philornis downsi) on the gut microbiota of nestling small ground finches (Geospiza fuliginosa) on San Cristóbal Island, Galápagos. We conducted a factorial study in which we experimentally manipulated parasite presence in an urban and nonurban area. Faeces were then collected from nestlings to characterize the gut microbiota (i.e. bacterial diversity and community composition). Although we did not find an interactive effect of urbanization and parasitism on the microbiota, we did find main effects of each variable. We found that urban nestlings had lower bacterial diversity and different relative abundances of taxa compared to nonurban nestlings, which could be mediated by introduction of the microbiota of the food items or changes in host physiology. Additionally, parasitized nestlings had lower bacterial richness than nonparasitized nestlings, which could be mediated by a change in the immune system. Overall, this study advances our understanding of the complex effects of anthropogenic stressors on the gut microbiota of birds.

Comparative analysis of the fecal microbiota of healthy and injured common kestrel (Falco tinnunculus) from the Beijing Raptor Rescue Center

The gut microbiota is a complex ecosystem that interacts with many other factors to affect the health and disease states of the host. The common kestrel (Falco tinnunculus) is protected at the national level in China. However, the available sequencing data of the gut microbiota from the feces of wild common kestrels, especially for being rescued individuals by professional organization, remains limited. In the present study, we characterized the fecal bacterial communities of healthy and injured common kestrels, and compared the structure of their fecal microbiota by analyzing the V3-V4 region of the 16S rRNA gene using high-throughput sequencing technology with the Illumina MiSeq platform. We found that Firmicutes, Proteobacteria and Actinobacteria were the most predominant phyla in common kestrels. Further, the beta diversity analysis showed that changes in gut microbes were associated with injuries to the common kestrel. The Bacteroides/Firmicutes ratio was significantly lower in the injured group. At the genus level, Glutamicibacter showed significant difference in the two groups. The aim of our current study was to characterize the basic bacterial composition and community structure in the feces of healthy common kestrels, and then compare the differences in the fecal microbiota between healthy and injured individuals. Patescibacteria, Spirochaetes, and Glutamicibacter may be studied as potential biomarkers for certain diseases in raptors. The results could provide the basic data for additional research on the fecal microbiota of common kestrels and contribute to the rescue of wild raptors in the future.

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.

The avian gut microbiota: Diversity, influencing factors, and future directions

The gut microbiota is viewed as the “second genome” of animals, sharing intricate relationships with their respective hosts. Because the gut microbial community and its diversity are affected by many intrinsic and extrinsic factors, studying intestinal microbes has become an important research topic. However, publications are dominated by studies on domestic or captive birds, while research on the composition and response mechanism of environmental changes in the gut microbiota of wild birds remains scarce. Therefore, it is important to understand the co-evolution of host and intestinal bacteria under natural conditions to elucidate the diversity, maintenance mechanisms, and functions of gut microbes in wild birds. Here, the existing knowledge of gut microbiota in captive and wild birds is summarized, along with previous studies on the composition and function, research methods employed, and factors influencing the avian gut microbial communities. Furthermore, research hotspots and directions were also discussed to identify the dynamics of the avian gut microbiota, aiming to contribute to studies of avian microbiology in the future.

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.

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.

Nutrient availability in urban food waste: carbohydrate bias in the Philadelphia–Camden urban matrix

Urban areas provide animals with both a unique set of challenges and resources. One of the novel resources available in urban areas is an abundance of human food waste. Although it is known that many urban-dwelling animals are consuming human food waste at some level, there is not a good understanding of the nutrients provided by this novel resource. Given that human food waste is unlikely to resemble an animal’s natural diet, there could be health consequences for an animal consuming human food waste. In some animals, nutritional imbalances can also lead to behavioral changes, making it important to understand more precisely what they are eating. To answer the question of what nutrients were available in urban food waste, we surveyed food waste in the Philadelphia–Camden urban matrix. We found that human food waste contained ∼1000% more carbohydrates than other nutrient types. Given the impact that carbohydrate-rich diets can have on human health, there may be important consequences for the animals in urban environments that consume this food waste. Therefore, it is possible that human food subsidies have cascading consequences for entire communities and their ecosystem services in cities.

A Four-Week Urban Diet Impairs Vasodilation but Not Nutritional Physiology in Wild-Caught Mourning Doves (Zenaida macroura)

AbstractBirds living in urban areas routinely consume anthropogenic foods, but the physiological consequences of this consumption are poorly understood. To address this question, we investigated the effects of an urban diet (UD) in wild, urban-caught mourning doves in a controlled environment. Since anthropogenic foods often contain a high proportion of refined carbohydrate and fat, we predicted that UD consumption alters body mass as well as plasma and tissue metabolites and that it impairs vasodilation. To test this prediction, we compared body mass, various nutritional physiology parameters, and peripheral vasodilation of doves fed an UD (1∶1 ratio of bird seeds and french fries; [Formula: see text]) with those of doves receiving a control diet (CON, bird seed diet; [Formula: see text]) for 4 wk. At the end of the dietary manipulation period, birds were euthanized, and we dissected cranial tibial arteries to measure ex vivo vasodilation in response to acetylcholine treatment after phenylephrine-induced vasoconstriction. We also collected cardiac blood as well as liver, pectoralis, and gastrocnemius muscle samples to measure nutritional metabolite concentrations. Vasodilation of tibial arteries was impaired in UD- compared to CON-fed birds ([Formula: see text]), suggesting the potential for UD consumption to alter cardiovascular function. Body mass, plasma osmolality, glucose, sodium, insulin, triglyceride, uric acid, liver glycogen and triglycerides, and muscle glycogen did not differ between groups. The results suggest that short-term consumption of a diet composed of 50% anthropogenic foods is not associated with major metabolic perturbations in urban mourning doves.

Preen gland microbiota of songbirds differ across populations but not sexes

Metabolites produced by symbiotic microbes can affect the odour of their hosts, providing olfactory cues of identity, sex or other salient features. In birds, preen oil is a major source of body odour that differs between populations and sexes. We hypothesized that population and sex differences in preen oil chemistry reflect underlying differences in preen gland microbiota, predicting that these microbes also differ among populations and between the sexes. We further predicted that pairwise similarity in the community composition of preen gland microbiota would covary with that of preen oil chemical composition, consistent with the fermentation hypothesis for chemical recognition. We analysed preen oil chemistry and preen gland bacterial communities of song sparrows Melospiza melodia. Birds were sampled at sites for which population and sex differences in preen oil have been reported, and at a third site that has been less studied. Consistent with prior work in this system, we found population and sex differences in preen oil chemistry. By contrast, we found population differences but not sex differences in the community composition of preen gland microbes. Overall similarity in the community composition of preen gland microbiota did not significantly covary with that of preen oil chemistry. However, we identified a subset of six microbial genera that maximally correlated with preen oil composition. Although both preen gland microbiota and preen oil composition differ across populations, we did not observe an overall association between them that would implicate symbiotic microbes in mediating variation in olfactory cues associated with preen oil. Instead, certain subsets of microbes may be involved in mediating olfactory cues in birds, but experiments are required to test this.

The evolutionary consequences of human-wildlife conflict in cities

Human-wildlife interactions, including human-wildlife conflict, are increasingly common as expanding urbanization worldwide creates more opportunities for people to encounter wildlife. Wildlife-vehicle collisions, zoonotic disease transmission, property damage, and physical attacks to people or their pets have negative consequences for both people and wildlife, underscoring the need for comprehensive strategies that mitigate and prevent conflict altogether. Management techniques often aim to deter, relocate, or remove individual organisms, all of which may present a significant selective force in both urban and nonurban systems. Management-induced selection may significantly affect the adaptive or nonadaptive evolutionary processes of urban populations, yet few studies explicate the links among conflict, wildlife management, and urban evolution. Moreover, the intensity of conflict management can vary considerably by taxon, public perception, policy, religious and cultural beliefs, and geographic region, which underscores the complexity of developing flexible tools to reduce conflict. Here, we present a cross-disciplinary perspective that integrates human-wildlife conflict, wildlife management, and urban evolution to address how social-ecological processes drive wildlife adaptation in cities. We emphasize that variance in implemented management actions shapes the strength and rate of phenotypic and evolutionary change. We also consider how specific management strategies either promote genetic or plastic changes, and how leveraging those biological inferences could help optimize management actions while minimizing conflict. Investigating human-wildlife conflict as an evolutionary phenomenon may provide insights into how conflict arises and how management plays a critical role in shaping urban wildlife phenotypes.

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

Habitats are changing rapidly around the globe and urbanization is one of the primary drivers. Urbanization changes food availability, environmental stressors, and the prevalence of disease for many species. These changes can lead to divergence in phenotypic traits, including behavioral, physiological, and morphological features between urban and rural populations. Recent research highlights that urbanization is also changing the gut microbial communities found in a diverse group of host species. These changes have not been uniform, leaving uncertainty as to how urban habitats are shaping gut microbial communities. To better understand these effects, we investigated the gut bacterial communities of White-Crowned Sparrow (Zonotrichia leucophrys) populations along an urbanization gradient in the San Francisco Bay area. We examined how gut bacterial communities vary with the local environment and host morphological characteristics. We found direct effects of environmental factors, including urban noise levels and territory land cover, as well as indirect effects through body size and condition, on alpha and beta diversity of gut microbial communities. We also found that urban and rural birds' microbiomes differed in which variables predicted their diversity, with urban communities driven by host morphology, and rural communities driven by environmental factors. Elucidating these effects provides a better understanding of how urbanization affects wild avian physiology.

Physiological and morphological correlates of blood parasite infection in urban and non-urban house sparrow populations

In the last decade, house sparrow populations have shown a general decline, especially in cities. Avian malaria has been recently suggested as one of the potential causes of this decline, and its detrimental effects could be exacerbated in urban habitats. It was initially thought that avian malaria parasites would not have large negative effects on wild birds because of their long co-evolution with their hosts. However, it is now well-documented that they can have detrimental effects at both the primo- and chronical infection stages. In this study, we examined avian malaria infection and its physiological and morphological consequences in four populations of wild house sparrows (2 urban and 2 rural). We did not find any relationship between the proportions of infected individuals and the urbanisation score calculated for our populations. However, we observed that the proportion of infected individuals increased during the course of the season, and that juveniles were less infected than adults. We did not detect a strong effect of malaria infection on physiological, morphological and condition indexes. Complex parasite dynamics and the presence of confounding factors could have masked the potential effects of infection. Thus, longitudinal and experimental studies are needed to understand the evolutionary ecology of this very common, but still poorly understood, wild bird parasite.

Fecal Sample Collection Method for Wild Birds-Associated Microbiome Research: Perspectives for Wildlife Studies

Simple Summary

This paper describes an easy-to-build box for the noninvasive collection of feces from wild birds or small wild animals (up to 1 kg), including a plastic storage box, a plastic tray, and a vinyl-coated hardware cloth. This method could minimize potential contamination and allow for cross-study comparisons on gut microbiomes for wildlife medicine, conservation, ecology, and evolutionary biology.

Abstract

Gut microbial communities play important roles in host health, modulating development, nutrient acquisition, immune and metabolic regulation, behavior and diseases. Wildlife microbiome studies and host–microbe interaction and exploration might be an important goal for evolutionary biology, conservation, and ecology. Therefore, collection and sampling methods must be considered before choosing a microbiome-based research plan. Since the fecal microbial community reflects the true gut community better than that of cloacal swab samples and only few nondestructive methods have been described, we propose an easy-to-build box for a noninvasive fecal collection method. The main components of the collection box include a plastic storage box, a plastic tray, a vinyl-coated hardware cloth, and a 10% bleach solution. In the plastic box, the tray is positioned under the raised grate, where the bird is placed, to reduce the risk of contamination of the fecal samples. This procedure could simplify handling and processing phases in wild birds or other animals. It might represent a cheap and useful method for research studies, wildlife rescue center activities, veterinary practices, and conservation practitioners.

Seasonal and elevational variation in glucose and glycogen in two songbird species

Birds naturally maintain high glucose concentrations in the blood and tissues, even when relying on fat to meet the metabolic demands of flight or thermogenesis. One possibility is that high glucose levels might be needed to deal with these metabolic demands. Thus, we hypothesized that birds chronically exposed to colder temperatures and higher elevations have higher circulating glucose and tissue free glucose and glycogen compared to conspecifics living at warmer temperatures and lower elevations. Adult House Sparrows (Passer domesticus) and House Finches (Haemorhous mexicanus) were captured from Phoenix, AZ (340 m elevation), and Albuquerque, NM (1600 m elevation), during the summer and winter months. We measured plasma glucose, as well as free glucose and glycogen from multiple tissues. In general, high elevation and colder temperatures were associated with higher tissue glycogen and higher free glucose concentrations in the brain. These findings indicate that glucose and glycogen are subject to seasonal phenotypic flexibility as well as geographic variations that may relate to local food availability and abundance.