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

Gadau, Alice; Crawford, Meli’sa; Mayek, Roman; Giraudeau, Mathieu; McGraw, Kevin J.; Whisner, Corrie M.; Kondrat-Smith, Christina; Sweazea, Karen L.

doi:10.1016/j.cbpb.2019.110332

Cited by 31 publications

(25 citation statements)

References 34 publications

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“…Urbanization clearly affected the eastern grey squirrel microbiome. This result is consistent with findings from birds [21,[23][24][25][26], reptiles [30], humans [51,52], insects [53], plants [54], and wild mammals [29]. Unlike previous studies, we demonstrate that convergence occurs across cities, but also that substantive variation exists both between and within cities.…”

Section: Discussionsupporting

confidence: 91%

“…Despite widespread evidence for an effect of urbanization on the microbiomes of wild plants and animals, reported patterns are inconsistent across host species [21][22][23][24][25][26][27][28][29].…”

Section: Introductionmentioning

confidence: 99%

“…Inconsistencies of urban effects are likely attributable to; 1) city-specific variation (most studies to-date have focused on populations residing within a single city); 2) differences in the operational definition of urbanization; 3) differences in the how host species interact with the urban environment. For example, among vertebrates, consumption of human food resources is hypothesized to be the primary driver of microbiome variation [24,26,30,31]. Dietary variation is likely an important contributor to urban microbiome variation for some wildlife, but not all species rely on human food subsidies to the same extent [32].…”

Section: Introductionmentioning

confidence: 99%

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Shades of grey: Coat-colour dependent effect of urbanization on the bacterial microbiome of a wild mammal

Stothart

Newman

2021

Preprint

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Background: Host-associated microbiota can be fundamental to the ecology of their host and may even help wildlife species colonize novel niches or 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 on the microbiome of eastern grey squirrels (Sciurus carolinensis). Eastern grey squirrels are ubiquitous in both 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). Many of the bacterial genera identified as characterizing the microbiomes of built-environment squirrels are though 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 phylogenetic expectations. Conclusions: Habitat heterogeneity at fine spatial scales affects host-associated microbiomes, however, we found little evidence that this pattern was the result of similar selective pressures acting on the microbiome within environments. Further, this result, those of phylogeny-independent analyses, and patterns of beta-dispersion lead us to suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. These patterns were partly mediated by squirrel coat colour phenotype, and therefore putatively, host physiology. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide an ideal free-living system with which to study how host genetics mediate environment x microbiome interactions.

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Section: Discussionsupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Shades of grey: Coat-colour dependent effect of urbanization on the bacterial microbiome of a wild mammal

Stothart

Newman

2021

Preprint

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“…Investigations on the composition and function of the gut microbiome of wild animals are growing. Climate change, land-use change, environmental contamination, new infectious disease, and antimicrobial resistance are some of the most crucial global threats to biodiversity and should indirectly modify the host-associated microbial diversity in wildlife populations [ 2 , 18 ]. Integrated microbiome, metabolomics, and multi-omics analyses reveal interactions between host and microbiota with the goal of obtaining and elaborating on the amount of information from biological samples.…”

Section: Discussionmentioning

confidence: 99%

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

Borrelli

Minichino

Pace

et al. 2020

Animals

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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.

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“…They also suffer from higher oxidative stress, and higher stress levels than rural sparrows [ 47 – 49 ]. These changes have been related to low food availability and quality [ 43 , 44 , 50 , but see 51 ], high rates of pollution [ 47 , 51 ], disturbance (traffic noise for example [ 52 ]), or even to a recent increase in predator pressure [ 53 , 54 ]. However, the potential impact of malaria infection on morphological and physiological attributes still needs to be clarified in wild bird populations (see [ 45 ] for a study on house sparrows and see [ 20 ] for a study on red-winged blackbirds, Agelaius phoeniceus ).…”

Section: Introductionmentioning

confidence: 99%

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

Bichet¹,

Brischoux²,

Ribout³

et al. 2020

PLoS ONE

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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.

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

Cited by 31 publications

References 34 publications

Shades of grey: Coat-colour dependent effect of urbanization on the bacterial microbiome of a wild mammal

Shades of grey: Coat-colour dependent effect of urbanization on the bacterial microbiome of a wild mammal

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

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

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