Non-invasive monitoring of multiple wildlife health factors by fecal microbiome analysis

The Faecal Microbiome Analysed from Healthy, Free-Roaming Giraffes (Giraffa camelopardalis)

Similar to other herbivores, healthy giraffes (Giraffa camelopardalis) rely on a variety of symbiotic microorganisms in their digestive systems to break down cellulose and hemicellulose. In this study, we investigate the impact that external stimuli might have on the faecal prokaryote composition of healthy, free-roaming giraffes. Faecal samples were collected from six male and seven female giraffe individuals, over a 2-year period, during the wet and dry seasons, from six locations within the Free State Province, South Africa. Giraffe populations were exposed to one of two feeding practices which included provision of supplemental feed or only naturally available vegetation. Seventeen (17) different prokaryotic phyla, consisting of 8370 amplicon sequence variants (ASVs), were identified from the 13 healthy, adult, free-roaming giraffes included in the study. Overall, the bacterial phyla with the largest relative abundance included Fusobacteria (22%), followed by Lentisphaera (17%) and Cyanobacteria (16%), which included 21 dominant prokaryotic ASVs. The relative abundance of Ruminococcaceae UCG 014 and Treponema 2 were found to be significantly (P < 0.05) higher and Escherichia / Shigella, Romboutsia and Ruminococcus 1 significantly lower for giraffes receiving supplemental feed compared to natural available vegetation. This is the first study to investigate the composition of the faecal prokaryotic communities of healthy, free-roaming giraffes. The analysis of faecal prokaryotes contributes to the development of non-invasive methods for assessing the nutritional status and identifying health issues in giraffe populations. Ultimately, such advances are beneficial towards the larger-scale conservation, determining nutritional needs and management of other sensitive wildlife species, as well.

Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance

Studies on wild animals, mostly undertaken using 16S metabarcoding, have yielded ambiguous evidence regarding changes in the gut microbiome (GM) with age and senescence. Furthermore, variation in GM function has rarely been studied in such wild populations, despite GM metabolic characteristics potentially being associated with host senescent declines. Here, we used 7 years of repeated sampling of individuals and shotgun metagenomic sequencing to investigate taxonomic and functional changes in the GM of Seychelles warblers (Acrocephalus sechellensis) with age. Our results suggest that taxonomic GM species richness declines with age and in the terminal year, with this terminal decline occurring consistently across all ages. Taxonomic and functional GM composition also shifted with host age. However, the changes we identified occurred linearly with age (or even mainly during early years prior to the onset of senescence in this species) with little evidence of accelerated change in later life or during their terminal year. Therefore, the results suggest that changes in the GM with age are not linked to senescence. Interestingly, we found a significant increase in the abundance of a group of transposase genes with age, which may accumulate passively or due to increased transposition induced as a result of stressors that arise with age. These findings reveal taxonomic and functional GM changes with age, but not senescence, in a wild vertebrate and provide a blueprint for future wild functional GM studies linked to age and senescence.

Advancements in noninvasive koala monitoring through combining Chlamydia detection with a targeted koala genotyping assay

Wildlife diseases are major players in local and global extinctions. Effective disease surveillance, management and conservation strategies require accurate estimates of pathogen prevalence. Yet pathogen detection in wild animals remains challenging. Current gold standards often require samples collected through veterinary examination, but this method is costly, intensive, invasive, and requires specialised staff and equipment. Collection of non-invasive samples, such as scats, is an effective monitoring tool which can be deployed at large scale, as scats contain DNA of both host and pathogens. The koala (Phascolarctos cinereus) is listed as 'endangered' under the EPBC Act 1999, with chlamydial disease representing a major threat. Here, we present a new approach that combines restriction-enzyme associated sequencing and targeted-sequence-capture genotyping, namely DArTcap, to detect Chlamydia pecorum in koala scats. We found this method has similar accuracy to current gold standards (qPCR of swab samples), with a sensitivity of 91.7% and a specificity of 100%. This method can be incorporated into existing koala genetic studies using marker panels, where population attributes can be estimated alongside C. pecorum presence, using the same scat samples, with the option to add further markers of interest. Such a one-stop-shop panel would considerably reduce processing times and cost.

First Insights into the Fecal Metabolome of Healthy, Free-Roaming Giraffes (Giraffa camelopardalis): An Untargeted GCxGC/TOF-MS Metabolomics Study

BACKGROUND/OBJECTIVES

This study provides the first insights to the fecal metabolome of the giraffe (Giraffa camelopardalis). By using untargeted metabolomics via gas chromatography time-of-flight mass spectrometry (GCxGC/TOF-MS), this study primarily aims to provide results of the impact that external stimuli, such as supplemental feeding (SF) practices, seasonal variation and sex, might have on the fecal metabolome composition of healthy, free-roaming giraffes.

METHODS

Untargeted GCxGC/TOF-MS analysis was applied to the feces collected from thirteen giraffes (six males and seven females) from six different locations within the central Free State Province of South Africa over a period of two years. Statistical analysis of the generated data was used to identify the metabolites that were significantly different between the giraffes located in environments that provided SF and others where the giraffes only fed on the natural available vegetation. The same metabolomics analysis was used to investigate metabolite concentrations that were significantly different between the wet and dry seasons for a single giraffe male provided with SF over the two-year period, as well as for age and sex differences.

RESULTS

A total of 2042 features were detected from 26 giraffe fecal samples. Clear variations between fecal metabolome profiles were confirmed, with higher levels of amino acid-related and carbohydrate-related metabolites for giraffes receiving SF. In addition, a separation between the obtained profiles of samples collected from a single adult male giraffe during the wet and dry seasons was identified. Differences, such as higher levels of carbohydrate-related metabolites and organic compounds during the wet season were noted. Distinct variations in profiles were also identified for the metabolites from fecal samples collected from the six males and seven females, with higher concentrations in carbohydrate-related metabolites and alkanes for female giraffes comparatively.

CONCLUSIONS

This is the first study to investigate the composition of the fecal metabolome of free-roaming giraffes, as well as the effects that external factors, such as environmental exposures, feeding practices, seasonal variations, age and sex, have on it. This novel use of fecal metabolomics assists in developing non-invasive techniques to determine giraffe populations' health that do not require additional stressors such as capture, restraint and blood collection. Ultimately, such non-invasive advances are beneficial towards the conservation of wildlife species on a larger scale.

Insights into the Gut Microbial Diversity of Wild Siberian Musk Deer (Moschus moschiferus) in Republic of Korea

The gut microbiota plays a crucial role in the health and well-being of wildlife. However, its composition and diversity remain unexplored, particularly in threatened species such as the Siberian musk deer (SMD). This study aimed to elucidate the gut microbiota composition within different wild SMD communities for assessing their health status. We conducted the first comprehensive fecal microbiome analysis of wild SMD inhabiting three distinct locations in Gangwon Province, Republic of Korea (Korea). Fecal samples were collected non-invasively and 16S rRNA gene sequencing was performed for gut microbiota characterization. Consistent with previous research, Firmicutes and Bacteroidetes were the dominant phyla in the gut microbiota of wild SMD. Planctomycetota was a prevalent phylum in wild SMD gut microbiota, warranting further investigation of its ecological significance. While significant differences were observed in the gut microbiota richness among the three groups, no significant disparities were detected in the beta diversity. Additionally, certain genera exhibited distinct relative abundances among the groups, suggesting potential associations with geographic factors, gut disorders, and dietary habits. Our findings provide valuable insights into the gut microbiome of wild SMD and offer a foundation for future microbiome-based conservation efforts for this vulnerable species.

Harnessing the gut microbiome: a potential biomarker for wild animal welfare

The welfare of wild animal populations is critically important to conservation, with profound implications for ecosystem health, biodiversity, and zoonotic disease transmission. Animal welfare is typically defined as the accumulated affective mental state of an animal over a particular time period. However, the assessment of animal welfare in the wild poses unique challenges, primarily due to the lack of universally applicable biomarkers. This perspective explores the potential role of the gut microbiome, a dynamic and non-invasive biomarker, as a novel avenue for evaluating animal welfare in wild animals. The gut microbiome, through interactions with the host's physiology, behavior, and cognition, offers a promising opportunity to gain insights into the well-being of animals. In this synthesis, we discuss the distinction between fitness and welfare, the complexities of assessing welfare in wild populations, and the linkages between the gut microbiome and aspects of animal welfare such as behavior and cognition. We lastly elucidate how the gut microbiome could serve as a valuable tool for wildlife managers, with the potential to serve as a non-invasive yet informative window into the welfare of wild animals. As this nascent field evolves, it presents unique opportunities to enhance our understanding of the well-being of wild animals and to contribute to the preservation of ecosystems, biodiversity, and human health.

Gut bacterial composition shows sex-specific shifts during breeding season in ex situ managed black-footed ferrets

The gut microbiome of mammals engages in a dynamic relationship with the body and contributes to numerous physiological processes integral to overall health. Understanding the factors shaping animal-associated bacterial communities is therefore paramount to the maintenance and management in ex situ wildlife populations. Here, we characterized the gut microbiome of 48 endangered black-footed ferrets (Mustela nigripes) housed at Smithsonian's National Zoo and Conservation Biology Institute (Front Royal, Virginia, USA). We collected longitudinal fecal samples from males and females across two distinct reproductive seasons to consider the role of host sex and reproductive physiology in shaping bacterial communities, as measured using 16S rRNA amplicon sequencing. Within each sex, gut microbial composition differed between breeding and non-breeding seasons, with five bacterial taxa emerging as differentially abundant. Between sexes, female and male microbiomes were similar during non-breeding season but significantly different during breeding season, which may result from sex-specific physiological changes associated with breeding. Finally, we found low overall diversity consistent with other mammalian carnivores alongside high relative abundances of potentially pathogenic microbes such as Clostridium, Escherichia, Paeniclostridium, and (to a lesser degree) Enterococcus-all of which have been associated with gastrointestinal or reproductive distress in mammalian hosts, including black-footed ferrets. We recommend further study of these microbes and possible therapeutic interventions to promote more balanced microbial communities. These results have important implications for ex situ management practices that can improve the gut microbial health and long-term viability of black-footed ferrets.

Temporal and Spatial Influences on Fawn Summer Survival in Pronghorn Populations: Management Implications from Noninvasive Monitoring

Monitoring vital rates allows managers to estimate trends in growth rates of ungulate populations. However, connecting the influence of nutrition on ungulate demography is challenging. Noninvasive sampling offers a low-cost, low-effort alternative for measuring nutritional indices, allowing for an increased understanding of the mechanistic relationships between environmental factors, nutrition, and specific population vital rates. We examined the temporal influence of intrinsic and extrinsic factors on pronghorn (Antilocapra americana) fawn recruitment. We collected fresh fecal samples from adult female pronghorn in five subpopulations spanning three sampling periods associated with critical maternal life-history stages (late gestation, early lactation, breeding season) for 2 years to investigate both intra- and interannual influences. Intrinsic factors were fecal glucocorticoid metabolites (FGMs), nutritional indices (fecal nitrogen (FN) and 2,6-diaminopimelic acid (DAPA)), and dietary composition (protein intake of forbs, graminoids, legumes, other, shrubs), while the extrinsic factor was vegetative greenness (normalized difference vegetation index (NDVI)). We found variations in DAPA, protein intake of forbs, variation in forb protein intake, and protein intake of legumes during late gestation positively influenced fawn recruitment. Fecal nitrogen during early lactation showed the strongest positive influence on the recruitment of any measured parameter. Finally, breeding season NDVI and the variation in DAPA values positively influenced the subsequent year's fawn recruitment. Our longitudinal study enabled us to investigate which parameter was most important to specific periods of fawn development and recruitment. We combined the results across five subpopulations, but interpretation and subsequent management decisions should be made at the subpopulation level such that pronghorn subpopulations with low recruitment can be positively influenced by increasing nitrogen on the landscape available to adult females during the early lactation period. As the use of noninvasive monitoring methods continues to expand, we believe our methodologies and results can be broadly applied to other ungulate monitoring programs.

A first characterization of the microbiota-resilience link in swine

BACKGROUND

The gut microbiome plays a crucial role in understanding complex biological mechanisms, including host resilience to stressors. Investigating the microbiota-resilience link in animals and plants holds relevance in addressing challenges like adaptation of agricultural species to a warming environment. This study aims to characterize the microbiota-resilience connection in swine. As resilience is not directly observable, we estimated it using four distinct indicators based on daily feed consumption variability, assuming animals with greater intake variation may face challenges in maintaining stable physiological status. These indicators were analyzed both as linear and categorical variables. In our first set of analyses, we explored the microbiota-resilience link using PERMANOVA, α-diversity analysis, and discriminant analysis. Additionally, we quantified the ratio of estimated microbiota variance to total phenotypic variance (microbiability). Finally, we conducted a Partial Least Squares-Discriminant Analysis (PLS-DA) to assess the classification performance of the microbiota with indicators expressed in classes.

RESULTS

This study offers four key insights. Firstly, among all indicators, two effectively captured resilience. Secondly, our analyses revealed robust relationship between microbial composition and resilience in terms of both composition and richness. We found decreased α-diversity in less-resilient animals, while specific amplicon sequence variants (ASVs) and KEGG pathways associated with inflammatory responses were negatively linked to resilience. Thirdly, considering resilience indicators in classes, we observed significant differences in microbial composition primarily in animals with lower resilience. Lastly, our study indicates that gut microbial composition can serve as a reliable biomarker for distinguishing individuals with lower resilience.

CONCLUSION

Our comprehensive analyses have highlighted the host-microbiota and resilience connection, contributing valuable insights to the existing scientific knowledge. The practical implications of PLS-DA and microbiability results are noteworthy. PLS-DA suggests that host-microbiota interactions could be utilized as biomarkers for monitoring resilience. Furthermore, the microbiability findings show that leveraging host-microbiota insights may improve the identification of resilient animals, supporting their adaptive capacity in response to changing environmental conditions. These practical implications offer promising avenues for enhancing animal well-being and adaptation strategies in the context of environmental challenges faced by livestock populations. Video Abstract.

Fecal and vaginal microbiota of vaccinated and non-vaccinated pregnant elk challenged with Brucella abortus

Introduction

Brucella abortus is the causative agent of brucellosis in cattle and in humans, resulting in economic losses in the agricultural sector and representing a major threat to public health. Elk populations in the American Northwest are reservoirs for this bacterium and transmit the agent to domestic cattle herds. One potential strategy to mitigate the transmission of brucellosis by elk is vaccination of elk populations against B. abortus; however, elk appear to be immunologically distinct from cattle in their responses to current vaccination strategies. The differences in host response to B. abortus between cattle and elk could be attributed to differences between the cattle and elk innate and adaptive immune responses. Because species-specific interactions between the host microbiome and the immune system are also known to affect immunity, we sought to investigate interactions between the elk microbiome and B. abortus infection and vaccination.

Methods

We analyzed the fecal and vaginal microbial communities of B. abortus-vaccinated and unvaccinated elk which were challenged with B. abortus during the periparturient period.

Results

We observed that the elk fecal and vaginal microbiota are similar to those of other ruminants, and these microbial communities were affected both by time of sampling and by vaccination status. Notably, we observed that taxa representing ruminant reproductive tract pathogens tended to increase in abundance in the elk vaginal microbiome following parturition. Furthermore, many of these taxa differed significantly in abundance depending on vaccination status, indicating that vaccination against B. abortus affects the elk vaginal microbiota with potential implications for animal reproductive health.

Discussion

This study is the first to analyze the vaginal microbiota of any species of the genus Cervus and is also the first to assess the effects of B. abortus vaccination and challenge on the vaginal microbiome.

Fecal Microbial Diversity of Coyotes and Wild Hogs in Texas Panhandle, USA

The ecology of infectious diseases involves wildlife, yet the wildlife interface is often neglected and understudied. Pathogens related to infectious diseases are often maintained within wildlife populations and can spread to livestock and humans. In this study, we explored the fecal microbiome of coyotes and wild hogs in the Texas panhandle using polymerase chain reactions and 16S sequencing methods. The fecal microbiota of coyotes was dominated by members of the phyla Bacteroidetes, Firmicutes, and Proteobacteria. At the genus taxonomic level, Odoribacter, Allobaculum, Coprobacillus, and Alloprevotella were the dominant genera of the core fecal microbiota of coyotes. While for wild hogs, the fecal microbiota was dominated by bacterial members of the phyla Bacteroidetes, Spirochaetes, Firmicutes, and Proteobacteria. Five genera, Treponema, Prevotella, Alloprevotella, Vampirovibrio, and Sphaerochaeta, constitute the most abundant genera of the core microbiota of wild hogs in this study. Functional profile of the microbiota of coyotes and wild hogs identified 13 and 17 human-related diseases that were statistically associated with the fecal microbiota, respectively (p < 0.05). Our study is a unique investigation of the microbiota using free-living wildlife in the Texas Panhandle and contributes to awareness of the role played by gastrointestinal microbiota of wild canids and hogs in infectious disease reservoir and transmission risk. This report will contribute to the lacking information on coyote and wild hog microbial communities by providing insights into their composition and ecology which may likely be different from those of captive species or domesticated animals. This study will contribute to baseline knowledge for future studies on wildlife gut microbiomes.

Composition and function of the Galapagos penguin gut microbiome vary with age, location, and a putative bacterial pathogen

Microbial colonization plays a direct role in host health. Understanding the ecology of the resident microbial community for a given host species is thus an important step for detecting population vulnerabilities like disease. However, the idea of integrating microbiome research into conservation is still relatively new, and wild birds have received less attention in this field than mammals or domesticated animals. Here we examine the composition and function of the gut microbiome of the endangered Galapagos penguin (Spheniscus mendiculus) with the goals of characterizing the normal microbial community and resistome, identifying likely pathogens, and testing hypotheses of structuring forces for this community based on demographics, location, and infection status. We collected fecal samples from wild penguins in 2018 and performed 16S rRNA gene sequencing and whole genome sequencing (WGS) on extracted DNA. 16S sequencing revealed that the bacterial phyla Fusobacteria, Epsilonbacteraeota, Firmicutes, and Proteobacteria dominate the community. Functional pathways were computed from WGS data, showing genetic functional potential primarily focused on metabolism-amino acid metabolism, carbohydrate metabolism, and energy metabolism are the most well-represented functional groups. WGS samples were each screened for antimicrobial resistance, characterizing a resistome made up of nine antibiotic resistance genes. Samples were screened for potential enteric pathogens using virulence factors as indicators; Clostridium perfringens was revealed as a likely pathogen. Overall, three factors appear to be shaping the alpha and beta diversity of the microbial community: penguin developmental stage, sampling location, and C. perfringens. We found that juvenile penguins have significantly lower alpha diversity than adults based on three metrics, as well as significantly different beta diversity. Location effects are minimal, but one site has significantly lower Shannon diversity than the other primary sites. Finally, when samples were grouped by C. perfringens virulence factors, we found dramatic changes in beta diversity based on operational taxonomic units, protein families, and functional pathways. This study provides a baseline microbiome for an endangered species, implicates both penguin age and the presence of a potential bacterial pathogen as primary factors associated with microbial community variance, and reveals widespread antibiotic resistance genes across the population.

DNA virome composition of two sympatric wild felids, bobcat (Lynx rufus) and puma (Puma concolor) in Sonora, Mexico

With viruses often having devastating effects on wildlife population fitness and wild mammals serving as pathogen reservoirs for potentially zoonotic diseases, determining the viral diversity present in wild mammals is both a conservation and One Health priority. Additionally, transmission from more abundant hosts could increase the extinction risk of threatened sympatric species. We leveraged an existing circular DNA enriched metagenomic dataset generated from bobcat (Lynx rufus, n = 9) and puma (Puma concolor, n = 13) scat samples non-invasively collected from Sonora, Mexico, to characterize fecal DNA viromes of each species and determine the extent that viruses are shared between them. Using the metaWRAP pipeline to co-assemble viral genomes for comparative metagenomic analysis, we observed diverse circular DNA viruses in both species, including circoviruses, genomoviruses, and anelloviruses. We found that differences in DNA virome composition were partly attributed to host species, although there was overlap between viruses in bobcats and pumas. Pumas exhibited greater levels of alpha diversity, possibly due to bioaccumulation of pathogens in apex predators. Shared viral taxa may reflect dietary overlap, shared environmental resources, or transmission through host interactions, although we cannot rule out species-specific host-virus coevolution for the taxa detected through co-assembly. However, our detection of integrated feline foamy virus (FFV) suggests Sonoran pumas may interact with domestic cats. Our results contribute to the growing baseline knowledge of wild felid viral diversity. Future research including samples from additional sources (e.g., prey items, tissues) may help to clarify host associations and determine the pathogenicity of detected viruses.

Comparing invasive and noninvasive faecal sampling in wildlife microbiome studies: A case study on wild common cranes

In ecological and conservation studies, responsible researchers strive to obtain rich data while minimizing disturbance to wildlife and ecosystems. We assessed if samples collected noninvasively can be used for faecal microbiome research, comparing microbiota of noninvasively collected faecal samples to those collected from trapped common cranes at the same sites over the same periods. We found significant differences in faecal microbial composition (alpha and beta diversity), which likely did not result from noninvasive sample exposure to soil contaminants, as assessed by comparing bacterial oxygen use profiles. Differences might result from trapped birds' exposure to sedatives or stress. We conclude that if all samples are collected in the same manner, comparative analyses are valid, and noninvasive sampling may better represent host faecal microbiota because there are no trapping effects. Experiments with fresh and delayed sample collection can elucidate effects of environmental exposures on microbiota. Further, controlled tests of stressing or sedation may unravel how trapping affects wildlife microbiota.

Gastrointestinal parasites in wild rodents in Chiloé Island-Chile

Gastrointestinal parasites are well-documented in small mammals from north-central Chile, but little is known about endoparasites of rodents in southern Chile. A survey was conducted between January and February 2018 to evaluate gastrointestinal parasites and risk factors of wild rodents that live in rural areas in Northern Chiloé Island, Chile. A total of 174 fecal samples from rodents of six native and one introduced species were collected and examined using the Mini-FLOTAC method. Also, 41 individuals of four native wild rodent species were examined furtherly to determinate adult parasites from gastrointestinal tracts. The overall prevalence of endoparasites was 89.65% (156). Helminth egg types included: Rodentolepis spp., Capillariidae, Trichuris sp., Syphacia sp., oxyurid-type eggs, Strongyloides sp., Spirurid-type eggs, Strongilid-type eggs, Moniliformis sp., and an unidentified nematode egg and larvae. Protozoa comprised coccidia, amoeba, and unidentified cysts. From necropsies, adult parasites involved Syphacia sp. Trichuris sp., Protospirura sp. and Physaloptera sp. In Abrothrix olivacea, individuals with low-body-mass index exhibited reduced infection probability for Spirurid-type and Strongilid-type eggs. Some parasites in this study may affect human health. In rural settings where environmental conditions are changing, more research should be undertaken to understand parasitic infections in wildlife and implications for public health and conservation.

Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations

Extensive research in well-studied animal models underscores the importance of commensal gastrointestinal (gut) microbes to animal physiology. Gut microbes have been shown to impact dietary digestion, mediate infection, and even modify behavior and cognition. Given the large physiological and pathophysiological contribution microbes provide their host, it is reasonable to assume that the vertebrate gut microbiome may also impact the fitness, health and ecology of wildlife. In accordance with this expectation, an increasing number of investigations have considered the role of the gut microbiome in wildlife ecology, health, and conservation. To help promote the development of this nascent field, we need to dissolve the technical barriers prohibitive to performing wildlife microbiome research. The present review discusses the 16S rRNA gene microbiome research landscape, clarifying best practices in microbiome data generation and analysis, with particular emphasis on unique situations that arise during wildlife investigations. Special consideration is given to topics relevant for microbiome wildlife research from sample collection to molecular techniques for data generation, to data analysis strategies. Our hope is that this article not only calls for greater integration of microbiome analyses into wildlife ecology and health studies but provides researchers with the technical framework needed to successfully conduct such investigations.

Analysis of Scat for Gut Microbiome Identification in Wolves from a Mediterranean and an Alpine Area

The gut microbiome can play a fundamental role in several processes associated with an organism’s ecology, and research on the microbiota of wild animals has flourished in the last decades. Microbiome composition can vary across and within species according to taxonomy and environmental variability, including the availability of food resources. Species with a large distribution may exhibit spatial patterns acting at local/regional scales. We considered one of the most widespread and ecologically important predators in the world, i.e., the grey wolf Canis lupus, for which microbiome data is unduly limited. We studied four packs in different ecological conditions in Italy—two packs from a Mediterranean coastal area and two packs from an Alpine range—using an amplicon sequencing barcoding approach. Overall, our results are consistent with food habits entailing a diet largely based on wild prey and agree with findings obtained on other species of canids. If confirmed through a larger sample, they would support the hypothesis of an influence of the shared evolutionary history across canids on the composition of the gut microbiome. Some emerging differences were observed among packs in terms of species composition (Jaccard) and diversity, providing partial support to recent indications on pack identity as a significant determinant of microbiome composition. These results should be considered preliminary results of gut microbiome composition in our study areas.

Gut Microbiome as a Mediator of Stress Resilience: A Reactive Scope Model Framework

Stress resilience is defined as the ability to rebound to a homeostatic state after exposure to a perturbation. Organisms modulate various physiological mediators to respond to unpredictable changes in their environment. The gut microbiome is a key example of a physiological mediator that coordinates a myriad of host functions including counteracting stressors. Here, we highlight the gut microbiome as a mediator of host stress resilience in the framework of the reactive scope model. The reactive scope model integrates physiological mediators with unpredictable environmental changes to predict how animals respond to stressors. We provide examples of how the gut microbiome responds to stressors within the four ranges of the reactive scope model (i.e., predictive homeostasis, reactive homeostasis, homeostatic overload, and homeostatic failure). We identify measurable metrics of the gut microbiome that could be used to infer the degree to which the host is experiencing chronic stress, including microbial diversity, flexibility, and gene richness. The goal of this perspective piece is to highlight the underutilized potential of measuring the gut microbiome as a mediator of stress resilience in wild animal hosts.

Host, microbiome, and complex space: applying population and landscape genetic approaches to gut microbiome research in wild populations

In recent years, emerging sequencing technologies and computational tools have driven a tidal wave of research on host-associated microbiomes, particularly the gut microbiome. These studies demonstrate numerous connections between the gut microbiome and vital host functions, primarily in humans, model organisms, and domestic animals. As the adaptive importance of the gut microbiome becomes clearer, interest in studying the gut microbiomes of wild populations has increased, in part due to the potential for discovering conservation applications. The study of wildlife gut microbiomes holds many new challenges and opportunities due to the complex genetic, spatial, and environmental structure of wild host populations, and the potential for these factors to interact with the microbiome. The emerging picture of adaptive coevolution in host-microbiome relationships highlights the importance of understanding microbiome variation in the context of host population genetics and landscape heterogeneity across a wide range of host populations. We propose a conceptual framework for understanding wildlife gut microbiomes in relation to landscape variables and host population genetics, including the potential of approaches derived from landscape genetics. We use this framework to review current research, synthesize important trends, highlight implications for conservation, and recommend future directions for research. Specifically, we focus on how spatial structure and environmental variation interact with host population genetics and microbiome variation in natural populations, and what we can learn from how these patterns of covariation differ depending on host ecological and evolutionary traits.