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Rapid changes in gene expression can result in physiological plasticity that assists animals in coping with environmental stressors. Increased capacity for physiological plasticity may then facilitate adaptation to stressful habitats like urban heat islands or invasion into novel ranges. Currently, temperature stress is a leading threat to organisms, especially ectotherms. While exposure to changing temperatures is known to shift gene expression patterns in ectothermic animals, many studies are conducted after lengthy acclimation times. However, exposure to thermal stress in nature can occur rapidly. We assessed the capacity for gene expression plasticity in response to a brief exposure to extreme thermal stress in an urban, introduced species, the common wall lizard (Podarcis muralis). Lizards were ramped to their critical thermal maximum (CTmax) or minimum (CTmin) followed by rapid recovery. We used RNA-sequencing to compare the transcriptomes of lizards exposed to CTmax, CTmin, or control conditions using heart, liver, and large intestine tissue. Exposure to heat stress induced a much stronger gene expression response across tissues than cold exposure. In response to heat, there was systemic upregulation of heat shock proteins and stress response pathways. Heat also induced changes in transcription, translation, and metabolic processes but these effects were more tissue specific. Although fewer gene expression changes were observed in response to cold, some genes were upregulated that could be beneficial under cooling stress. Our data suggests gene expression plasticity could facilitate range expansion in this species, but more work is needed to assess the transcriptomic response to temperature stress in nature. 

Vertebrates house dense and diverse communities of microorganisms in their gastrointestinal tracts. These communities shape host physiological and ecological phenotypes in diverse ways, with implications for animal fitness in nature. Exposure to microbes during the earliest stages of life is particularly important because, during critical developmental windows, the microbiome is exceptionally plastic and interactions with microbes can have long-lasting physiological impacts on the host. Despite our understanding that early-life microbial interactions are important to host function broadly, the majority of research in this area has been performed in human or model organisms that are not representative of animals in the wild. Specifically, most gut microbiome studies in wildlife are cross-sectional and compare microbial communities across life stages using different individuals, as opposed to tracking the microbial communities and phenotypes of the same individuals from early to later life. This knowledge gap may hinder wildlife microbiome research, as the current model lacks an early-life perspective that can contextualize host phenotypic and fitness differences observed between animals at later life stages. Further, considering early-life microbial dynamics may offer insights to applied research, such as determining the optimal age to manipulate microbiomes for desired conservation outcomes. In this Commentary, we consider current understanding of the importance of early-life host–microbe interactions to vertebrate physiology across the lifespan, discuss why this perspective is necessary in wildlife studies, and provide practical recommendations for experimental designs that can address these questions, including field and laboratory approaches. 

ABSTRACT Diet and host identity play fundamental roles in digestive physiology and the assembly of gut microbial communities. Research shows that microbial communities are plastic, with abundances of taxa and community interactions exhibiting changes in response to diet. Few studies considering the influence of diet on host and microbial plasticity disentangle the unique roles of specific nutrients, such as protein and fiber. Additionally, in the context of host–microbiome interactions, few studies have explored how host dietary strategies shape the plastic responses of microbial communities within the host digestive tract. To address these current gaps, we fed rodents with distinct dietary strategies (Peromyscus leucopus, Microtus montanus and Onychomys torridus) diets varying in fiber and protein content. Species varied in the degree of cecum size plasticity, with the carnivore showing no significant changes and the omnivore responding to both fiber and protein manipulation. There were also differences in the diversity indices of bacterial and fungal communities across hosts, and the microbes driving those differences were largely unique across rodent species. Additionally, community network interactions varied across treatments, and hub taxa that play a role in regulating network properties were identified. For example, bacteria in the Eubacterium groups, which are known to aid in fiber fermentation, were identified as hub taxa in all three species, but no group shared the same Eubacterium as a hub taxa. Overall, our data suggest that hosts with unique dietary strategies and their microbiomes respond uniquely to changes in the nutrient composition of their diets. 

ABSTRACT To efficiently digest food resources that may vary spatially and temporally, animals maintain physiological flexibility across levels of organization. For example, in response to dietary shifts, animals may exhibit changes in the expression of digestive enzymes, the size of digestive organs or the structure of their gut microbiome. A ‘Grand Challenge’ in comparative physiology is to understand how components of flexibility across organizational levels may scale to cumulatively determine organismal performance. Here, we conducted feeding trials on three rodent species with disparate feeding strategies: herbivorous montane voles (Microtus montanus), omnivorous white-footed mice (Peromyscus leucopus) and carnivorous grasshopper mice (Onychomys torridus). For each species, four groups of individuals were presented with diets that varied in carbohydrate, fiber and protein content. After 4–5 weeks, we measured organismal performance in the form of nutrient digestibility (dry matter, nitrogen, fiber). We also measured gut anatomy and organ size, and conducted enzyme assays on various tissues to measure activities of carbohydrases and peptidases. We found some shared physiological responses, e.g. fiber generally increased gut size across species. However, the specifics of these responses were distinct across species, suggesting different capacities for flexibility. Thus, in the context of digestion, we still lack an understanding of how flexibility across organizational levels may scale to determine whole-animal performance. 

Abstract The role of species interactions, as well as genetic and environmental factors, all likely contribute to the composition and structure of the gut microbiome; however, disentangling these independent factors under field conditions represents a challenge for a functional understanding of gut microbial ecology. Avian brood parasites provide unique opportunities to investigate these questions, as brood parasitism results in parasite and host nestlings being raised in the same nest, by the same parents. Here we utilized obligate brood parasite brown‐headed cowbird nestlings (BHCO;Molothrus ater) raised by several different host passerine species to better understand, via 16S rRNA sequencing, the microbial ecology of brood parasitism. First, we compared faecal microbial communities of prothonotary warbler nestlings (PROW;Protonotaria citrea) that were either parasitized or non‐parasitized by BHCO and communities among BHCO nestlings from PROW nests. We found that parasitism by BHCO significantly altered both the community membership and community structure of the PROW nestling microbiota, perhaps due to the stressful nest environment generated by brood parasitism. In a second dataset, we compared faecal microbiotas from BHCO nestlings raised by six different host passerine species. Here, we found that the microbiota of BHCO nestlings was significantly influenced by the parental host species and the presence of an inter‐specific nestmate. Thus, early rearing environment is important in determining the microbiota of brood parasite nestlings and their companion nestlings. Future work may aim to understand the functional effects of this microbiota variability on nestling performance and fitness. 

Diet selection is a fundamental aspect of animal behavior with numerous ecological and evolutionary implications. While the underlying mechanisms are complex, the availability of essential dietary nutrients can strongly influence diet selection behavior. The gut microbiome has been shown to metabolize many of these same nutrients, leading to the untested hypothesis that intestinal microbiota may influence diet selection. Here, we show that germ-free mice colonized by gut microbiota from three rodent species with distinct foraging strategies differentially selected diets that varied in macronutrient composition. Specifically, we found that herbivore-conventionalized mice voluntarily selected a higher protein:carbohydrate (P:C) ratio diet, while omnivore- and carnivore-conventionalized mice selected a lower P:C ratio diet. In support of the long-standing hypothesis that tryptophan—the essential amino acid precursor of serotonin—serves as a peripheral signal regulating diet selection, bacterial genes involved in tryptophan metabolism and plasma tryptophan availability prior to the selection trial were significantly correlated with subsequent voluntary carbohydrate intake. Finally, herbivore-conventionalized mice exhibited larger intestinal compartments associated with microbial fermentation, broadly reflecting the intestinal morphology of their donor species. Together, these results demonstrate that gut microbiome can influence host diet selection behavior, perhaps by mediating the availability of essential amino acids, thereby revealing a mechanism by which the gut microbiota can influence host foraging behavior. 

Abstract Measurements of fecal pellet size can provide important information about wild mammals, such as body size and demographic information. Previous studies have not rigorously tested whether diet can confound these measurements. Furthermore, it is unknown whether diet might alter fecal dimensions directly or through changes in animal physiology. Here, we studied three closely related rodent species that differ in natural feeding strategies. Individuals were fed diets that varied in protein and fiber content for 5 weeks. We then measured body size, fecal widths and lengths, and the radius of the large intestine. Diet composition significantly changed fecal widths in all species. High-fiber content significantly increased fecal widths and would cause overestimations of body size if applied to wild feces. Using path analysis, we found that fiber can increase fecal widths both directly and indirectly through increasing the large intestine radius. Protein affected each species differently, suggesting that protein effects vary by species feeding strategy and existing physiology. Overall, diet and large intestine morphology can alter fecal pellet measurements. Studies using fecal measurements therefore must consider these effects in their conclusions.