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1. Large-scale surveys of woodrats ( Neotoma spp.) reveal constraints on diet breadth in herbivorous mammals

   https://doi.org/10.1073/pnas.2413556122  

   Weinstein, Sara B; Klure, Dylan M; Symeonidi, Efthymia; Greenhalgh, Robert; Mayes, Marc T; Doolin, Margaret L; Stapleton, Tess E; Swei, Andrea; Cove, Michael V; Dearing, M Denise (September 2025, Proceedings of the National Academy of Sciences)

   Characterizing niche space is critical for predicting species interactions and responses to environmental change. To enhance our understanding of dietary niche breadth, we used DNA metabarcoding to examine how diets of a widespread, model herbivore (woodrats, genusNeotoma) respond to changing resources and the extent to which dietary specialization is conserved across space and time. We used diet data from 13 species, 57 populations, and over 500 individuals to examine predictors of niche breadth and interindividual diet variation at a landscape scale. Then, to test whether these patterns are conserved across scales, we explored the same questions using a single population sampled over 5 y and mark-recapture data from individuals sampled at least three times. We found that woodrats exhibited a continuum of dietary specialization that included species-level dietary generalists and specialists. Specialist species maintained narrow population-level niche breadths with little evidence of interindividual diet variation. In contrast, generalist species consisted of populations with varying degrees of dietary specialization and interindividual diet variation. Across sampling scales, increased population-level niche breadth was explained by both increased interindividual diet variation and increased diet richness. These results are consistent with the Niche Variation Hypothesis and suggest that diet breadth is constrained by costs of both specialization and generalization. 

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2. Environment impacts gut microbiome richness in hybridizing chickadees, while ancestry influences community composition

   https://doi.org/10.1002/ecs2.70611  

   Russell, Austin C; Vohsen, Samuel A; Spinelli, Joan_Marie C; Martinez, Noel; Curry, Robert L; Roth, Timothy C; Semenov, Georgy A; Taylor, Scott A; Rice, Amber M (April 2026, Ecosphere)

   Abstract Among closely related species, host phylogenetic relationships are typically a stronger predictor of gut microbiome composition than environmental variation. However, the relative impact of genetic admixture caused by hybridization versus environmental variation on gut microbiome communities is poorly understood. To explore this knowledge gap, we used fecal metabarcoding to characterize chickadee gut microbiomes along a hybrid zone transect in natural environments and after transfer to a common, controlled environment. We collected fecal samples from nestling black‐capped (Poecile atricapillus), Carolina (Poecile carolinensis), and hybrid chickadees immediately after removal from their nests and twice after entering captivity and experiencing common diet and environmental conditions. To characterize gut microbiome communities, we extracted fecal DNA and sequenced the V3–V4 region of the 16S rRNA gene using Illumina MiSeq. Overall,FirmicutesandProteobacteriawere the major microbial phyla present across host species groups. Our analysis of alpha diversity showed that the transition to common environmental conditions significantly impacted host gut microbiome richness. In contrast, the change in host environment did not impact the community composition (i.e., beta diversity) of the gut microbiomes. Although not statistically significant, host ancestry may influence the microbiome composition more than host environment. Additional analyses suggest chloroplast 16S rRNA sequences accurately characterized host diets in captivity. In certain cases, 16S rRNA sequences can provide reliable characterization of habitat and dietary variation in wild birds. Although environment more strongly shapes microbiome richness and evenness, host ancestry may have a greater influence on the specific microbes present in the microbiome. 

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3. Covariation of diet and gut microbiome in African megafauna

   https://doi.org/10.1073/pnas.1905666116  

   Kartzinel, Tyler R.; Hsing, Julianna C.; Musili, Paul M.; Brown, Bianca R.; Pringle, Robert M. (November 2019, Proceedings of the National Academy of Sciences)

   A major challenge in biology is to understand how phylogeny, diet, and environment shape the mammalian gut microbiome. Yet most studies of nonhuman microbiomes have relied on relatively coarse dietary categorizations and have focused either on individual wild populations or on captive animals that are sheltered from environmental pressures, which may obscure the effects of dietary and environmental variation on microbiome composition in diverse natural communities. We analyzed plant and bacterial DNA in fecal samples from an assemblage of 33 sympatric large-herbivore species (27 native, 6 domesticated) in a semiarid East African savanna, which enabled high-resolution assessment of seasonal variation in both diet and microbiome composition. Phylogenetic relatedness strongly predicted microbiome composition ( r = 0.91) and was weakly but significantly correlated with diet composition ( r = 0.20). Dietary diversity did not significantly predict microbiome diversity across species or within any species except kudu; however, diet composition was significantly correlated with microbiome composition both across and within most species. We found a spectrum of seasonal sensitivity at the diet−microbiome nexus: Seasonal changes in diet composition explained 25% of seasonal variation in microbiome composition across species. Species’ positions on (and deviations from) this spectrum were not obviously driven by phylogeny, body size, digestive strategy, or diet composition; however, domesticated species tended to exhibit greater diet−microbiome turnover than wildlife. Our results reveal marked differences in the influence of environment on the degree of diet−microbiome covariation in free-ranging African megafauna, and this variation is not well explained by canonical predictors of nutritional ecology. 

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4. Trophic level and proteobacteria abundance drive antibiotic resistance levels in fish from coastal New England

   https://doi.org/10.1186/s42523-023-00236-w  

   Korry, Benjamin J.; Belenky, Peter (December 2023, Animal Microbiome)

   Abstract Background The natural marine environment represents a vast reservoir of antimicrobial resistant bacteria. The wildlife that inhabits this environment plays an important role as the host to these bacteria and in the dissemination of resistance. The relationship between host diet, phylogeny, and trophic level and the microbiome/resistome in marine fish is not fully understood. To further explore this relationship, we utilize shotgun metagenomic sequencing to define the gastrointestinal tract microbiomes of seven different marine vertebrates collected in coastal New England waters. Results We identify inter and intraspecies differences in the gut microbiota of these wild marine fish populations. Furthermore, we find an association between antibiotic resistance genes and host dietary guild, which suggests that higher trophic level organisms have a greater abundance of resistance genes. Additionally, we demonstrate that antibiotic resistance gene burden is positively correlated with Proteobacteria abundance in the microbiome. Lastly, we identify dietary signatures within the gut of these fish and find evidence of possible dietary selection for bacteria with specific carbohydrate utilization potential. Conclusions This work establishes a link between host lifestyle/dietary guild, and microbiome composition and the abundance of antibiotic resistance genes within the gastrointestinal tract of marine organisms. We expand the current understanding of marine organism-associated microbial communities and their role as reservoirs of antimicrobial resistance genes. 

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5. Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas

   https://doi.org/10.1186/s40168-020-00977-9  

   Baniel, Alice; Amato, Katherine R.; Beehner, Jacinta C.; Bergman, Thore J.; Mercer, Arianne; Perlman, Rachel F.; Petrullo, Lauren; Reitsema, Laurie; Sams, Sierra; Lu, Amy; et al (December 2021, Microbiome)

   null (Ed.)

   Abstract Background Adaptive shifts in gut microbiome composition are one route by which animals adapt to seasonal changes in food availability and diet. However, outside of dietary shifts, other potential environmental drivers of gut microbial composition have rarely been investigated, particularly in organisms living in their natural environments. Results Here, we generated the largest wild nonhuman primate gut microbiome dataset to date to identify the environmental drivers of gut microbial diversity and function in 758 samples collected from wild Ethiopian geladas ( Theropithecus gelada ). Because geladas live in a cold, high-altitude environment and have a low-quality grass-based diet, they face extreme thermoregulatory and energetic constraints. We tested how proxies of food availability (rainfall) and thermoregulatory stress (temperature) predicted gut microbiome composition of geladas. The gelada gut microbiome composition covaried with rainfall and temperature in a pattern that suggests distinct responses to dietary and thermoregulatory challenges. Microbial changes were driven by differences in the main components of the diet across seasons: in rainier periods, the gut was dominated by cellulolytic/fermentative bacteria that specialized in digesting grass, while during dry periods the gut was dominated by bacteria that break down starches found in underground plant parts. Temperature had a comparatively smaller, but detectable, effect on the gut microbiome. During cold and dry periods, bacterial genes involved in energy, amino acid, and lipid metabolism increased, suggesting a stimulation of fermentation activity in the gut when thermoregulatory and nutritional stress co-occurred, and potentially helping geladas to maintain energy balance during challenging periods. Conclusion Together, these results shed light on the extent to which gut microbiota plasticity provides dietary and metabolic flexibility to the host, and might be a key factor to thriving in changing environments. On a longer evolutionary timescale, such metabolic flexibility provided by the gut microbiome may have also allowed members of Theropithecus to adopt a specialized diet, and colonize new high-altitude grassland habitats in East Africa. 

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