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Microbiome science has provided groundbreaking insights into human and animal health. Similarly, evolutionary medicine - the incorporation of eco-evolutionary concepts into primarily human medical theory and practice - is increasingly recognised for its novel perspectives on modern diseases. Studies of host-microbe relationships have been expanded beyond humans to include a wide range of animal taxa, adding new facets to our understanding of animal ecology, evolution, behaviour, and health. In this review, we propose that a broader application of evolutionary medicine, combined with microbiome science, can provide valuable and innovative perspectives on animal care and conservation. First, we draw on classic ecological principles, such as alternative stable states, to propose an eco-evolutionary framework for understanding variation in animal microbiomes and their role in animal health and wellbeing. With a focus on mammalian gut microbiomes, we apply this framework to populations of animals under human care, with particular relevance to the many animal species that suffer diseases linked to gut microbial dysfunction (e.g. gut distress and infection, autoimmune disorders, obesity). We discuss diet and microbial landscapes (i.e. the microbes in the animal's external environment), as two factors that are (i) proposed to represent evolutionary mismatches for captive animals, (ii) linked to gut microbiome structure and function, and (iii) potentially best understood from an evolutionary medicine perspective. Keeping within our evolutionary framework, we highlight the potential benefits - and pitfalls - of modern microbial therapies, such as pre- and probiotics, faecal microbiota transplants, and microbial rewilding. We discuss the limited, yet growing, empirical evidence for the use of microbial therapies to modulate animal gut microbiomes beneficially. Interspersed throughout, we propose 12 actionable steps, grounded in evolutionary medicine, that can be applied to practical animal care and management. We encourage that these actionable steps be paired with integration of eco-evolutionary perspectives into our definitions of appropriate animal care standards. The evolutionary perspectives proposed herein may be best appreciated when applied to the broad diversity of species under human care, rather than when solely focused on humans. We urge animal care professionals, veterinarians, nutritionists, scientists, and others to collaborate on these efforts, allowing for simultaneous care of animal patients and the generation of valuable empirical data., (© 2023 Cambridge Philosophical Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

Host-associated microbiomes are influenced by evolutionary history and proximate factors such as diet and environment. Zoos house animals in relatively standardized and manipulatable environments, making zoo populations valuable for studying microbiomes. Using a small population of five, closely related primate species housed under nearly identical environments, we investigated gut microbiome variation regarding (a) congruence between host evolutionary history and gut bacterial composition (i.e. phylosymbiosis), (b) a longitudinal reduction in dietary sugar intake, and (c) ingestion of bacteria from dietary sources. We found that the primate gut microbiomes varied across individuals and showed phylosymbiosis. When animals were fed diets with reduced sugar and increased fibre, we found host-specific changes in taxonomically distinct microbes (Phascolarctobacterium, Megasphaera, and Sharpea). Yet, these bacterial genera share similar functional potential (fibre degradation), indicating that the distinct bacterial communities may fulfill similar functions. Although all individuals received the same diet, the diet-associated bacteria in primate gut microbiomes were distinct across individuals of different species, suggesting a mechanism that selects for unique dietary microbes to persist in animal guts. Our findings show that the microbiomes of a small, captive primate population housed under uniform environmental conditions still show patterns congruent with combined influences of evolutionary history and diet., (© The Author(s) 2023. Published by Oxford University Press on behalf of FEMS.)

European starlings (Sturnus vulgaris) were used as a passerine bird model to examine the effect of dietary iron on the level of hepatic iron in birds. Nestling and fledgling starlings (n = 56) were raised on a controlled-iron diet. When birds maintained constant body weight, they were assigned in pairs to cages, and baseline sampling was performed. Pairs were then assigned to one of two diets: the controlled-iron diet (168 ppm, dry basis) or a high-iron diet (3,035 ppm, dry basis). Dry-matter intake and iron consumption were recorded. Dry-matter intake did not differ between the dietary treatment groups and was stable during treatment periods. Iron intake was higher in the high-iron group (P < 0.05). Birds were euthanized at baseline, 8 wk, and 16 wk. Body, liver, and spleen weights were measured. Hepatic iron and copper concentrations were determined. Body weight did not differ between the two treatment groups or among individuals for the study duration. Liver iron concentration differed over time and between treatment groups. Birds receiving both treatments had similar liver iron content at week 8 (3,107 +/- 228.6 ppm and 3,122 +/- 306.2 ppm high and controlled iron, respectively; P > 0.05), but by week 16, birds consuming the high-iron diet had greater hepatic iron levels than those consuming the controlled-iron diet (5,929 +/- 937.2 ppm and 3,683 +/- 229.5 ppm high and controlled iron, respectively; P < 0.05). Birds on the controlled-iron diet also had higher hepatic iron at 16 wk than at 8 wk. Liver copper decreased over time in all birds regardless of treatment. Results show that both dietary iron level and duration of time influenced hepatic iron storage. The controlled-iron diets still allowed accumulation of hepatic iron in an 8-wk period.