Microbiome-driven adaptations are fundamental to how both domesticated and wild animals respond to environmental challenges. The gut microbiota plays a central role in regulating nutrition, immune function, and resilience to environmental stressors. Notably, significant differences in microbiome composition and functionality are observed between wild and domesticated species, largely influenced by diet, habitat, and human interaction.
Differences in Microbiome Diversity and Function
Wild animals typically exhibit greater gut microbiota diversity and abundance than their domesticated counterparts. Domestication and captivity are associated with a reduction in microbial diversity, particularly among beneficial bacterial families such as Ruminococcaceae and Lachnospiraceae, which are essential for digestion and immune regulation (Alessandri et al., 2019; Glazko et al., 2021; Kuthyar et al., 2023; Qin et al., 2020; Prabhu et al., 2020).
The microbiota of wild animals is enriched with metabolic and cellular pathways that support adaptation to nutrient scarcity and harsh environmental conditions. In contrast, domesticated animals tend to harbor microbial genes associated with carbohydrate metabolism, reflecting their reliance on commercial feed (Alessandri et al., 2019; Glazko et al., 2021; Levin et al., 2021; Qin et al., 2020).
Drivers of Microbiome Shifts
Diet and living conditions are primary drivers of microbiome composition. Domestication and urbanization lead to notable shifts in gut microbial communities, with diet playing a particularly influential role. Reciprocal feeding experiments have demonstrated that altering the diet of domesticated animals can partially restore microbiota profiles resembling those of wild animals (Das et al., 2023; Kuthyar et al., 2023; Reese et al., 2020). Moreover, domestication often favors microbial taxa that enhance feed efficiency and may involve horizontal transmission of bacteria from humans to animals (Alessandri et al., 2019; Glazko et al., 2021).
Implications for Adaptation and Health
The gut microbiome plays a pivotal role in host adaptability by regulating energy balance, supporting immune function, and enhancing resilience to environmental stressors. In wild animals, a diverse and metabolically versatile microbiota enables the digestion of complex and sometimes toxic food sources, bolsters disease resistance, and facilitates survival in challenging environments (Kuthyar et al., 2023; Levin et al., 2021; Prabhu et al., 2020; Qin et al., 2020). In contrast, domesticated animals often exhibit reduced microbial diversity due to controlled diets, limited environmental exposure, and human-mediated selective pressures. This reduction in diversity has been associated with increased susceptibility to metabolic disorders, allergies, and gastrointestinal diseases.
Domestication tends to favor microbial taxa that enhance feed efficiency and carbohydrate metabolism, reflecting the nutrient composition of commercial diets. However, this shift may come at the cost of losing microbial functions critical for immune modulation and detoxification. Studies have shown that domesticated animals may harbor higher levels of opportunistic pathogens and exhibit altered immune markers, suggesting a compromised ability to respond to infections and environmental stress (Glazko et al., 2021; Kuthyar et al., 2023).
Moreover, the gut microbiome’s influence extends beyond digestion and immunity—it also affects behavior, stress response, and overall physiological homeostasis. The simplification of microbial communities in domesticated species may therefore have cascading effects on health and fitness, underscoring the importance of microbiome diversity in maintaining robust biological systems.
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