The gut microbiome is increasingly recognized as a welfare-relevant system whose composition reflects and influences animal health, stress resilience, and behavioral wellbeing across species.
Gut microbiome research is expanding our understanding of animal welfare by revealing how experiences of stress, disruption, and recovery leave biological traces measurable in microbiome composition. Animals with diverse, stable microbiomes are more resilient to disease and behavioral disturbance, reflecting the relationship between gut health and overall welfare. Management practices that cause microbiome disruption, including routine antibiotic use, unnecessary social upheaval, and poor nutrition, have downstream welfare costs that operate through this biological system. Microbiome analysis may become a powerful objective welfare assessment tool, providing biological evidence of stress history alongside behavioral observations.