Simple SummaryThe body is home to a complex, finely balanced ecological community containing commensal, symbiotic, and pathogenic microorganisms that are collectively termed the microbiota. This system of living organisms plays a crucial role in integrating the neural, endocrine, and immune systems via a bidirectional communication pathway known as the gut-brain-immune axis. In concert with these pathways, the microbiota can influence their hosts’ neurological system to have a profound influence on mental health, mood, and behaviour. Despite the abundance of research in human medicine, there is limited literature exploring the connection between abnormal behavioural phenotypes and disturbances in the gut microbiota of animals. This review provides the first compilation of the current progress of gut microbiota analysis in production, performance, and companion animal studies. We assessed the similarities of gut microbiota between animal categories and compared them to the gut microbiota population shifts already associated with human mental health disorders.AbstractThe literature has identified poor nutrition as the leading factor in the manifestation of many behavioural issues in animals, including aggression, hyperalertness, and stereotypies. Literature focused on all species of interest consistently reported that although there were no significant differences in the richness of specific bacterial taxa in the microbiota of individual subjects with abnormal behaviour (termed alpha diversity), there was variability in species diversity between these subjects compared to controls (termed beta diversity). As seen in humans with mental disorders, animals exhibiting abnormal behaviour often have an enrichment of pro-inflammatory and lactic acid-producing bacteria and a reduction in butyrate-producing bacteria. It is evident from the literature that an association exists between gut microbiota diversity (and by extension, the concurrent production of microbial metabolites) and abnormal behavioural phenotypes across various species, including pigs, dogs, and horses. Similar microbiota population changes are also evident in human mental health patients. However, there are insufficient data to identify this association as a cause or effect. This review provides testable hypotheses for future research to establish causal relationships between gut microbiota and behavioural issues in animals, offering promising potential for the development of novel therapeutic and/or preventative interventions aimed at restoring a healthy gut-brain-immune axis to mitigate behavioural issues and, in turn, improve health, performance, and production in animals.