Sensory variation and behavioural degeneracy: a framework for interpreting heterogeneity in the gut-brain axis
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Gut microbiome differences are frequently interpreted as reflecting underlying biological differences between individuals. When outcomes are mediated by behaviour, however, this mapping may be fundamentally non-unique. This limits causal inference in gut-brain research, where microbiome differences in autism and depression are routinely attributed to intrinsic neurobiology despite highly variable, overlapping findings. I built a minimal agent-based model grounded in the known sensory variation across the autism spectrum. Dietary behaviour emerges from latent sensory traits, including sensory drive, predictability preference, and context sensitivity, through reinforcement learning and environmental interaction. This behaviour shapes gut microbiome composition. Behavioural variation organizes endogenously into a continuum of specialist, opportunist, and explorer strategies that maps onto the autism sensory spectrum. The system is fundamentally degenerate. Similar microbiome states arise from distinct behavioural pathways. Similar dietary patterns emerge from divergent latent traits. This many-to-one mapping reflects the structural interaction of behaviour, learning, and environmental variability, not stochasticity alone. Microbiome similarity therefore does not uniquely identify underlying cause. As such, the model provides a theoretical framework for interpreting heterogeneity in gut microbiome research, particularly in autism, and generalizes to any condition where behaviour mediates between neural processes and ecological outcomes.
Significance Statement
Biological patterns are often interpreted as direct reflections of underlying mechanisms. This study shows that when outcomes are mediated by behaviour, this mapping becomes intrinsically non-unique, limiting causal inference. Using a minimal agent-based model, I demonstrate that dietary behaviour emerging from sensory traits, environmental context, and learning can generate similar microbial communities via distinct behavioural pathways. Consequently, microbiome similarity does not uniquely identify underlying causes. By identifying behaviour as a mechanistic intermediate linking neural processes to ecological outcomes, this work provides a general framework for interpreting heterogeneity and overlap in gut microbiome research, including in autism and other neurodevelopmental and psychiatric conditions.
