Resilient but Unreliable: Cross-Generational Restructuring of the Tribolium castaneum Gut Microbiome Under Contrasting Nutritional Regimes

Abstract

Microbial communities are frequently exposed to environmental disturbances, yet recovery does not always lead to a single, predictable outcome. Distinguishing resilience, the capacity to recover following perturbation, from reliability, the predictability of that recovery, is essential for understanding microbiome dynamics. Here, we investigated cross-generational gut microbiome responses in the red flour beetle, Tribolium castaneum , a globally significant stored-product pest exposed to frequent environmental and dietary shifts. Using a four-generation experimental design (G0–G3), we examined how gut microbial communities respond to a major environmental transition from commercial to laboratory rearing, followed by dietary perturbations. The shift to laboratory conditions produced the largest change in gut microbiome composition, occurring within a single generation and exceeding the effects of dietary shifts. Following this disturbance, microbial communities stabilized across subsequent generations, consistent with strong ecological resilience. However, recovery trajectories and endpoints differed among treatments, with replicate lineages stabilizing toward multiple, partially distinct community configurations rather than a single shared state, indicating low reliability. Diet influenced overall community composition and diversity trajectories, but these effects were smaller in magnitude than the dominant generational restructuring. Together, these results show that the T. castaneum gut microbiome is resilient but not strictly reliable, stabilizing after rapid reorganization toward multiple partially distinct community configurations associated with environmental history rather than a single shared state. These findings underscore the importance of environmental context in shaping host-associated microbiomes and suggest that the capacity for rapid microbiome restructuring may contribute to the ecological success of insect pests in variable environments.