Exposure to natural heat stress is associated with delayed changes of the composition of the fecal microbiota in goats

Heat stress represents a multifaceted environmental challenge for ruminants, yet the longitudinal dynamics of distal gut microbial ecosystems following thermal perturbation remain largely unexplored. Here, we conducted a longitudinal observation of a goat herd exposed to a natural summer heatwave, tracking fecal microbiota trajectories across pre-stress, acute thermal exposure, and post-stress recovery phases. While overall alpha diversity remained stable, community composition exhibited progressive temporal shifts. Crucially, the most pronounced divergence from baseline profiles emerged not during peak thermal exposure, but following the normalization of ambient temperatures, indicating a pronounced temporal lag. This reorganization featured a decreased representation of Bacillota alongside increased abundances of Bacteroidota and Verrucomicrobiota. Functional inference revealed persistent alterations in predicted metabolic capacities, characterized by enhanced fermentative potential and reduced hindgut methanogenesis-related pathways that outlasted the thermal challenge. Together, these patterns demonstrate that natural heatwave exposure coincides with delayed and incomplete fecal microbiota reorganization, corresponding to a hysteresis-like ecological response. These findings emphasize that evaluating post-stress trajectories is essential for understanding the resilience and stability of host-associated microbial ecosystems under climate-related disturbances. This dataset includes the source data obtained from processing the 16S rRNA gene sequencing results, including the PICRUSt2 profiling results.