The present study aimed at investigating the impact of heat challenges on gut microbiota composition in growing pigs and its relationship with pigs’ performance and thermoregulation responses. From a total of 10 F1 sire families, 558 and 564 backcross Large White × Créole pigs were raised and phenotyped from 11 to 23 wk of age in temperate (TEMP) and in tropical (TROP) climates, respectively. In TEMP, all pigs were subjected to an acute heat challenge (3 wk at 29 °C) from 23 to 26 wk of age. Feces samples were collected at 23 wk of age both in TEMP and TROP climate (TEMP23 and TROP23 samples, respectively) and at 26 wk of age in TEMP climate (TEMP26 samples) for 16S rRNA analyses of fecal microbiota composition. The fecal microbiota composition significantly differed between the 3 environments. Using a generalized linear model on microbiota composition, 182 operational taxonomic units (OTU) and 2 pathways were differentially abundant between TEMP23 and TEMP26, and 1,296 OTU and 20 pathways between TEMP23 and TROP23. Using fecal samples collected at 23 wk of age, pigs raised under the 2 climates were discriminated with 36 OTU using a sparse partial least square discriminant analysis that had a mean classification error-rate of 1.7%. In contrast, pigs in TEMP before the acute heat challenge could be discriminated from the pigs in TEMP after the heat challenge with 32 OTU and 9.3% error rate. The microbiota can be used as biomarker of heat stress exposition. Microbiota composition revealed that pigs were separated into 2 enterotypes. The enterotypes were represented in both climates. Whatever the climate, animals belonging to the Turicibacter–Sarcina–Clostridium sensu stricto dominated enterotype were 3.3 kg heavier (P < 0.05) at 11 wk of age than those belonging to the Lactobacillus-dominated enterotype. This latter enterotype was related to a 0.3 °C lower skin temperature (P < 0.05) at 23 wk of age. Following the acute heat challenge in TEMP, this enterotype had a less-stable rectal temperature (0.34 vs. 0.25 °C variation between weeks 23 and 24, P < 0.05) without affecting growth performance (P > 0.05). Instability of the enterotypes was observed in 34% of the pigs, switching from an enterotype to another between 23 and 26 wk of age after heat stress. Despite a lower microbial diversity, the Turicibacter–Sarcina–Clostridium sensu stricto dominated enterotype was better adapted to heat stress conditions with lower thermoregulation variations.