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Background  High-altitude ecosystems are extreme environments that generate specific physiological, morphological, and behavioral adaptations in ectotherms. The shifts in gut microbiota of the ectothermic hosts as an adaptation to environmental changes are still largely unknown. We investigated the food ingested and the bacterial, fungal, and protistan communities in feces of the lizard  Sceloporus grammicus  inhabiting an altitudinal range using metabarcoding approaches.    Results  The bacterial phyla  Bacteroidetes  and  Firmicutes , and the genera  Bacteroides  and  Parabacteroides  dominated the core fecal bacteriome, while  Zygomycota  and  Ascomycota , and the species  Basidiobolus ranarum  and  Basidiobolus magnus  dominated the core fecal mycobiome. The diet of  S .  grammicus  included 29 invertebrate families belonging to  Arachnida ,  Chilopoda , and  Insecta . The diversity and abundance of its diet decreased sharply at high altitudes, while the abundance of plant material and  Agaricomycetes  was significantly higher at the highest site. The composition of the fecal microbiota of  S .  grammicus  was different at the three altitudes, but not between females and males. Dietary restriction in  S .  grammicus  at 4150 m might explain the high fecal abundance of  Akkermansia  and  Oscillopira , bacteria characteristic of long fasting periods, while low temperature favored  B .  magnus . A high proportion of bacterial functions were digestive in  S .  grammicus  at 2600 and 3100, while metabolism of aminoacids, vitamins, and key intermediates of metabolic pathways were higher at 4150 m. Different assemblages of fungal species in the lizard reflect differences in the environments at different elevations. Pathogens were more prevalent at high elevations than at the low ones.    Conclusions  Limiting food resources at high elevations might oblige  S .  grammicus  to exploit other food resources and its intestinal microbiota have degradative and detoxifying capacities.  Sceloporus grammicus  might have acquired  B .  ranarum  from the insects infected by the fungus, but its commensal relationship might be established by the quitinolytic capacities of  B .  ranarum.  The mycobiome participate mainly in digestive and degradative functions while the bacteriome in digestive and metabolic functions.

Dietary effects on gut microbiota of the mesquite lizard Sceloporus grammicus (Wiegmann, 1828) across different altitudes