Homeotherm animals adapt to external temperature fluctuations to maintain a constant body temperature. We hypothesised that the gut microbiota is involved in this adaptation, and identified change in the gut flora population in conditions of cold (6°C) and warm (34°C) temperatures. We showed that cold adapted gut microbiota could promote white adipose tissue browning associated with a better cold tolerance, improved insulin sensitivity and fat loss. The extinction of the bacteria A. muciniphila mediated by cold was sufficient to increase intestinal, villi and microvilli lengths that maximise the absorptive capacity of the intestine, thus helping compensating for the increased energy expenditure. In contrast, warm adapted gut microbiota induced whitening of adipose tissue and reduced body temperature. Additionally, warm exposure or warm adapted microbiota transplantation could improve the structural parameters and strength of the bone. Accordingly, both warm exposure and warm microbiota transplantation were effective in the prevention of osteoporosis.