Efficient animal production with a reduced environmental impact requires healthy animals, higher performance, increased feed conversion, and the use of available nutrients. The improvement of those traits could be accomplished by understanding how the gut microbiome plays a vital role in nutrient digestion and feed efficiency. Also, applying a reliable sorting tool allows identifying pigs according to their feed digestibility capacity (near infrared spectroscopy = NIRS) and muscle deposition level (Computer tomography scan = CT scan) with minimal sample preparation, avoid serial carcass dissection and reduced time consumption, which can provide a clear picture of how their possible role is in pork growth performance and carcass/meat quality. The findings may allow us to modulate the gut microbiome to raise more efficient animals or modulate carcass/meat quality traits, as well as might be useful in identifying high-efficiency animals and facilitating the proper selection of pigs for breeding programs.