The effect of intrinsic factors and mechanisms in shaping human gut microbiota

The human body harbors a myriad of microbial communities with the highest concentration and diversity found within the intestine whose disturbance is associated with many diseases. The potential of gut microbiota modulation to confer health benefits has resulted in tremendous efforts of testing extrinsic materials, e.g., probiotics, prebiotics, diet modulation and fecal microbiota transplantation. Meanwhile, the assembly of gut microbiota follows its intrinsic rules, including host selective pressures, bacteria-bacteria interactions, fungi-bacteria interactions, and virus-bacteria interactions. Understanding how these intrinsic factors and mechanisms shape the indigenous gut microbiota can provide crucial knowledge to guide evidence-based microbiota modulation therapies. Hence, this review focuses on our current understanding of the gut microbiota assemblage shaped by host, resident bacteria, fungi as well as virus.