Current Understanding of the Gut Microbiota Shaping Mechanisms

J Biomed Sci. 2019 Aug 21;26(1):59. doi: 10.1186/s12929-019-0554-5.


Increasing evidences have shown strong associations between gut microbiota and many human diseases, and understanding the dynamic crosstalks of host-microbe interaction in the gut has become necessary for the detection, prevention, or therapy of diseases. Many reports have showed that diet, nutrient, pharmacologic factors and many other stimuli play dominant roles in the modulation of gut microbial compositions. However, it is inappropriate to neglect the impact of host factors on shaping the gut microbiota. In this review, we highlighted the current findings of the host factors that could modulate the gut microbiota. Particularly the epithelium-associated factors, including the innate immune sensors, anti-microbial peptides, mucus barrier, secretory IgAs, epithelial microvilli, epithelial tight junctions, epithelium metabolism, oxygen barrier, and even the microRNAs are discussed in the context of the microbiota shaping. With these shaping factors, the gut epithelial cells could select the residing microbes and affect the microbial composition. This knowledge not only could provide the opportunities to better control many diseases, but may also be used for predicting the success of fecal microbiota transplantation clinically.

Keywords: Barrier; Gut microbiota; Intestinal epithelium; Microbiota shaping.

Publication types

  • Review

MeSH terms

  • Antimicrobial Cationic Peptides / physiology*
  • Epithelium / physiology*
  • Gastrointestinal Microbiome / physiology*
  • Humans
  • Immunity, Innate*
  • Immunoglobulin A, Secretory / physiology*
  • MicroRNAs / physiology
  • Microvilli / physiology
  • Mucus / physiology*
  • Tight Junctions / physiology


  • Antimicrobial Cationic Peptides
  • Immunoglobulin A, Secretory
  • MicroRNAs