Role of Microbiome and Antibiotics in Autoimmune Diseases

Nutr Clin Pract. 2020 Jun;35(3):406-416. doi: 10.1002/ncp.10489. Epub 2020 Apr 22.


The global rise in the incidence of autoimmune diseases has paralleled the widespread use of antibiotics. Recently, the gut microbiome has been shown to be key in the development and maturation of a normal immune system, and a range of microbial disturbances have been associated with the development and activity of several autoimmune diseases. Here, we aim to provide an overview of the mechanistic crosstalk between the human microbiome, the immune system, and antibiotics. The disease-associated microbial gut dysbiosis, the potential role of antibiotics in the development and treatment of autoimmune diseases, and the manipulation of the gut microbiome with prebiotics and probiotics is discussed using 2 key autoimmune diseases as an example: inflammatory bowel disease and type 1 diabetes. Although some data suggest that widespread use of antibiotics may facilitate autoimmunity through gut dysbiosis, there are also data to suggest antibiotics may hold the potential to improve disease activity. Currently, the effect of fecal microbiota transplantation on several autoimmune diseases is being studied in clinical trials, and several preclinical studies are revealing promising results with probiotic and prebiotic therapies.

Keywords: antibacterial agents; antibiotics; autoimmune diseases; dysbiosis; gastrointestinal microbiome; microbiota; prebiotics; probiotics.

Publication types

  • Review

MeSH terms

  • Animals
  • Anti-Bacterial Agents* / adverse effects
  • Anti-Bacterial Agents* / therapeutic use
  • Autoimmune Diseases* / drug therapy
  • Autoimmune Diseases* / microbiology
  • Autoimmune Diseases* / therapy
  • Diabetes Mellitus, Type 1 / immunology
  • Diabetes Mellitus, Type 1 / microbiology
  • Dysbiosis / chemically induced
  • Dysbiosis / microbiology
  • Fecal Microbiota Transplantation
  • Gastrointestinal Microbiome / drug effects
  • Gastrointestinal Microbiome / immunology
  • Gastrointestinal Microbiome / physiology*
  • Humans
  • Immune System / drug effects
  • Immune System / microbiology
  • Immune System / physiology
  • Inflammatory Bowel Diseases / immunology
  • Inflammatory Bowel Diseases / microbiology
  • Lymphoid Tissue / immunology
  • Lymphoid Tissue / microbiology
  • Prebiotics / administration & dosage
  • Probiotics / therapeutic use


  • Anti-Bacterial Agents
  • Prebiotics