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Updated: Dec 23, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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Role of Microbiome and Antibiotics in Autoimmune Diseases

Roman Vangoitsenhoven1,2, Gail A M Cresci3,4

  • 1Bariatric and Metabolic Institute, Cleveland Clinic, Cleveland, Ohio, USA.

Nutrition in Clinical Practice : Official Publication of the American Society for Parenteral and Enteral Nutrition
|April 23, 2020
PubMed

Insights

Antibiotic use and gut microbiome changes may influence autoimmune diseases. Research explores how microbial imbalances and treatments like probiotics could impact conditions such as inflammatory bowel disease and type 1 diabetes.

Area of Science:

  • Immunology
  • Microbiology
  • Gastroenterology

Background:

  • The global increase in autoimmune diseases coincides with widespread antibiotic use.
  • The gut microbiome is crucial for immune system development and function.
  • Microbial disturbances (dysbiosis) are linked to autoimmune disease onset and progression.

Purpose of the Study:

  • To overview the mechanistic interactions between the human microbiome, immune system, and antibiotics.
  • To discuss the role of gut dysbiosis and antibiotics in autoimmune diseases.
  • To explore microbiome manipulation strategies for autoimmune conditions.

Main Methods:

  • Review of existing literature on microbiome-immune system-antibiotic interactions.
  • Case examples of inflammatory bowel disease and type 1 diabetes.
  • Discussion of prebiotics, probiotics, and fecal microbiota transplantation.

Main Results:

  • Antibiotic-induced gut dysbiosis may contribute to autoimmunity.
  • Antibiotics may also possess therapeutic potential in certain autoimmune diseases.
  • Emerging therapies like fecal microbiota transplantation show promise in clinical trials.

Conclusions:

  • The relationship between antibiotics, the microbiome, and autoimmunity is complex and bidirectional.
  • Targeting the gut microbiome offers potential therapeutic avenues for autoimmune diseases.
  • Further research into microbiome modulation is warranted for autoimmune disease management.
Keywords:
antibacterial agentsantibioticsautoimmune diseasesdysbiosisgastrointestinal microbiomemicrobiotaprebioticsprobiotics

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