Review Article Volume 21 Issue 9 - 2025

Autoimmune Diseases and their Correlation with the Intestinal Microbiome and Fecal Microbiota Transplantation

Álvaro Zamudio Tiburcio1*, Héctor Bermúdez Ruiz2, Silverio Alonso López3 and Pedro Antonio Reyes López4

1Department of Gastroenterology, Intestinal Microbiota Transplantation, Medical Specialties, Naples Unit, Mexico

2Endoscopy Service, Oncology Hospital, National Medical Center, XXI Century, Mexican Social Security Institute, Mexico

3Department of Urologist, Chairman Medical Specialties Naples in Mexico City, Mexico

4Immunologist, Rheumatologist, National Institute of Cardiology “I. Chávez” Mexico City, Mexico

*Corresponding Author: Álvaro Zamudio Tiburcio, Department of Gastroenterology, Intestinal Microbiota Transplantation, Medical Specialties, Naples Unit, Mexico.
Received: August 04, 2025; Published: August 25, 2025



Autoimmune diseases are complex and diverse processes that arise from a lack of recognition by the immune system. They affect cytokines, immune cells, and protein kinases, generating monoclonal antibodies and small molecule inhibitors targeting these molecules. The purpose of this review is to analyze the impact of the Gut Microbiome (GI) on different autoimmune diseases and to leverage it in the management of these complex processes. A significant number of these processes are analyzed, but not all, since they total approximately more than 80.

 Keywords: Autoimmune Diseases (AD); Gut Microbiome (GM); Short-Chain Fatty Acids (SCFA); Intestinal Dysbiosis (ID); Fecal Microbiota Transplant (FMT)

  1. Baba M., et al. “Similarity of autoimmune diseases based on the profile of immune complex antigens”. Rheumatology International 2 (2019): 323-325.
  2. Cleveland Clinic. Diseases & Conditions.
  3. Everything to know about autoimmune diseases.
  4. Martins K and Sheikh Z. Medical Review (2023).
  5. Pasha SF., et al. Mayo clinic biobank immune disorders. Biobank study in inflammatory bowel disease.
  6. De Widt L. “New study calculates autoimmune disease prevalence in U.S.”. MAYO CLINIC (2025).
  7. Kumar K. 10 Diseases of the Immune System | Autoimmune Disorders. Hematologist (2024).
  8. Rare diseases: a global health priority for equity and inclusion. EB156/CONF./2 (2025).
  9. Thursby E and Juge N. “Introduction to the human gut microbiota”. Biochemical Journal 11 (2017): 1823-1836.
  10. Rodriguez Alpizar., et al. “Prevotella copri in individuals at risk for rheumatoid arthritis”. Annals of Rheumatic Diseases5 (2019): 590-593.
  11. Shan Y., et al. “The gut microbiome and inflammatory bowel diseases”. Annual Review of Medicine 73 (2022): 455-468.
  12. Castañeda GC. “Intestinal microbiota and celiac disease. Part 1: Update. ECIMED”. Revista Cubana de Pediatría 97 (2025): e7461.
  13. Chen L., et al. “Skin and gut microbiome in psoriasis: gaining insight into the pathophysiology of it and finding novel therapeutic strategies”. Frontiers in Microbiology 11 (2020): 589726.
  14. Trevor O Kirby and Javier Ochoa Repáraz. “The gut microbiome in multiple sclerosis: a potential therapeutic avenue”. Medical Sciences (Basel)3 (2018): 69.
  15. Ochoa-Repáraz J., et al. “The gut microbiome and multiple sclerosis”. Cold Spring Harbor Perspectives in Medicine 6 (2018): a029017.
  16. Katz-Agranov N and Zandman-Goddard G. “The microbiome and systemic lupus erythematosus”. Immunologic Research 2 (2017): 432-437.
  17. Furio CM., et al. “Auto-immunity and the gut microbiome in type 1 diabetes: Lessons from rodent and human studies”. Best Practice and Research Clinical Endocrinology and Metabolism3 (2021): 101544.
  18. Zhang YY., et al. “Association between gut microbiota and adrenal disease: a two-sample Mendelian randomized study”. Frontiers in Cellular and Infection Microbiology 14 (2024): 1421128.
  19. Deng Y., et al. “Correlation between gut microbiota and the development of Graves’ disease: A prospective study”. i Science7 (2023): 107188.
  20. Yuan X., et al. “Microbiome alterations in primary Sjögren's syndrome: Regional dysbiosis and microbiome-targeted therapeutic strategies”. Clinical Immunology 273 (2025): 110444.
  21. García RD. “Enfermedades tiroideas autoinmunes y, microbiota intestinal”. Universidad Michoacana de San Nicolás de Hidalgo.
  22. Morrris G., et al. “Fecal microbiota profile in a group of myasthenia gravis patients”. Scientific Reports 8 (2018): 14384.
  23. Espinosa G. “Síndrome de Behçet”. Medicina Clínica1 (2025): 106983.
  24. De Paz R and Hernández Navarro F. “Recomendaciones terapéuticas. Manejo, prevención y control de la anemia perniciosa”. Nutrición Hospitalaria 6 (2005).
  25. Carding S., et al. “Dysbiosis of the gut microbiota in disease”. Microbial Ecology in Health and Disease 26 (2015): 26191.
  26. Huang Y., et al. “Severe intestinal dysbiosis in rat models of short bowel syndrome with ileocecal resection”. Digestive Diseases and Sciences2 (2020): 431-441.
  27. Wilkins LJ., et al. “Defining dysbiosis for a cluster of chronic diseases”. Scientific Reports 9 (2019): 12918.
  28. Jian Tan., et al. Chapter Three – The Role of Short-Chain Fatty Acids in Health and Disease, Editor(s).
  29. Zhou T., et al. “Bile acids in autoimmune liver disease: unveiling the nexus of inflammation, inflammatory cells, and treatment strategies”. Cells 23 (2023): 2725.
  30. An J., et al. “The role of intestinal mucosal barrier in autoimmune disease: a potential target”. Frontiers in Immunology 13 (2022): 871713.
  31. Ananieva MM., et al. “Indicators of quantitative and qualitative composition of the gut commensal microbiota as biomarkers of homeostasis”. Актуальні проблеми сучасної медицини Вісник Української медичної стоматологічної академії 2 (2024): 277-283.
  32. Bodkhe R., et al. “The role of microbiome in rheumatoid arthritis treatment”. Therapeutic Advances in Musculoskeletal Disease 11 (2019): 1759720X19844632.
  33. Li Y., et al. “Editorial: Interaction between the gut flora and immunity in intestinal diseases”. Frontiers in Immunology 15 (2024): 1458526.
  34. Yang R., et al. “Fecal microbiota transplantation: Emerging applications in autoimmune diseases”. Journal of Autoimmunity 141 (2023): 103038.
  35. Xiaomin Liu., et al. “Fecal microbiota transplantation for the management of autoimmune diseases: Potential mechanisms and challenges”. Journal of Autoimmunity 141 (2023): 103109.

Álvaro Zamudio Tiburcio., et al. “Autoimmune Diseases and their Correlation with the Intestinal Microbiome and Fecal Microbiota Transplantation”. EC Microbiology  21.9 (2025): 01-11.