THE ROLE OF THE MICROBIOME IN HASHIMOTO’S DISEASE - PATHOGENESIS AND THERAPEUTIC IMPLICATIONS: NARRATIVE REVIEW
DOI:
https://doi.org/10.31435/ijitss.2(50).2026.6108Keywords:
Hashimoto’s Disease, Hashimoto’s Thyroiditis, Microbiome, Microbiota, Autoimmune Thyroid DiseaseAbstract
Objective: The aim of this narrative review was to summarize the current state of knowledge regarding the role of the gut microbiome in the pathogenesis of Hashimoto’s disease and to discuss potential microbiome-targeted therapeutic strategies.
Methods: A narrative literature review was conducted using publications indexed in the PubMed, Google Scholar and Scopus databases. Original research articles, systematic reviews, and meta-analyses focusing on Hashimoto’s disease and gut microbiota interactions were included. Most studies were selected from the past 10-15 years, with approximately 80% of the included literature published within the last five years (2021–2025), ensuring up-to-date evidence.
Key findings: Available evidence indicates that patients with Hashimoto’s disease exhibit gut dysbiosis characterized by reduced microbial diversity, decreased abundance of short-chain fatty acid-producing bacteria, and an overrepresentation of potentially pathogenic microorganisms. These alterations are associated with impaired intestinal barrier integrity, increased systemic inflammation, and dysregulation of immune responses, particularly an imbalance between regulatory T cells and Th17 lymphocytes. Furthermore, microbiome disturbances may contribute to thyroid autoimmunity through mechanisms such as molecular mimicry and translocation of bacterial antigens. Emerging studies suggest that dietary modification, probiotic and synbiotic supplementation, and fecal microbiota transplantation may positively influence thyroid function and immune regulation.
Conclusions: Although levothyroxine replacement remains the standard treatment for Hashimoto’s disease, modulation of the gut microbiome represents a promising adjunctive therapeutic approach. Further well-designed clinical trials are required to clarify causal relationships and evaluate the efficacy of microbiome-targeted interventions in autoimmune thyroid disease.
References
Antonini, S., Birtolo, M. F., Lania, A., & Longhi, E. V. (2025). Hashimoto thyroiditis. Managing Psychosexual Consequences in Chronic Diseases, 95–102. https://doi.org/10.1007/978-3-031-31307-3_9
Asnicar, F., Manghi, P., Fackelmann, G., Baldanzi, G., Bakker, E., Ricci, L., Piccinno, G., Piperni, E., Mladenovic, K., Amati, F., Arrè, A., Ganesh, S., Giordano, F., Davies, R., Wolf, J., Bermingham, K. M., Berry, S. E., Spector, T. D., & Segata, N. (2025). Gut micro-organisms associated with health, nutrition and dietary interventions. Nature, 1–9. https://doi.org/10.1038/s41586-025-09854-7
Aversa, T., Messina, M. F., Mazzanti, L., Salerno, M., Mussa, A., Faienza, M. F., Scarano, E., De Luca, F., & Wasniewska, M. (2015). The association with Turner syndrome significantly affects the course of Hashimoto’s thyroiditis in children, irrespective of karyotype. Endocrine, 50(3), 777–782. https://doi.org/10.1007/S12020-014-0513-6
Avramidou, E., Gkantaras, A., Dermitzakis, I., Sapalidis, K., Manthou, M. E., & Theotokis, P. (2023). Histological alterations in Hashimoto’s disease: A case-series ultrastructural study. Medicines, 10(9), 51. https://doi.org/10.3390/MEDICINES10090051
Barb, J. J., & Wallen, G. R. (2025). Emerging research on the relationship between diet, gut microbes, and human health. Nutrients, 17(16), 2627. https://doi.org/10.3390/NU17162627
Caturegli, P., De Remigis, A., Chuang, K., Dembele, M., Iwama, A., & Iwama, S. (2013). Hashimoto’s thyroiditis: Celebrating the centennial through the lens of the Johns Hopkins hospital surgical pathology records. Thyroid, 23(2), 142–150. https://doi.org/10.1089/THY.2012.0554
Cheng, Z., Zhang, L., Yang, L., & Chu, H. (2022). The critical role of gut microbiota in obesity. Frontiers in Endocrinology, 13, 1025706. https://doi.org/10.3389/FENDO.2022.1025706
Danailova, Y., Velikova, T., Nikolaev, G., Mitova, Z., Shinkov, A., Gagov, H., & Konakchieva, R. (2022). Nutritional management of thyroiditis of Hashimoto. International Journal of Molecular Sciences, 23(9), 5144. https://doi.org/10.3390/IJMS23095144
Ehlers, M., Thiel, A., Bernecker, C., Porwol, D., Papewalis, C., Willenberg, H. S., Schinner, S., Hautzel, H., Scherbaum, W. A., & Schott, M. (2012). Evidence of a combined cytotoxic thyroglobulin and thyroperoxidase epitope-specific cellular immunity in Hashimoto’s thyroiditis. The Journal of Clinical Endocrinology and Metabolism, 97(4), 1347–1354. https://doi.org/10.1210/JC.2011-2178
Fang, L., & Ning, J. (2024). Recent advances in gut microbiota and thyroid disease: Pathogenesis and therapeutics in autoimmune, neoplastic, and nodular conditions. Frontiers in Cellular and Infection Microbiology, 14. https://doi.org/10.3389/FCIMB.2024.1465928
Feng, Z., Burgermeister, E., Philips, A., Zuo, T., & Wen, W. (2025). The gut virome in association with the bacteriome in gastrointestinal diseases and beyond: Roles, mechanisms, and clinical applications. Precision Clinical Medicine, 8(2), 10. https://doi.org/10.1093/PCMEDI/PBAF010
Fenneman, A. C., Rampanelli, E., Van Der Spek, A. H., Fliers, E., & Nieuwdorp, M. (2023). Protocol for a double-blinded randomised controlled trial to assess the effect of faecal microbiota transplantations on thyroid reserve in patients with subclinical autoimmune hypothyroidism in the Netherlands: The IMITHOT trial. BMJ Open, 13(9). https://doi.org/10.1136/BMJOPEN-2023-073971
Fujimoto, K., Miyaoka, D., & Uematsu, S. (2022). Characterization of the human gut virome in metabolic and autoimmune diseases. Inflammation and Regeneration, 42(1), 32. https://doi.org/10.1186/S41232-022-00218-6/TABLES/2
Fusco, W., Lorenzo, M. B., Cintoni, M., Porcari, S., Rinninella, E., Kaitsas, F., Lener, E., Mele, M. C., Gasbarrini, A., Collado, M. C., Cammarota, G., & Ianiro, G. (2023). Short-chain fatty-acid-producing bacteria: Key components of the human gut microbiota. Nutrients, 15(9), 2211. https://doi.org/10.3390/NU15092211
Gong, B., Meng, F., Wang, X., Han, Y., Yang, W., Wang, C., & Shan, Z. (2024). Effects of iodine intake on gut microbiota and gut metabolites in Hashimoto thyroiditis-diseased humans and mice. Communications Biology, 7(1), 136. https://doi.org/10.1038/s42003-024-05813-6
Grice, E. A., & Segre, J. A. (2012). The human microbiome: Our second genome. Annual Review of Genomics and Human Genetics, 13, 151–170. https://doi.org/10.1146/ANNUREV-GENOM-090711-163814
Hollywood, J. B., Hutchinson, D., Feehery-Alpuerto, N., Whitfield, M., Davis, K., & Johnson, L. M. (2023). The effects of the paleo diet on autoimmune thyroid disease: A mixed methods review. Journal of the American Nutrition Association, 42(8), 727–736. https://doi.org/10.1080/27697061.2022.2159570
Hou, K., Wu, Z. X., Chen, X. Y., Wang, J. Q., Zhang, D., Xiao, C., Zhu, D., Koya, J. B., Wei, L., Li, J., & Chen, Z. S. (2022). Microbiota in health and diseases. Signal Transduction and Targeted Therapy, 7(1), 135. https://doi.org/10.1038/s41392-022-00974-4
Hu, X., Chen, Y., Shen, Y., Tian, R., Sheng, Y., & Que, H. (2022). Global prevalence and epidemiological trends of Hashimoto’s thyroiditis in adults: A systematic review and meta-analysis. Frontiers in Public Health, 10, 1020709. https://doi.org/10.3389/FPUBH.2022.1020709/TEXT
Huwiler, V. V., Maissen-Abgottspon, S., Stanga, Z., Mühlebach, S., Trepp, R., Bally, L., & Bano, A. (2024). Selenium supplementation in patients with Hashimoto thyroiditis: A systematic review and meta-analysis of randomized clinical trials. Thyroid, 34(3), 295. https://doi.org/10.1089/THY.2023.0556
Jiang, T., Yang, X., Wu, B., Tao, R., Chen, R., Jin, L., Sun, D., & Weng, H. (2025). Gut microbiota in hypothyroidism: Pathogenic mechanisms and opportunities for precision microbiome interventions. Frontiers in Microbiology, 16, 1661211. https://doi.org/10.3389/FMICB.2025.1661211/XML
Karimi, M., Rabiei, R., Kazemi, K., Motlagh, R. B., & Asbaghi, O. (2025). Effects of probiotics and synbiotics oral supplementation on thyroid function in adults: A GRADE-assessed systematic review and meta-analysis. Thyroid Research, 18(1), 39. https://doi.org/10.1186/S13044-025-00257-4/TABLES/3
Kim, C. H. (2023). Complex regulatory effects of gut microbial short-chain fatty acids on immune tolerance and autoimmunity. Cellular and Molecular Immunology, 20(4), 341. https://doi.org/10.1038/S41423-023-00987-1
Kim, S., Ndwandwe, C., Devotta, H., Kareem, L., Yao, L., & O’Mahony, L. (2025). Role of the microbiome in regulation of the immune system. Allergology International, 74(2), 187–196. https://doi.org/10.1016/J.ALIT.2024.12.006
Kovenskiy, A., Katkenov, N., Ramazanova, A., Vinogradova, E., Jarmukhanov, Z., Mukhatayev, Z., & Kushugulova, A. (2025). Bacteroides fragilis and Microbacterium as microbial signatures in Hashimoto’s thyroiditis. International Journal of Molecular Sciences, 26(17), 8724. https://doi.org/10.3390/IJMS26178724/S1
Liu, H. Y., Li, S., Ogamune, K. J., Ahmed, A. A., Kim, I. H., Zhang, Y., & Cai, D. (2025). Fungi in the gut microbiota: Interactions, homeostasis, and host physiology. Microorganisms, 13(1), 70. https://doi.org/10.3390/MICROORGANISMS13010070
Liu, J., Qin, X., Lin, B., Cui, J., Liao, J., Zhang, F., & Lin, Q. (2022). Analysis of gut microbiota diversity in Hashimoto’s thyroiditis patients. BMC Microbiology, 22(1). https://doi.org/10.1186/S12866-022-02739-Z
Mady, E. A., Doghish, A. S., El-Dakroury, W. A., Elkhawaga, S. Y., Ismail, A., El-Mahdy, H. A., Elsakka, E. G. E., & El-Husseiny, H. M. (2023). Impact of the mother’s gut microbiota on infant microbiome and brain development. Neuroscience & Biobehavioral Reviews, 150, 105195. https://doi.org/10.1016/J.NEUBIOREV.2023.105195
Milani, C., Duranti, S., Bottacini, F., Casey, E., Turroni, F., Mahony, J., Belzer, C., Palacio, S. D., Montes, S. A., Mancabelli, L., Lugli, G. A., Rodriguez, J. M., Bode, L., de Vos, W., Gueimonde, M., Margolles, A., van Sinderen, D., & Ventura, M. (2017). The first microbial colonizers of the human gut: Composition, activities, and health implications of the infant gut microbiota. Microbiology and Molecular Biology Reviews, 81(4), e00036-17. https://doi.org/10.1128/MMBR.00036-17
Olvera-Rosales, L. B., Cruz-Guerrero, A. E., Ramírez-Moreno, E., Quintero-Lira, A., Contreras-López, E., Jaimez-Ordaz, J., Castañeda-Ovando, A., Añorve-Morga, J., Calderón-Ramos, Z. G., Arias-Rico, J., & González-Olivares, L. G. (2021). Impact of the gut microbiota balance on the health–disease relationship: The importance of consuming probiotics and prebiotics. Foods, 10(6), 1261. https://doi.org/10.3390/FOODS10061261
Osowiecka, K., & Myszkowska-Ryciak, J. (2023). The influence of nutritional intervention in the treatment of Hashimoto’s thyroiditis—A systematic review. Nutrients, 15(4), 1041. https://doi.org/10.3390/NU15041041
Osowiecka, K., Skrypnik, D., & Myszkowska-Ryciak, J. (2025). Probiotic supplementation enhances the effects of a nutritional intervention on quality of life in women with Hashimoto’s thyroiditis—A double-blind randomised study. Nutrients, 17(21), 3387. https://doi.org/10.3390/NU17213387/S1
Pahirah, N., Narkwichean, A., Taweechotipatr, M., Wannaiampikul, S., Duang-Udom, C., & Laosooksathit, W. (2024). Comparison of gut microbiomes between neonates born by cesarean section and vaginal delivery: Prospective observational study. BioMed Research International, 2024(1), 8302361. https://doi.org/10.1155/BMRI/8302361
Parveen, N., Chittawar, S., & Khandelwal, D. (2025). Gut-thyroid axis and emerging role of probiotics in thyroid disorders. Thyroid Research and Practice, 21(1), 4–12. https://doi.org/10.4103/TRP.TRP_12_24
Pyzik, A., Grywalska, E., Matyjaszek-Matuszek, B., & Roliński, J. (2015). Immune disorders in Hashimoto’s thyroiditis: What do we know so far? Journal of Immunology Research, 2015. https://doi.org/10.1155/2015/979167
Rawat, H. K., Nath, S., Sharma, I., & Kango, N. (2024). Recent developments in the production of prebiotic fructooligosaccharides using fungal fructosyltransferases. Mycology, 15(4), 564–584. https://doi.org/10.1080/21501203.2024.2323713
Rehner, J., Molano, L. A. G., Christodoulou, C., Holländer, S., Förster, M. O., Keller, V., Jäger, J., Volz-Willems, S., Becker, S. L., Glanemann, M., & Jelden, M. (2025). Examining spatial microbiome variations across gastrointestinal tract regions in obesity. Scientific Reports, 15(1), 25423. https://doi.org/10.1038/S41598-025-10931-0
Rinninella, E., Tohumcu, E., Raoul, P., Fiorani, M., Cintoni, M., Mele, M. C., Cammarota, G., Gasbarrini, A., & Ianiro, G. (2023). The role of diet in shaping human gut microbiota. Best Practice & Research Clinical Gastroenterology, 62–63, 101828. https://doi.org/10.1016/J.BPG.2023.101828
Rydzewska, M., Jaromin, M., Pasierowska, I. E., Stozek, K., & Bossowski, A. (2018). Role of the T and B lymphocytes in pathogenesis of autoimmune thyroid diseases. Thyroid Research, 11(1). https://doi.org/10.1186/S13044-018-0046-9
Sawicka-Gutaj, N., Gruszczyński, D., Zawalna, N., Nijakowski, K., Muller, I., Karpiński, T., Salvi, M., & Ruchała, M. (2022). Microbiota alterations in patients with autoimmune thyroid diseases: A systematic review. International Journal of Molecular Sciences, 23(21). https://doi.org/10.3390/IJMS232113450
Sender, R., Fuchs, S., & Milo, R. (2016). Revised estimates for the number of human and bacteria cells in the body. PLOS Biology, 14(8), e1002533. https://doi.org/10.1371/JOURNAL.PBIO.1002533
Sessa, L., Malavolta, E., Sodero, G., Cipolla, C., & Rigante, D. (2025). The conspiring role of gut microbiota as primer of autoimmune thyroid diseases: A scoping focus. Autoimmunity Reviews, 24(5). https://doi.org/10.1016/J.AUTREV.2025.103780
Sommer, F., & Bäckhed, F. (2013). The gut microbiota—Masters of host development and physiology. Nature Reviews Microbiology, 11(4), 227–238. https://doi.org/10.1038/NRMICRO2974
Sun, W., Zhang, Y., Guo, R., Sha, S., Chen, C., Ullah, H., Zhang, Y., Ma, J., You, W., Meng, J., Lv, Q., Cheng, L., Fan, S., Li, R., Mu, X., Li, S., & Yan, Q. (2024). A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases. npj Biofilms and Microbiomes, 10(1), 96. https://doi.org/10.1038/s41522-024-00567-9
Tian, H., Wang, X., Fang, Z., Li, L., Wu, C., Bi, D., Li, N., Chen, Q., & Qin, H. (2024). Fecal microbiota transplantation in clinical practice: Present controversies and future prospects. HLife, 2(6), 269–283. https://doi.org/10.1016/J.HLIFE.2024.01.006
Walker, R. W., Clemente, J. C., Peter, I., & Loos, R. J. F. (2017). The prenatal gut microbiome: Are we colonized with bacteria in utero? Pediatric Obesity, 12(Suppl. 1), 3. https://doi.org/10.1111/IJPO.12217
Wiersinga, W. M. (2016). Clinical relevance of environmental factors in the pathogenesis of autoimmune thyroid disease. Endocrinology and Metabolism, 31(2), 213–222. https://doi.org/10.3803/ENM.2016.31.2.213
Zaletel, K., & Gaberscek, S. (2011). Hashimoto’s thyroiditis: From genes to the disease. Current Genomics, 12(8), 576–588. https://doi.org/10.2174/138920211798120763
Zhang, S., Zhao, X., Wang, X., Jin, H., Chen, L., Ma, Y., Chi, Y., Zhang, J., Zhang, J., & Gao, Y. (2024). Gut microecology may be involved in the pathogenesis of Hashimoto thyroiditis by reducing production of hydrogen sulfide. The Journal of Clinical Endocrinology and Metabolism, 109(3), 792–801. https://doi.org/10.1210/CLINEM/DGAD588
Zhu, X., Zhang, C., Feng, S., He, R., & Zhang, S. (2024). Intestinal microbiota regulates the gut-thyroid axis: The new dawn of improving Hashimoto thyroiditis. Clinical and Experimental Medicine, 24(1). https://doi.org/10.1007/S10238-024-01304-4
Downloads
Published
Issue
Section
License
Copyright (c) 2026 Zuzanna Michalska, Julia Maria Kuczkowska, Judyta Bordakiewicz, Michalina Chodór, Maciej Kokoszka, Donata Pokorska, Julia Świechowska, Zuzanna Zarzycka, Ingrid Samberger, Magdalena Wiciak

This work is licensed under a Creative Commons Attribution 4.0 International License.
All articles are published in open-access and licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0). Hence, authors retain copyright to the content of the articles.
CC BY 4.0 License allows content to be copied, adapted, displayed, distributed, re-published or otherwise re-used for any purpose including for adaptation and commercial use provided the content is attributed.

