Autoimmune thyroid diseases (AITDs) are among the most prevalent organ-specific autoimmune disorders, with thyroid hormones playing a pivotal role in the gastrointestinal system’s structure and function. Emerging evidence suggests a link between AITDs and the gut microbiome, which is a diverse community of organisms that are essential for digestion, absorption, intestinal homeostasis, and immune defense. Recent studies using 16S rRNA and metagenomic sequencing of fecal samples from AITD patients have revealed a significant correlation between a gut microbiota imbalance and the severity of AITDs. Progress in animal models of autoimmune diseases has shown that intervention in the gut microbiota can significantly alter the disease severity. The gut microbiota influences T cell subgroup differentiation and modulates the pathological immune response to AITDs through mechanisms involving short-chain fatty acids (SCFAs), lipopolysaccharides (LPSs), and mucosal immunity. Conversely, thyroid hormones also influence gut function and microbiota composition. Thus, there is a bidirectional relationship between the thyroid and the gut ecosystem. This review explores the pathogenic mechanisms of the gut microbiota and its metabolites in AITDs, characterizes the gut microbiota in Graves’ disease (GD) and Hashimoto’s thyroiditis (HT), and examines the interactions between the gut microbiota, thyroid hormones, T cell differentiation, and trace elements. The review aims to enhance understanding of the gut microbiota–thyroid axis and proposes novel approaches to mitigate AITD severity through gut microbiota modulation.

Diabetes mellitus (DM) is a complex metabolic disease characterized by significantly elevated blood glucose levels as a result of dysfunctional or impaired pancreatic β-cells, leading to insulin deficiency. This condition can result in severe complications, including cardiovascular diseases, kidney failure, vision impairment, and nerve damage. Currently available anti-diabetic drugs do not fully prevent the progression of these complications. Moreover, they often have significant side effects. The gut microbiota plays a crucial role in influencing diet, energy metabolism, and blood glucose levels. Research shows a strong link between microbiota dysbiosis and DM, as well as the severity of its complications. Commensal bacteria can help manage blood glucose levels, reduce inflammation, regulate metabolism, and enhance the gut barrier. Conversely, opportunistic pathogens can worsen insulin resistance, promote metabolic disorders, disrupt gut integrity, and affect appetite and weight. This article describes the characteristics of gut microbiota in various types of DM and explores the role of the “gut microbiota–metabolite–signaling pathway” axis in DM and its complications. In addition, it highlights the therapeutic potential of traditional Chinese medicine and dietary interventions through modulation of the gut microbiota and metabolites. The aim is to provide comprehensive evidence supporting the integration of TCM dietary therapy, targeted dietary strategies, and specific probiotics as alternative and complementary therapies for DM and its complications.