Research into the gut microbiota has rapidly advanced our understanding of immune system regulation in vertebrates, demonstrating the vital role that diverse microbial communities play in both maintaining health and contributing to disease. Over the past decade, accumulating evidence has revealed that disruptions in the gut microbiome—known as dysbiosis—are closely linked to the onset and exacerbation of numerous autoimmune disorders, such as rheumatoid arthritis, systemic lupus erythematosus, type 1 diabetes, and inflammatory bowel disease. Despite a growing recognition of the complexity and importance of these microbe-immune interactions, key questions remain unanswered, including how specific microbial signals affect immune cell differentiation, regulate mucosal and systemic responses, and influence disease outcomes. Recent studies have highlighted a range of mechanisms, from microbial metabolite production (e.g., short-chain fatty acids) to antigen presentation and mucosal barrier integrity, yet the field lacks a unified understanding of the precise molecular and cellular pathways involved. Notably, emerging comparative research across vertebrate species is uncovering evolutionary patterns and species-specific dynamics but gaps persist regarding the translation of these findings into clinical or veterinary applications.

This Research Topic aims to deepen our understanding of the gut microbiota’s multifaceted influence on vertebrate autoimmunity by elucidating the cellular and molecular mechanisms that mediate host-microbe crosstalk. The main objectives are to clarify the principles governing microbial modulation of immune development, to dissect how dysbiosis contributes to disease susceptibility and progression, and to identify strategies for leveraging microbiota-driven processes in the prevention, diagnosis, and treatment of autoimmune diseases. The topic seeks to bridge gaps between ecological, functional, and evolutionary perspectives, fostering integrative research that advances both basic and translational science in this domain.

While the primary focus of this Research Topic is the gut-immune axis and its relevance to autoimmunity in vertebrates, it also encompasses fundamental and applied research across species and methodologies that investigate other mucosal microbial communities (such as the oral microbiota and salivary microbiota), given their emerging and significant roles in modulating immune responses and contributing to autoimmune diseases. Manuscripts can address mechanistic, ecological, translational, or comparative aspects and may use experimental, computational, or integrative approaches (including in vivo/in vitro models). We welcome articles on—but not limited to—the following themes:

o Mechanisms of microbial regulation of immune responses
o Impact of gut microbiota dysbiosis on autoimmune disease onset and progression
o Comparative analyses of gut-immune interactions across vertebrate taxa
o Functional profiling using metagenomics, metatranscriptomics, and metabolomics
o Development and evaluation of microbiota-targeted interventions and therapies
o Integration of microbial composition, functional outputs, and immune phenotyping
o Identification and validation of microbial biomarkers for autoimmunity

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Microbial Influences on Autoimmunity: Unraveling the Gut-Immune Axis in Vertebrates