Immune System and Commensal Microbiota

Dear Colleagues,

The immune system and commensal microbiota engage in a complex and dynamic interplay that is essential for maintaining host health. The human body harbors a vast and diverse microbial ecosystem, particularly in the gut, skin, respiratory tract, and other mucosal surfaces, which constantly interacts with the host immune system. These interactions shape immune responses, contribute to the development of immune tolerance, and play a pivotal role in protecting us against pathogenic infections.

In recent years, advances in microbiome research and immunology have deepened our understanding of how commensal microbes influence both innate and adaptive immunity. Certain microbial species and their metabolites have been shown to modulate immune cell differentiation, regulate inflammatory pathways, and even impact systemic immune responses. However, disruptions in this delicate balance—often referred to as dysbiosis—have been implicated in a wide range of diseases, including inflammatory bowel disease, allergies, autoimmune conditions, metabolic disorders, and chronic inflammatory diseases.

One particularly intriguing area of research is how certain commensal bacteria, which are normally well tolerated by the immune system, may act as immune triggers under specific conditions. For example, skin-associated bacteria such as Cutibacterium acnes have been hypothesized to play a role in chronic granulomatous diseases, highlighting the potential for commensal microbes to influence inflammatory and fibrotic processes. Understanding how the immune system maintains tolerance to these bacteria in healthy individuals—and why this tolerance sometimes fails—remains an important question in immunology and microbiome research.

This Special Issue of Microorganisms aims to provide a platform for cutting-edge research that explores the bidirectional interactions between commensal microbiota and the immune system. We seek studies that elucidate fundamental mechanisms of host–microbiota communication, the role of microbiota in immune homeostasis, and potential therapeutic interventions targeting microbiota–immune system interactions. We particularly encourage the submission of interdisciplinary approaches that integrate microbiology, immunology, systems biology, and clinical research to uncover novel insights into this critical field.

Topics of interest include, but are not limited to, the following:

• The role of commensal microbiota in immune system development and regulation;
• Mechanisms of immune tolerance to commensal microorganisms;
• Microbial metabolites and their immunomodulatory effects on host cells;
• Dysbiosis and its contribution to autoimmune diseases, allergies, chronic inflammation, and granulomatous diseases;
• Gut–brain–immune axis: the role of microbiota in neuroinflammation and neurodegenerative diseases;
• Microbiota–host crosstalk beyond the gut: interactions at the skin, respiratory, and oral mucosal interfaces;
• The impact of host genetics and environmental factors on microbiota–immune interactions;
• Therapeutic strategies targeting microbiota, including probiotics, prebiotics, postbiotics, and fecal microbiota transplantation (FMT).

By bringing together original research and comprehensive reviews, this Special Issue aims to bridge the gap between microbiome science and immunology and pave the way for new therapeutic approaches for immune-mediated diseases. We welcome contributions from researchers in microbiology, immunology, molecular biology, and clinical medicine to advance our collective understanding of this critical area of biomedical research.

Dr. Yoshinobu Eishi
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

• commensal microbiota
• immune system
• mechanisms of immune tolerance
• microbial metabolites
• therapeutic strategies