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Microorganisms
Special Issues
The Gut Microbiota and Autoimmune Disease
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The Gut Microbiota and Autoimmune Disease

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Gut Microbiota".

Deadline for manuscript submissions: closed (31 July 2025) | Viewed by 5199

Special Issue Editors

Dr. Pascale Alard

E-Mail Website
Guest Editor
Department of Microbiology and Immunology, University of Louisville, 505 South Hancock St, Rm 611, Louisville, KY 40202, USA
Interests: autoimmune disease; gut microbiota; immunoregulation; immunity
Dr. Michele M. Kosiewicz

E-Mail Website
Guest Editor
Department of Microbiology and Immunology, University of Louisville, Louisville, KY 40202, USA
Interests: immunoregulation; tolerance; autoimmunity and microbiota

Special Issue Information

Dear Colleagues,

The intestinal microbiota is an important component of the body that exists in symbiosis with the host and helps with various functions, e.g., digesting insoluble fibers. More importantly, the intestinal microbiota is necessary for the proper development of the immune response and a dysbiotic intestinal microbiota has been associated with development of autoimmune diseases. Furthermore, intestinal microbiota is not only associated with induction of autoimmunity but also its prevention. High-throughput human multi-omics data, including metagenomics and metabolomics data, have shed some light on potential mechanisms by which autoimmune diseases can be induced or prevented. Through this issue, we will discuss the current knowledge of how the intestinal microbiota and derived microbial compounds may be associated with pathogenesis or prevention of autoimmunity.

The aim of this Special Issue of Microorganisms is to present a collection of articles that provide a snapshot of current research into the effects of the gut microbiota on autoimmunity and inflammatory disease such as colitis. Manuscripts covering all aspects of research relating to this area are welcome.

Dr. Pascale Alard
Dr. Michele M. Kosiewicz
Guest Editors

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.

Keywords

  • intestinal microbiota
  • autoimmune diseases
  • inflammatory disease
  • immune regulation

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Published Papers (3 papers)

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Research

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22 pages, 4320 KB  
Article
Characterization of Sex-Based Differences in Gut Microbiota That Correlate with Suppression of Lupus in Female BWF1 Mice
by James W. Harder, Jing Ma, James Collins, Pascale Alard, Venkatakrishna R. Jala, Haribabu Bodduluri and Michele M. Kosiewicz
Microorganisms 2025, 13(5), 1023; https://doi.org/10.3390/microorganisms13051023 - 29 Apr 2025
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Abstract
Systemic lupus erythematosus (SLE) is more prevalent in female mice and humans and is associated with microbiota dysbiosis. We analyzed the fecal microbiota composition in female and male NZBxNZWF1 (BWF1) mice, a model of SLE, using 16S RNA gene sequencing. Composition of gut [...] Read more.
Systemic lupus erythematosus (SLE) is more prevalent in female mice and humans and is associated with microbiota dysbiosis. We analyzed the fecal microbiota composition in female and male NZBxNZWF1 (BWF1) mice, a model of SLE, using 16S RNA gene sequencing. Composition of gut microbiota differed between adult disease-prone female (pre-disease) and disease-resistant male mice. Transfer of male cecal contents by gavage into female mice suppressed kidney disease (decreased proteinuria) and improved survival. After our mouse colony was moved to a new barrier facility with similar housing, male cecal transplants failed to suppress disease in female recipients. After two years, the protective phenotype reemerged: male cecal transplants once again suppressed disease in female mice. We compared the gut microbiota composition in female and male BWF1 mice for the three different periods, during which the male microbiota either protected or failed to protect female recipients. In female vs. male mice and in female mice receiving male cecal transplants, we found Bacteroides was high, Clostridium was low (high Bacteroides/Clostridium ratio), and Alistipes was present during periods when male cecal transplants suppressed disease. These data suggest that specific bacterial populations may have opposing effects on disease suppression in a model of microbiota transplantation. Full article
(This article belongs to the Special Issue The Gut Microbiota and Autoimmune Disease)
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Review

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15 pages, 1351 KB  
Review
Role of the Microbiome and Its Metabolites in Primary Sjögren’s Syndrome
by Jazz Alan Corona-Angeles, Roxana Lizbeth Martínez-Pulido, Edith Oregon-Romero and Claudia Azucena Palafox-Sánchez
Microorganisms 2025, 13(9), 1979; https://doi.org/10.3390/microorganisms13091979 - 25 Aug 2025
Viewed by 822
Abstract
Primary Sjögren’s syndrome (pSS) is a chronic, autoimmune rheumatic disease characterized by progressive lymphocytic infiltration of the exocrine glands, leading to inflammation and subsequent tissue damage. As a multifactorial disease, its etiology is complex, making it difficult to predict disease progression. Among the [...] Read more.
Primary Sjögren’s syndrome (pSS) is a chronic, autoimmune rheumatic disease characterized by progressive lymphocytic infiltration of the exocrine glands, leading to inflammation and subsequent tissue damage. As a multifactorial disease, its etiology is complex, making it difficult to predict disease progression. Among the environmental factors implicated in pSS, the involvement of microorganisms has gained increasing attention. Since the launch of the Human Microbiome Project, growing evidence has highlighted the role of dysbiosis in the pathogenesis of various autoimmune diseases, including pSS. Shifts in the abundance of specific bacterial phyla can lead to corresponding changes in the levels of key microbial metabolites involved in tissue homeostasis and immune regulation—such as short-chain fatty acids (SCFAs), choline, taurine, serine, lactate, and tryptophan and their metabolites. Understanding the mechanisms by which these metabolites influence immune processes may provide deeper insights into the progression of the disease. Therefore, this review aims to explore the mechanisms through which microbiota-derived metabolites contribute to the pathophysiology of primary Sjögren’s syndrome. Full article
(This article belongs to the Special Issue The Gut Microbiota and Autoimmune Disease)
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26 pages, 1070 KB  
Review
Dysregulated Intestinal Host–Microbe Interactions in Systemic Lupus Erythematosus: Insights from Patients and Mouse Models
by Miki Kume, Jin Din and Daniel F. Zegarra-Ruiz
Microorganisms 2025, 13(3), 556; https://doi.org/10.3390/microorganisms13030556 - 1 Mar 2025
Viewed by 3130
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by chronic inflammation that affects multiple organs, with its prevalence varying by ethnicity. Intestinal dysbiosis has been observed in both SLE patients and murine models. Additionally, intestinal barrier impairment is thought to contribute to [...] Read more.
Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by chronic inflammation that affects multiple organs, with its prevalence varying by ethnicity. Intestinal dysbiosis has been observed in both SLE patients and murine models. Additionally, intestinal barrier impairment is thought to contribute to the ability of pathobionts to evade and breach immune defenses, resulting in antigen cross-reactivity, microbial translocation, subsequent immune activation, and, ultimately, multiple organ failure. Since the detailed mechanisms underlying these processes are difficult to examine using human samples, murine models are crucial. Various SLE murine models, including genetically modified spontaneous and inducible murine models, offer insights into pathobionts and how they dysregulate systemic immune systems. Furthermore, since microbial metabolites modulate systemic immune responses, bacteria and their metabolites can be targeted for treatment. Based on human and mouse research insights, this review examines how lupus pathobionts trigger intestinal and systemic immune dysregulation. Therapeutic approaches, such as fecal microbiota transplantation and dietary adjustments, show potential as cost-effective and safe methods for preventing and treating SLE. Understanding the complex interactions between the microbiota, host factors, and immune dysregulation is essential for developing novel, personalized therapies to tackle this multifaceted disease. Full article
(This article belongs to the Special Issue The Gut Microbiota and Autoimmune Disease)
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