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      Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s Disease

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          Abstract

          Secretory immunoglobulin A (sIgA) plays an important role in gut barrier protection by shaping the resident microbiota community, restricting the growth of bacterial pathogens, and enhancing host protective immunity via immunological exclusion. Here, we found that a portion of microbiota-driven sIgA response is induced by and directed towards intestinal fungi. Analysis of the human gut mycobiota bound by sIgA revealed a preference for hyphae; a fungal morphotype associated with virulence. C. albicans was a potent inducer of IgA class switch recombination (CSR) among plasma cells, through an interaction dependent on intestinal phagocytes and hyphal programming. Characterization of sIgA affinity and polyreactivity showed that hyphae-associated virulence factors were bound by these antibodies and that sIgA influenced C. albicans morphotypes in the murine gut. Furthermore, an increase of granular hyphal morphologies in Crohn’s Disease (CD) patients compared to healthy controls, correlated with a decrease of antifungal sIgA antibody titers with affinity to hyphae-associated virulence factors. Thus, in addition to their importance in gut bacterial regulation, sIgA targets the uniquely fungal phenomenon of hyphal formation. Our findings indicate that antifungal sIgA produced in the gut can play a role in regulating intestinal fungal commensalism by coating fungal morphotypes linked to virulence, thereby providing a protective mechanism that might be dysregulated in CD patients.

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          Most cited references91

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          Regional specialization within the intestinal immune system.

          The intestine represents the largest compartment of the immune system. It is continually exposed to antigens and immunomodulatory agents from the diet and the commensal microbiota, and it is the port of entry for many clinically important pathogens. Intestinal immune processes are also increasingly implicated in controlling disease development elsewhere in the body. In this Review, we detail the anatomical and physiological distinctions that are observed in the small and large intestines, and we suggest how these may account for the diversity in the immune apparatus that is seen throughout the intestine. We describe how the distribution of innate, adaptive and innate-like immune cells varies in different segments of the intestine and discuss the environmental factors that may influence this. Finally, we consider the implications of regional immune specialization for inflammatory disease in the intestine.
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            Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease.

            Specific members of the intestinal microbiota dramatically affect inflammatory bowel disease (IBD) in mice. In humans, however, identifying bacteria that preferentially affect disease susceptibility and severity remains a major challenge. Here, we used flow-cytometry-based bacterial cell sorting and 16S sequencing to characterize taxa-specific coating of the intestinal microbiota with immunoglobulin A (IgA-SEQ) and show that high IgA coating uniquely identifies colitogenic intestinal bacteria in a mouse model of microbiota-driven colitis. We then used IgA-SEQ and extensive anaerobic culturing of fecal bacteria from IBD patients to create personalized disease-associated gut microbiota culture collections with predefined levels of IgA coating. Using these collections, we found that intestinal bacteria selected on the basis of high coating with IgA conferred dramatic susceptibility to colitis in germ-free mice. Thus, our studies suggest that IgA coating identifies inflammatory commensals that preferentially drive intestinal disease. Targeted elimination of such bacteria may reduce, reverse, or even prevent disease development. Copyright © 2014 Elsevier Inc. All rights reserved.
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              Fungal microbiota dysbiosis in IBD

              Objective The bacterial intestinal microbiota plays major roles in human physiology and IBDs. Although some data suggest a role of the fungal microbiota in IBD pathogenesis, the available data are scarce. The aim of our study was to characterise the faecal fungal microbiota in patients with IBD. Design Bacterial and fungal composition of the faecal microbiota of 235 patients with IBD and 38 healthy subjects (HS) was determined using 16S and ITS2 sequencing, respectively. The obtained sequences were analysed using the Qiime pipeline to assess composition and diversity. Bacterial and fungal taxa associated with clinical parameters were identified using multivariate association with linear models. Correlation between bacterial and fungal microbiota was investigated using Spearman's test and distance correlation. Results We observed that fungal microbiota is skewed in IBD, with an increased Basidiomycota/Ascomycota ratio, a decreased proportion of Saccharomyces cerevisiae and an increased proportion of Candida albicans compared with HS. We also identified disease-specific alterations in diversity, indicating that a Crohn's disease-specific gut environment may favour fungi at the expense of bacteria. The concomitant analysis of bacterial and fungal microbiota showed a dense and homogenous correlation network in HS but a dramatically unbalanced network in IBD, suggesting the existence of disease-specific inter-kingdom alterations. Conclusions Besides bacterial dysbiosis, our study identifies a distinct fungal microbiota dysbiosis in IBD characterised by alterations in biodiversity and composition. Moreover, we unravel here disease-specific inter-kingdom network alterations in IBD, suggesting that, beyond bacteria, fungi might also play a role in IBD pathogenesis.
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                Author and article information

                Journal
                101674869
                44774
                Nat Microbiol
                Nat Microbiol
                Nature microbiology
                2058-5276
                22 September 2021
                22 November 2021
                December 2021
                22 May 2022
                : 6
                : 12
                : 1493-1504
                Affiliations
                [1 ]Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
                [2 ]The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA.
                [3 ]Department of Microbiology and Parasitology-IRYCIS, Faculty of Pharmacy, Universidad Complutense de Madrid, 28040 Madrid, Spain
                [4 ]Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago IL.
                [5 ]Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA.
                [6 ]Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
                Author notes

                Author contribution

                I.D. and I.D.I. conceived and designed experiments, I.D., M.M., D.G.S., X. V. L., I.L., T.K, W.D.F., W.Y.L., E.R. and M.B.C. performed experiments. J.P., R.S.L. and P.C.W., generated key research materials and contributed to experiment interpretation. I.D. and I.D.I. generated figures and legends from analyzed data. I.D.I acquired funding for the project. I.D. and I.D.I. wrote the manuscript.

                [* ]Correspondence to: iliev@ 123456med.cornell.edu
                Article
                NIHMS1741825
                10.1038/s41564-021-00983-z
                8622360
                34811531
                087dcea7-5322-4412-8fae-afbf13ef0a63

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                Categories
                Article

                mycobiome,iga antibodies,crohn’s disease,fungal commensalism,hyphae,candida albicans

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