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  1. Article ; Online: Translating the human microbiome: a path to improving health.

    Xavier, Ramnik J

    Genome medicine

    2021  Volume 13, Issue 1, Page(s) 78

    MeSH term(s) Diet ; Disease Susceptibility ; Energy Metabolism ; Homeostasis ; Host Microbial Interactions ; Humans ; Metagenome ; Metagenomics/methods ; Microbiota/physiology ; T-Lymphocytes/immunology ; T-Lymphocytes/metabolism
    Language English
    Publishing date 2021-05-05
    Publishing country England
    Document type Editorial ; Introductory Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2484394-5
    ISSN 1756-994X ; 1756-994X
    ISSN (online) 1756-994X
    ISSN 1756-994X
    DOI 10.1186/s13073-021-00896-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Untangling the CD4 T cell response to the microbiota.

    Mayassi, Toufic / Xavier, Ramnik J

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 16, Page(s) e2303351120

    MeSH term(s) CD4-Positive T-Lymphocytes ; Microbiota ; Gastrointestinal Microbiome
    Language English
    Publishing date 2023-04-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2303351120
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Conditioning of the immune system by the microbiome.

    Graham, Daniel B / Xavier, Ramnik J

    Trends in immunology

    2023  Volume 44, Issue 7, Page(s) 499–511

    Abstract: The human intestinal microbiome has coevolved with its host to establish a stable homeostatic relationship with hallmark features of mutualistic symbioses, yet the mechanistic underpinnings of host-microbiome interactions are incompletely understood. ... ...

    Abstract The human intestinal microbiome has coevolved with its host to establish a stable homeostatic relationship with hallmark features of mutualistic symbioses, yet the mechanistic underpinnings of host-microbiome interactions are incompletely understood. Thus, it is an opportune time to conceive a common framework for microbiome-mediated regulation of immune function. We propose the term conditioned immunity to describe the multifaceted mechanisms by which the microbiome modulates immunity. In this regard, microbial colonization is a conditioning exposure that has durable effects on immune function through the action of secondary metabolites, foreign molecular patterns, and antigens. Here, we discuss how spatial niches impact host exposure to microbial products at the level of dose and timing, which elicit diverse conditioned responses.
    MeSH term(s) Humans ; Microbiota ; Intestines ; Gastrointestinal Microbiome ; Immune System ; Symbiosis
    Language English
    Publishing date 2023-05-24
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2036831-8
    ISSN 1471-4981 ; 1471-4906
    ISSN (online) 1471-4981
    ISSN 1471-4906
    DOI 10.1016/j.it.2023.05.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Cytotoxic Th1 cells mushroom after fungal exposures in Crohn's disease.

    Stražar, Martin / Xavier, Ramnik J

    Immunity

    2023  Volume 56, Issue 12, Page(s) 2679–2681

    Abstract: Fungi are consistently enriched in inflamed intestines, with elusive effects on host immunity. In a recent issue of Nature Medicine, Martini et al. identify a subset of Th1 cells able to lyse the epithelium, enriched in Crohn's disease patient samples ... ...

    Abstract Fungi are consistently enriched in inflamed intestines, with elusive effects on host immunity. In a recent issue of Nature Medicine, Martini et al. identify a subset of Th1 cells able to lyse the epithelium, enriched in Crohn's disease patient samples after fungal exposure.
    MeSH term(s) Humans ; Crohn Disease ; Th1 Cells ; Agaricales ; Intestines/microbiology
    Language English
    Publishing date 2023-12-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1217235-2
    ISSN 1097-4180 ; 1074-7613
    ISSN (online) 1097-4180
    ISSN 1074-7613
    DOI 10.1016/j.immuni.2023.11.012
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Growth and the Microbiome - Integrating Global Health with Basic Science.

    Xavier, Ramnik J

    The New England journal of medicine

    2020  Volume 383, Issue 4, Page(s) 391–393

    MeSH term(s) Child ; Duodenum ; Global Health ; Humans ; Intestinal Diseases ; Microbiota
    Language English
    Publishing date 2020-07-24
    Publishing country United States
    Document type Editorial ; Comment
    ZDB-ID 207154-x
    ISSN 1533-4406 ; 0028-4793
    ISSN (online) 1533-4406
    ISSN 0028-4793
    DOI 10.1056/NEJMe2017496
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Gut microbiome lipid metabolism and its impact on host physiology.

    Brown, Eric M / Clardy, Jon / Xavier, Ramnik J

    Cell host & microbe

    2023  Volume 31, Issue 2, Page(s) 173–186

    Abstract: Metabolites produced by commensal gut microbes impact host health through their recognition by the immune system and their influence on numerous metabolic pathways. Notably, the gut microbiota can both transform and synthesize lipids as well as break ... ...

    Abstract Metabolites produced by commensal gut microbes impact host health through their recognition by the immune system and their influence on numerous metabolic pathways. Notably, the gut microbiota can both transform and synthesize lipids as well as break down dietary lipids to generate secondary metabolites with host modulatory properties. Although lipids have largely been consigned to structural roles, particularly in cell membranes, recent research has led to an increased appreciation of their signaling activities, with potential impacts on host health and physiology. This review focuses on studies that highlight the functions of bioactive lipids in mammalian physiology, with a special emphasis on immunity and metabolism.
    MeSH term(s) Animals ; Gastrointestinal Microbiome/physiology ; Lipid Metabolism ; Immune System ; Lipids ; Mammals
    Chemical Substances Lipids
    Language English
    Publishing date 2023-02-10
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2278004-X
    ISSN 1934-6069 ; 1931-3128
    ISSN (online) 1934-6069
    ISSN 1931-3128
    DOI 10.1016/j.chom.2023.01.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Pathway paradigms revealed from the genetics of inflammatory bowel disease.

    Graham, Daniel B / Xavier, Ramnik J

    Nature

    2020  Volume 578, Issue 7796, Page(s) 527–539

    Abstract: Inflammatory bowel disease (IBD) is a complex genetic disease that is instigated and amplified by the confluence of multiple genetic and environmental variables that perturb the immune-microbiome axis. The challenge of dissecting pathological mechanisms ... ...

    Abstract Inflammatory bowel disease (IBD) is a complex genetic disease that is instigated and amplified by the confluence of multiple genetic and environmental variables that perturb the immune-microbiome axis. The challenge of dissecting pathological mechanisms underlying IBD has led to the development of transformative approaches in human genetics and functional genomics. Here we describe IBD as a model disease in the context of leveraging human genetics to dissect interactions in cellular and molecular pathways that regulate homeostasis of the mucosal immune system. Finally, we synthesize emerging insights from multiple experimental approaches into pathway paradigms and discuss future prospects for disease-subtype classification and therapeutic intervention.
    MeSH term(s) Animals ; Cytokines/immunology ; Exome/genetics ; Fibrosis/immunology ; Fibrosis/pathology ; Genetic Predisposition to Disease ; Homeostasis ; Humans ; Immunity, Cellular ; Immunity, Humoral ; Immunity, Innate ; Immunity, Mucosal/genetics ; Immunity, Mucosal/immunology ; Inflammation/immunology ; Inflammation/pathology ; Inflammatory Bowel Diseases/genetics ; Inflammatory Bowel Diseases/immunology ; Inflammatory Bowel Diseases/pathology ; Inflammatory Bowel Diseases/therapy ; Intestinal Mucosa/immunology ; Intestinal Mucosa/microbiology ; Single-Cell Analysis
    Chemical Substances Cytokines
    Language English
    Publishing date 2020-02-26
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-020-2025-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Tuning in to inflammation: A path forward for precise and efficacious microbiome medicines?

    Subramanian, Sathish / Xavier, Ramnik J

    Med (New York, N.Y.)

    2020  Volume 2, Issue 8, Page(s) 892–894

    Abstract: Gut microbes sense various external cues, including those found in inflammatory conditions, yielding possibilities for connecting sensory circuits to effector pathways to engineer precise and scaled interventions to target pathway activity. Scott et al. ... ...

    Abstract Gut microbes sense various external cues, including those found in inflammatory conditions, yielding possibilities for connecting sensory circuits to effector pathways to engineer precise and scaled interventions to target pathway activity. Scott et al. combined directed evolution and a synthetic gene circuit in yeast to fine-tune sensing of extracellular ATP, showing promise as a live therapeutic in two murine models of chemical colitis and a murine model of antibody-mediated enteritis.
    MeSH term(s) Animals ; Colitis/chemically induced ; Enteritis ; Inflammation/drug therapy ; Mice ; Microbiota ; Time
    Language English
    Publishing date 2020-07-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Comment
    ISSN 2666-6340
    ISSN (online) 2666-6340
    DOI 10.1016/j.medj.2021.07.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Microbiota as Therapeutic Targets.

    Xavier, Ramnik J

    Digestive diseases (Basel, Switzerland)

    2016  Volume 34, Issue 5, Page(s) 558–565

    Abstract: Background: Inflammatory bowel disease (IBD) represents a family of diseases including Crohn's disease and ulcerative colitis. IBD has garnered significant attention in recent years due to successes in 2 areas of basic science: complex human genetics ... ...

    Abstract Background: Inflammatory bowel disease (IBD) represents a family of diseases including Crohn's disease and ulcerative colitis. IBD has garnered significant attention in recent years due to successes in 2 areas of basic science: complex human genetics and host-microbe interactions. Advances in understanding the genetics of IBD, mainly driven by genome-wide association studies, have identified more than 160 genetic loci that modulate the risk of disease. Notably, several of these genes have pointed to alterations in host-microbe interactions as being critical factors in pathogenesis. Investigations into the microbial communities of the gastrointestinal tract (or the 'gut microbiome') in IBD have yielded important insights into several aspects of interactions between microbiota and the host immune system, including how alterations to microbial community composition and function have important consequences for immune homeostasis.
    Key messages: The anatomy of the gastrointestinal tract plays a role in defining not only intestinal function, but also the microbial ecosystem that lives within the gut. Careful investigations into the composition and function of these microbial communities have suggested that patients with IBD have an imbalance in their gut microbiota, termed dysbiosis. These studies, as well as studies using samples from healthy individuals, have begun to uncover mechanisms of crosstalk between particular microbes (and microbial products) and immunomodulatory pathways, alterations which may drive immune diseases such as IBD.
    Conclusions: Investigations into the role of the microbiome in IBD have provided important clues to potential pathogenic mechanisms. Harnessing this knowledge to develop therapeutics and identify biomarkers is currently a major translational goal, holding great promise for clinically meaningful progress.
    MeSH term(s) Colitis, Ulcerative/genetics ; Colitis, Ulcerative/microbiology ; Crohn Disease/genetics ; Crohn Disease/microbiology ; Dysbiosis/genetics ; Dysbiosis/microbiology ; Gastrointestinal Microbiome ; Homeostasis/immunology ; Humans ; Inflammatory Bowel Diseases/genetics ; Inflammatory Bowel Diseases/microbiology
    Language English
    Publishing date 2016
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 632798-9
    ISSN 1421-9875 ; 0257-2753
    ISSN (online) 1421-9875
    ISSN 0257-2753
    DOI 10.1159/000445263
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Innate host defense mechanisms SAC bacteria by regulating phosphoinositide kinases and phosphatases.

    Carey, Kimberly L / Liu, Kai / Xavier, Ramnik J

    Autophagy

    2021  Volume 18, Issue 2, Page(s) 452–454

    Abstract: Human genetics and loss-of-function studies revealed a critical role for macroautophagy/autophagy in host defense. The autophagic delivery of intracellular pathogens to lysosomes is a central mechanism of innate immunity; thus, augmentation of host ... ...

    Abstract Human genetics and loss-of-function studies revealed a critical role for macroautophagy/autophagy in host defense. The autophagic delivery of intracellular pathogens to lysosomes is a central mechanism of innate immunity; thus, augmentation of host xenophagy represents a promising and powerful approach to combat infections. The precise mechanisms required for autophagosome biogenesis and maturation, however, remain unclear. Using a targeted genetic screen against phosphoinositide kinases and phosphatases, our recent work identified an essential role for the phosphoinositide phosphatase SACM1L/SAC1 in xenophagy. Re-expression of wild-type or catalytically-dead SACM1L in CRISPR knockout cells confirmed that SACM1L enzymatic activity is required to suppress replication of intracellular
    MeSH term(s) 1-Phosphatidylinositol 4-Kinase/metabolism ; Autophagosomes/metabolism ; Autophagy/genetics ; Bacteria/metabolism ; Defense Mechanisms ; Humans ; Lysosomes/metabolism ; Phosphoric Monoester Hydrolases/genetics ; Phosphoric Monoester Hydrolases/metabolism ; Salmonella/metabolism
    Chemical Substances 1-Phosphatidylinositol 4-Kinase (EC 2.7.1.67) ; Phosphoric Monoester Hydrolases (EC 3.1.3.2)
    Language English
    Publishing date 2021-11-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2454135-7
    ISSN 1554-8635 ; 1554-8627
    ISSN (online) 1554-8635
    ISSN 1554-8627
    DOI 10.1080/15548627.2021.2002102
    Database MEDical Literature Analysis and Retrieval System OnLINE

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