An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases

Diet rapidly and reproducibly alters the human gut microbiome

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Human gut microbiome viewed across age and geography

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Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease

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Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

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The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic T reg Cell Homeostasis

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A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease

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Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation

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Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases

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Autophagy and Viruses: Adversaries or Allies?

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Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve

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Gut microbiome structure and metabolic activity in inflammatory bowel disease

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Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients

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Impact of the Gut Microbiota on Intestinal Immunity Mediated by Tryptophan Metabolism

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The Human Gut Microbiome: From Association to Modulation

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Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches

Sartor, R. B., & Wu, G. D. (2017) · Gastroenterology · doi:10.1053/j.gastro.2016.10.012 · Cited by 808

Mechanisms and consequences of intestinal dysbiosis

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Adhesion mechanisms mediated by probiotics and prebiotics and their potential impact on human health

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Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals

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Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease

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Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis

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Human genetic variation and the gut microbiome in disease

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Signalling cognition: The gut microbiota and hypothalamic-pituitary-adrenal axis

Rusch, J. A., Layden, B. T., & Dugas, L. R. (2023) · Frontiers in Endocrinology · doi:10.3389/fendo.2023.1130689 · Cited by 415

Faecal microbiota study reveals specific dysbiosis in spondyloarthritis

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Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts

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Escherichia coli Pathobionts Associated with Inflammatory Bowel Disease

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Microbiome therapeutics — Advances and challenges

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Gut Microbiota Regulation of T Cells During Inflammation and Autoimmunity

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The role of the gut microbiota in development, function and disorders of the central nervous system and the enteric nervous system

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Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course

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Autophagy protein ATG16L1 prevents necroptosis in the intestinal epithelium

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Dual Role of Indoles Derived From Intestinal Microbiota on Human Health

Ye, X., Li, H., Anjum, K., Zhong, X., Miao, S., Zheng, G., Liu, W., & Li, L. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.903526 · Cited by 288

Anti-Inflammatory and Intestinal Microbiota Modulation Properties of Jinxiang Garlic ( Allium sativum L.) Polysaccharides toward Dextran Sodium Sulfate-Induced Colitis

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Mucosal Barrier Depletion and Loss of Bacterial Diversity are Primary Abnormalities in Paediatric Ulcerative Colitis

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A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers

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A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice

Chiaro, T. R., Soto, R., Stephens, W. Z., Kubinak, J. L., Petersen, C., Gogokhia, L., Bell, R. S., Delgado, J. C., Cox, J. E., Voth, W. P., et al. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aaf9044 · Cited by 237

Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning

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Lactobacillus johnsonii alleviates colitis by TLR1/2-STAT3 mediated CD206 + macrophages IL-10 activation

Jia, D., Wang, Q.-W., Hu, Y., He, J., Ge, Q., Qi, Y., Chen, L.-Y., Zhang, Y., Fan, L., Lin, Y., et al. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2145843 · Cited by 222

The Effects of Nutrition on the Gastrointestinal Microbiome of Cats and Dogs: Impact on Health and Disease

Wernimont, S. M., Radosevich, J., Jackson, M. I., Ephraim, E., Badri, D. V., MacLeay, J. M., Jewell, D. E., & Suchodolski, J. S. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01266 · Cited by 244

Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe

Lamichhane, S., Sen, P., Dickens, A. M., Orešič, M., & Bertram, H. C. (2018) · Methods · doi:10.1016/j.ymeth.2018.04.029 · Cited by 207

5-Aminosalicylic Acid Alters the Gut Bacterial Microbiota in Patients With Ulcerative Colitis

Xu, J., Chen, N., Wu, Z., Song, Y., Zhang, Y., Wu, N., Zhang, F., Ren, X., & Liu, Y. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01274 · Cited by 187

Polysaccharides, proteins, and their complex as microencapsulation carriers for delivery of probiotics: A review on carrier types and encapsulation techniques

Xie, A., Zhao, S., Liu, Z., Yue, X., Shao, J., Li, M., & Li, Z. (2023) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2023.124784 · Cited by 180

A Review of Inflammatory Bowel Disease: A Model of Microbial, Immune and Neuropsychological Integration

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Determinants of IBD Heritability: Genes, Bugs, and More

Turpin, W., Goethel, A., Bedrani, L., & Croitoru, M. K. (2018) · Inflammatory Bowel Diseases · doi:10.1093/ibd/izy085 · Cited by 170

Altered Immunity of Laboratory Mice in the Natural Environment Is Associated with Fungal Colonization

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Alcohol, Inflammation, and Microbiota in Alcoholic Liver Disease

Dukić, M., Radonjić, T., Jovanović, I., Zdravkovic, M. D., Todorović, Z., Kraišnik, N., Aranđelović, B., Mandić, O., Popadić, V., Nikolić, N., et al. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24043735 · Cited by 164

Modulation of the microbiota-gut-brain axis by probiotics in a murine model of inflammatory bowel disease

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Helicobacter species are potent drivers of colonic T cell responses in homeostasis and inflammation

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Attenuation of DSS induced colitis by Dictyophora indusiata polysaccharide (DIP) via modulation of gut microbiota and inflammatory related signaling pathways

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Gut mucosal DAMPs in IBD: from mechanisms to therapeutic implications

Boyapati, R. K., Rossi, A. G., Satsangi, J., & Ho, G. (2016) · Mucosal Immunology · doi:10.1038/mi.2016.14 · Cited by 150

Ursodeoxycholic Acid and Its Taurine- or Glycine-Conjugated Species Reduce Colitogenic Dysbiosis and Equally Suppress Experimental Colitis in Mice

den Bossche, L. V., Hindryckx, P., Devisscher, L., Devriese, S., Welden, S. V., Holvoet, T., Vilchez‐Vargas, R., Vital, M., Pieper, D. H., Bussche, J. V., et al. (2017) · Applied and Environmental Microbiology · doi:10.1128/aem.02766-16 · Cited by 146

Carcinogenesis and therapeutics: the microbiota perspective

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Camellia sinensis and Litsea coreana Ameliorate Intestinal Inflammation and Modulate Gut Microbiota in Dextran Sulfate Sodium‐Induced Colitis Mice

Liu, Y., Wang, X., Chen, Q., Luo, L., Ma, M., Xiao, B., & Zeng, L. (2020) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201900943 · Cited by 135

Generation of axenic Aedes aegypti demonstrate live bacteria are not required for mosquito development

Correa, M. A., Matusovsky, B., Brackney, D. E., & Steven, B. T. (2018) · Nature Communications · doi:10.1038/s41467-018-07014-2 · Cited by 134

Mucin O-glycans facilitate symbiosynthesis to maintain gut immune homeostasis

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Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease

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Sesamol Supplementation Attenuates DSS-Induced Colitis via Mediating Gut Barrier Integrity, Inflammatory Responses, and Reshaping Gut Microbiome

Zhao, B., Xia, B., Li, X., Zhang, L., Liu, X., Shi, R., Kou, R.-W., Liu, Z., & Liu, X. (2020) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.0c04370 · Cited by 116

The human gastrointestinal tract and oral microbiota in inflammatory bowel disease: a state of the science review

López, R. L., Burgos, M. J. G., Gálvez, A., & Pulido, R. P. (2016) · Apmis · doi:10.1111/apm.12609 · Cited by 116

Research Gaps in Diet and Nutrition in Inflammatory Bowel Disease. A Topical Review by D-ECCO Working Group [Dietitians of ECCO]

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A correlation between intestinal microbiota dysbiosis and osteoarthritis

Szychlinska, M. A., Rosa, M. D., Castorina, A., Mobasheri, A., & Musumeci, G. (2019) · Heliyon · doi:10.1016/j.heliyon.2019.e01134 · Cited by 117

Health benefits of edible mushroom polysaccharides and associated gut microbiota regulation

Ma, G., Du, H., Hu, Q., Yang, W., Pei, F., & Xiao, H. (2021) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2021.1903385 · Cited by 114

Cellular stress and innate inflammation in organ‐specific autoimmunity: lessons learned from vitiligo

Harris, J. E. (2015) · Immunological Reviews · doi:10.1111/imr.12369 · Cited by 113

Role of Microbiota-Derived Metabolites in Alcoholic and Non-Alcoholic Fatty Liver Diseases

Park, J. W., Kim, S. E., Lee, N. Y., Kim, J. H., Jung, J.-H., Jang, M.-K., Park, S.-H., Lee, M.-S., Kim, D.-J., Kim, H.-S., et al. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms23010426 · Cited by 110

Deep Metaproteomics Approach for the Study of Human Microbiomes

Zhang, X., Chen, W., Ning, Z., Mayne, J., Mack, D. R., Stintzi, A., Tian, R., & Figeys, D. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b02224 · Cited by 109

Australian consensus statements for the regulation, production and use of faecal microbiota transplantation in clinical practice

Haifer, C., Kelly, C. R., Paramsothy, S., Andresen, D. N., Papanicolas, L. E., McKew, G. L., Borody, T. J., Kamm, M. A., Costello, S. P., Andrews, J. M., et al. (2020) · Gut · doi:10.1136/gutjnl-2019-320260 · Cited by 108

Silk as a Biomaterial to Support Long-Term Three-Dimensional Tissue Cultures

Abbott, R. D., Kimmerling, E. P., Cairns, D. M., & Kaplan, D. L. (2016) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.5b12114 · Cited by 101

“I Am I and My Bacterial Circumstances”: Linking Gut Microbiome, Neurodevelopment, and Depression

Lima‐Ojeda, J. M., Rupprecht, R., & Baghai, T. C. (2017) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2017.00153 · Cited by 104

Gut microbiota modulation and anti-inflammatory properties of mixed lactobacilli in dextran sodium sulfate-induced colitis in mice

Shi, J., Xie, Q., Yue, Y., Chen, Q., Zhao, L., Evivie, S. E., Li, B., & Huo, G. (2021) · Food & Function · doi:10.1039/d1fo00317h · Cited by 98

Intestinal Microbiota Mediates High-Fructose and High-Fat Diets to Induce Chronic Intestinal Inflammation

Tan, R., Dong, H., Chen, Z., Jin, M., Yin, J., Li, H., Shi, D., Shao, Y., Wang, H., Chen, T., et al. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.654074 · Cited by 100

Microbiota and Autoimmunity: Exploring New Avenues

Yurkovetskiy, L., Pickard, J. M., & Chervonsky, A. V. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.010 · Cited by 99

Protective and pro-inflammatory roles of intestinal bacteria

Webb, C. R., Koboziev, I., Furr, K. L., & Grisham, M. B. (2016) · Pathophysiology · doi:10.1016/j.pathophys.2016.02.002 · Cited by 102

Absorption ofCodonopsis pilosulaSaponins by Coexisting Polysaccharides Alleviates Gut Microbial Dysbiosis with Dextran Sulfate Sodium-Induced Colitis in Model Mice

Jing, Y., Li, A., Liu, Z., Yang, P., Wei, J., Chen, X., Zhao, T., Bai, Y., Zha, L., & Zhang, C. (2018) · BioMed Research International · doi:10.1155/2018/1781036 · Cited by 91

Dietary Tangeretin Alleviated Dextran Sulfate Sodium-Induced Colitis in Mice via Inhibiting Inflammatory Response, Restoring Intestinal Barrier Function, and Modulating Gut Microbiota

Chen, B., Luo, J., Han, Y., Du, H., Liu, J., He, W., Zhu, J., Xiao, J., Wang, J., Cao, Y., et al. (2021) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.1c03046 · Cited by 92

Gut microbiome: a new player in gastrointestinal disease

Gorkiewicz, G., & Moschen, A. R. (2017) · Archiv für Pathologische Anatomie und Physiologie und für Klinische Medicin · doi:10.1007/s00428-017-2277-x · Cited by 95

Enlisting commensal microbes to resist antibiotic-resistant pathogens

Keith, J. W., & Pamer, E. G. (2018) · The Journal of Experimental Medicine · doi:10.1084/jem.20180399 · Cited by 93

Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview

Sen, P., & Orešič, M. (2019) · Metabolites · doi:10.3390/metabo9020022 · Cited by 84

Synbiotics for Improved Human Health: Recent Developments, Challenges, and Opportunities

Krumbeck, J. A., Walter, J., & Hutkins, R. W. (2018) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-030117-012757 · Cited by 84

Microbiota-derived tryptophan metabolism: Impacts on health, aging, and disease

Gupta, S. K., Vyavahare, S. S., Blanes, I. L. D., Berger, F. G., Isales, C. M., & Fulzele, S. (2023) · Experimental Gerontology · doi:10.1016/j.exger.2023.112319 · Cited by 96

The Safety of Fecal Microbiota Transplantation for Crohn’s Disease: Findings from A Long-Term Study

Wang, H., Cui, B., Li, Q., Ding, X. L., Li, P., Zhang, T., Yang, X., Ji, G., & Zhang, F. (2018) · Advances in Therapy · doi:10.1007/s12325-018-0800-3 · Cited by 88

Rewilding Nod2 and Atg16l1 Mutant Mice Uncovers Genetic and Environmental Contributions to Microbial Responses and Immune Cell Composition

Lin, J.-D., Devlin, J. C., Yeung, F., McCauley, C., Leung, J. M., Chen, Y.-H., Cronkite, A., Hansen, C., Drake-Dunn, C., Ruggles, K. V., et al. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.03.001 · Cited by 82

Pediococcus pentosaceus LI05 alleviates DSS‐induced colitis by modulating immunological profiles, the gut microbiota and short‐chain fatty acid levels in a mouse model

Bian, X., Yang, L., Wu, W., Lv, L., Jiang, X., Wang, Q., Wu, J., Li, Y., Ye, J., Fang, D., et al. (2020) · Microbial Biotechnology · doi:10.1111/1751-7915.13583 · Cited by 84

Serum Metabolomics Identifies Altered Bioenergetics, Signaling Cascades in Parallel with Exposome Markers in Crohn’s Disease

Lai, Y., Xue, J., Liu, C., Gao, B., Chi, L., Tu, P., Lü, K., & Ru, H. (2019) · Molecules · doi:10.3390/molecules24030449 · Cited by 81

Effects of four food hydrocolloids on colitis and their regulatory effect on gut microbiota

Zhang, S., Sun, Y., Nie, Q., Hu, J., Li, Y., Shi, Z., Ji, H., Zhang, H., Zhao, M., Chen, C., et al. (2023) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2023.121368 · Cited by 81

The mouse gut microbiome revisited: From complex diversity to model ecosystems

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Interactions of tea catechins with intestinal microbiota and their implication for human health

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