Intestinal homeostasis and its breakdown in inflammatory bowel disease

A role for mitochondria in nlrp3 inflammasome activation

Zhou, R., Yazdi, A. S., Menu, P., & Tschopp, J. (2011) · Nature · doi:10.1038/nature09663 · Cited by 5,602

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

Atarashi, K., Tanoue, T., Shima, T., Imaoka, A., Kuwahara, T., Momose, Y., Cheng, G., Yamasaki, S., Saito, T., Ohba, Y., et al. (2011) · Science · doi:10.1126/science.1198469 · Cited by 3,752

A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells

Cadwell, K., Liu, J. Y., Brown, S. L., Miyoshi, H., Loh, J., Lennerz, J. K., Kishi, C., Kc, W., Carrero, J. A., Hunt, S., et al. (2008) · Nature · doi:10.1038/nature07416 · Cited by 1,542

Nod1 and Nod2 direct autophagy by recruiting ATG16L1 to the plasma membrane at the site of bacterial entry

Travassos, L. H., Carneiro, L. A. M., Ramjeet, M., Hussey, S., Kim, Y.-G., Magalhães, J. G., Yuan, L., Soares, F., Chea, E., Le Bourhis, L., et al. (2010) · Nature Immunology · doi:10.1038/ni.1823 · Cited by 1,306

Diet, gut microbiota and immune responses

Maslowski, K. M., & Mackay, C. R. (2011) · Nature Immunology · doi:10.1038/ni0111-5 · Cited by 1,261

Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut

Artis, D. (2008) · Nature reviews. Immunology · doi:10.1038/nri2316 · Cited by 1,136 · cited 1×

STAT3 links IL-22 signaling in intestinal epithelial cells to mucosal wound healing

Pickert, G., Neufert, C., Leppkes, M., Zheng, Y., Wittkopf, N., Warntjen, M., Lehr, H.-A., Hirth, S., Weigmann, B., Wirtz, S., et al. (2009) · Journal of Experimental Medicine · doi:10.1084/jem.20082683 · Cited by 1,043

Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface

Vaishnava, S., Behrendt, C. L., Ismail, A. S., Eckmann, L., & Hooper, L. V. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808723105 · Cited by 1,019

CD4 + Regulatory T Cells Control T H 17 Responses in a Stat3-Dependent Manner

Chaudhry, A., Rudra, D., Treuting, P., Samstein, R. M., Liang, Y., Kas, A., & Rudensky, A. Y. (2009) · Science · doi:10.1126/science.1172702 · Cited by 1,000

TLR activation of the transcription factor XBP1 regulates innate immune responses in macrophages

Martinon, F., Chen, X., Lee, A.-H., & Glimcher, L. H. (2010) · Nature Immunology · doi:10.1038/ni.1857 · Cited by 996 · cited 1×

DADA2: High–resolution sample inference from Illumina amplicon data

Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698

Role of the microbiota in immunity and inflammation.

Belkaid, Y., & Hand, T. W. (2014) · Cell · doi:10.1016/j.cell.2014.03.011 · Cited by 5,385

Protective and pathogenic functions of macrophage subsets

Murray, P. J., & Wynn, T. A. (2011) · Nature Reviews Immunology · doi:10.1038/nri3073 · Cited by 5,269

Oxidative Stress: An Essential Factor in the Pathogenesis of Gastrointestinal Mucosal Diseases

Bhattacharyya, A., Chattopadhyay, R., Mitra, S., & Crowe, S. E. (2014) · Physiological Reviews · doi:10.1152/physrev.00040.2012 · Cited by 2,484

Inflammasomes in health and disease

Strowig, T., Henao-Mejia, J., Elinav, E., & Flavell, R. (2012) · Nature · doi:10.1038/nature10759 · Cited by 2,230

The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition.

Chang, P. V., Hao, L., Offermanns, S., & Medzhitov, R. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1322269111 · Cited by 2,175

Mechanisms Regulating Intestinal Barrier Integrity and Its Pathological Implications

Chelakkot, C., Ghim, J., & Ryu, S. H. (2018) · Experimental & Molecular Medicine · doi:10.1038/s12276-018-0126-x · Cited by 2,017

The keystone-pathogen hypothesis

Hajishengallis, G., Darveau, R. P., & Curtis, M. A. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2873 · Cited by 1,790

Symbiotic bacterial metabolites regulate gastrointestinal barrier function via the xenobiotic sensor PXR and Toll-like receptor 4

Venkatesh, M., Mukherjee, S., Wang, H., Li, H., Sun, K., Benechet, A. P., Qiu, Z., Maher, L., Redinbo, M. R., Phillips, R. S., et al. (2014) · Immunity · doi:10.1016/j.immuni.2014.06.014 · Cited by 1,066

The role of JAK/STAT signaling pathway and its inhibitors in diseases.

Xin, P., Xu, X., Deng, C., Liu, S., Wang, Y., Zhou, X., Ma, H., Wei, D., & Sun, S. (2020) · International Immunopharmacology · doi:10.1016/j.intimp.2020.106210 · Cited by 1,010

Microbiota-dependent crosstalk between macrophages and ILC3 promotes intestinal homeostasis

Mortha, A., Chudnovskiy, A., Hashimoto, D., Bogunovic, M., Spencer, S. P., Belkaid, Y., & Merad, M. (2014) · Science · doi:10.1126/science.1249288 · Cited by 820

Natural aryl hydrocarbon receptor ligands control organogenesis of intestinal lymphoid follicles

Kiss, E. A., Vonarbourg, C., Kopfmann, S., Hobeika, E., Finke, D., Esser, C., & Diefenbach, A. (2011) · Science · doi:10.1126/science.1214914 · Cited by 801

Paneth cells as a site of origin for intestinal inflammation

Adolph, T. E., Tomczak, M. F., Niederreiter, L., Ko, H.-J., Böck, J., Martinez-Naves, E., Glickman, J. N., Tschurtschenthaler, M., Hartwig, J., Hosomi, S., et al. (2013) · Nature · doi:10.1038/nature12599 · Cited by 732

Fecal microbiota transplantation and emerging applications

Borody, T. J., & Khoruts, A. (2012) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2011.244 · Cited by 677

Microbial tryptophan metabolites regulate gut barrier function via the aryl hydrocarbon receptor

Scott, S. A., Fu, J., & Chang, P. V. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2000047117 · Cited by 696

Regulation of intestinal inflammation by microbiota following allogeneic bone marrow transplantation

Jenq, R. R., Ubeda, C., Taur, Y., Menezes, C. C., Khanin, R., Dudakov, J. A., Liu, C., West, M. L., Singer, N. V., Equinda, M. J., et al. (2012) · Journal of Experimental Medicine · doi:10.1084/jem.20112408 · Cited by 626

A wave of regulatory T cells into neonatal skin mediates tolerance to commensal microbes

Scharschmidt, T. C., Vasquez, K. S., Truong, H.-A., Gearty, S. V., Pauli, M. L., Nosbaum, A., Gratz, I. K., Otto, M., Moon, J. J., Liese, J., et al. (2015) · Immunity · doi:10.1016/j.immuni.2015.10.016 · Cited by 586

Development and maintenance of intestinal regulatory T cells

Tanoue, T., Atarashi, K., & Honda, K. (2016) · Nature Reviews Immunology · doi:10.1038/nri.2016.36 · Cited by 553

Development of an enhanced human gastrointestinal epithelial culture system to facilitate patient-based assays

VanDussen, K. L., Marinshaw, J. M., Shaikh, N., Miyoshi, H., Moon, C., Tarr, P. I., Ciorba, M. A., & Stappenbeck, T. S. (2015) · Gut · doi:10.1136/gutjnl-2013-306651 · Cited by 525

Microbiome and Anticancer Immunosurveillance

Zitvogel, L., Ayyoub, M., Routy, B., & Kroemer, G. (2016) · Cell · doi:10.1016/j.cell.2016.03.001 · Cited by 478

Molecular Pathways of Colon Inflammation Induced by Cancer Immunotherapy

Luoma, A. M., Suo, S., Williams, H. L., Sharova, T., Sullivan, K., Manos, M., Bowling, P., Hodi, F. S., Rahma, O., Sullivan, R. J., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.001 · Cited by 484

Molecular physiology of bile acid signaling in health, disease, and aging

Perino, A., Demagny, H., Velazquez-Villegas, L., & Schoonjans, K. (2021) · Physiological Reviews · doi:10.1152/physrev.00049.2019 · Cited by 481

Apoptosis, necrosis and necroptosis: cell death regulation in the intestinal epithelium

Günther, C., Neumann, H., Neurath, M. F., & Becker, C. (2013) · Gut · doi:10.1136/gutjnl-2011-301364 · Cited by 462

Modulation of the human gut microbiota by dietary fibres occurs at the species level

Chung, W. S. F., Walker, A. W., Louis, P., Parkhill, J., Vermeiren, J., Bosscher, D., Duncan, S. H., & Flint, H. J. (2016) · BMC Biology · doi:10.1186/s12915-015-0224-3 · Cited by 409

Strain-Specific Anti-inflammatory Properties of Two Akkermansia muciniphila Strains on Chronic Colitis in Mice

Zhai, R., Xue, X., Zhang, L., Yang, X., Zhao, L., & Zhang, C. (2019) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2019.00239 · Cited by 368

Association between polycystic ovary syndrome and gut microbiota

Guo, Y., Qi, Y., Yang, X., Zhao, L., Wen, S., Liu, Y., & Tang, L. (2016) · PLOS ONE · doi:10.1371/journal.pone.0153196 · Cited by 350

Loss of Gut Microbiota Alters Immune System Composition and Cripples Postinfarction Cardiac Repair

Tang, T. W. H., Chen, H.-C., Chen, C.-Y., Yen, C. Y. T., Lin, C.-J., Prajnamitra, R. P., Chen, L.-L., Ruan, S.-C., Lin, J.-H., Lin, P.-J., et al. (2019) · Circulation · doi:10.1161/circulationaha.118.035235 · Cited by 348

Circulating and Tissue-Resident CD4+ T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function Is Altered During Inflammation

Hegazy, A. N., West, N. R., Stubbington, M. J. T., Wendt, E., Suijker, K. I. M., Datsi, A., This, S., Danne, C., Campion, S., Duncan, S. H., et al. (2017) · Gastroenterology · doi:10.1053/j.gastro.2017.07.047 · Cited by 338

Gut Microbiota and Iron: The Crucial Actors in Health and Disease

Yilmaz, B., & Li, H. (2018) · Pharmaceuticals · doi:10.3390/ph11040098 · Cited by 317

Microbiota-dependent sequelae of acute infection compromise tissue-specific immunity

Fonseca, D. M. D., Hand, T. W., Han, S.-J., Gerner, M. Y., Zaretsky, A. G., Byrd, A. L., Harrison, O. J., Ortiz, A. M., Quinones, M., Trinchieri, G., et al. (2015) · Cell · doi:10.1016/j.cell.2015.08.030 · Cited by 281

Gut microbiome response to sucralose and its potential role in inducing liver inflammation in mice

Bian, X., Chi, L., Gao, B., Tu, P., Ru, H., & Lu, K. (2017) · Frontiers in Physiology · doi:10.3389/fphys.2017.00487 · Cited by 258

Targeted deletion of MyD88 in intestinal epithelial cells results in compromised antibacterial immunity associated with downregulation of polymeric immunoglobulin receptor, mucin-2, and antibacterial peptides

Frantz, A. L., Rogier, E. W., Weber, C. R., Shen, L., Cohen, D. A., Fenton, L. A., Bruno, M. E. C., & Kaetzel, C. S. (2012) · Mucosal Immunology · doi:10.1038/mi.2012.23 · Cited by 230

Intestinal Epithelial Cell Autophagy Is Required to Protect against TNF-Induced Apoptosis during Chronic Colitis in Mice

Pott, J., Kabat, A. M., & Maloy, K. J. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2017.12.017 · Cited by 205

The autophagy gene Atg16l1 differentially regulates Treg and TH2 cells to control intestinal inflammation

Kabat, A. M., Harrison, O. J., Riffelmacher, T., Moghaddam, A. E., Pearson, C. F., Laing, A., Abeler-Dörner, L., Forman, S. P., Grencis, R. K., Sattentau, Q., et al. (2016) · eLife · doi:10.7554/elife.12444 · Cited by 193

Dietary advanced glycation end products modify gut microbial composition and partially increase colon permeability in rats

Qu, W., Yuan, X., Zhao, J., Zhang, Y., Hu, J., Wang, J., & Li, J. (2017) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201700118 · Cited by 195

Mechanism and Intervention Measures of Iron Side Effects on the Intestine

Qi, X., Zhang, Y., Guo, H., Hai, Y., Luo, Y., & Yue, T. (2020) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2019.1630599 · Cited by 142

Host-Microbiota Interactions Shape Local and Systemic Inflammatory Diseases

Grigg, J. B., & Sonnenberg, G. F. (2017) · The Journal of Immunology · doi:10.4049/jimmunol.1601621 · Cited by 130

A Large Polysaccharide Produced by Helicobacter hepaticus Induces an Anti-inflammatory Gene Signature in Macrophages

Danne, C., Ryzhakov, G., Martínez-López, M., Ilott, N. E., Franchini, F., Cuskin, F., Lowe, E. C., Bullers, S. J., Arthur, J. S. C., & Powrie, F. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.11.002 · Cited by 120

Bidirectional gut-brain-microbiota axis as a potential link between inflammatory bowel disease and ischemic stroke

Zhao, L., Xiong, Q., Stary, C. M., Mahgoub, O. K., Ye, Y., Gu, L., Xiong, X., & Zhu, S. (2018) · Journal of Neuroinflammation · doi:10.1186/s12974-018-1382-3 · Cited by 113

Human retinoic acid–regulated CD161+ regulatory T cells support wound repair in intestinal mucosa

Povoleri, G. A. M., Nova-Lamperti, E., Scottà, C., Fanelli, G., Chen, Y.-C., Becker, P. D., Boardman, D., Costantini, B., Romano, M., Pavlidis, P., et al. (2018) · Nature Immunology · doi:10.1038/s41590-018-0230-z · Cited by 114

Translatability of helminth therapy in inflammatory bowel diseases

Weinstock, J. V., & Elliott, D. E. (2013) · International Journal for Parasitology · doi:10.1016/j.ijpara.2012.10.016 · Cited by 110

Identification of trypsin-degrading commensals in the large intestine

Li, Y., Watanabe, E., Kawashima, Y., Plichta, D. R., Wang, Z., Ujike, M., Ang, Q. Y., Wu, R., Furuichi, M., Takeshita, K., et al. (2022) · Nature · doi:10.1038/s41586-022-05181-3 · Cited by 106

The Yin and Yang of Bacterial Resilience in the Human Gut Microbiota

Gibson, M. K., Pesesky, M. W., & Dantas, G. (2014) · Journal of Molecular Biology · doi:10.1016/j.jmb.2014.05.029 · Cited by 71

Temporal microbiota changes of high-protein diet intake in a rat model

Mu, C., Yang, Y., Luo, Z., & Zhu, W. (2017) · Anaerobe · doi:10.1016/j.anaerobe.2017.06.003 · Cited by 67

Inflammatory cues enhance TGFβ activation by distinct subsets of human intestinal dendritic cells via integrin αvβ8

Fenton, T. M., Kelly, A., Shuttleworth, E. E., Smedley, C., Atakilit, A., Powrie, F., Campbell, S., Nishimura, S. L., Sheppard, D., Levison, S., et al. (2017) · Mucosal Immunology · doi:10.1038/mi.2016.94 · Cited by 64

Metformin Improves Ileal Epithelial Barrier Function in Interleukin-10 Deficient Mice

Xue, Y., Zhang, H., Sun, X., & Zhu, M.-J. (2016) · PLOS ONE · doi:10.1371/journal.pone.0168670 · Cited by 61

Microbiome influences on allergy in mice and humans

Marsland, B. J., & Salami, O. (2015) · Current Opinion in Immunology · doi:10.1016/j.coi.2015.07.005 · Cited by 49

Alterations in cecal microbiota and intestinal barrier function of laying hens fed on fluoride supplemented diets

Miao, L., Gong, Y., Li, H., Xie, C., Xu, Q., Dong, X., Elwan, H. A. M., & Zou, X. (2020) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2020.110372 · Cited by 45

Modulation of TCR Signaling by Tyrosine Phosphatases: From Autoimmunity to Immunotherapy

Castro-Sanchez, P., Teagle, A. R., Prade, S., & Zamoyska, R. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.608747 · Cited by 44

Regulation of Th1/Th2 and Th17/Treg by pDC/mDC imbalance in primary immune thrombocytopenia.

Li, Q., Liu, Y., Wang, X., Sun, M., Wang, L., Wang, X., Liu, Y., Fan, W., Zhang, K., Sui, X., et al. (2021) · Experimental Biology and Medicine · doi:10.1177/15353702211009787 · Cited by 41

Piezo1-specific deletion in macrophage protects the progression of chronic inflammatory bowel disease in mice

Wang, Y., Chu, T., Meng, C., Bian, Y., & Li, J. (2025) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2025.101495 · Cited by 32

The chemical interactome space between the human host and the genetically defined gut metabotypes

Jacobsen, U. P., Nielsen, H. B., Hildebrand, F., Raes, J., Sicheritz-Ponten, T., Kouskoumvekaki, I., & Panagiotou, G. (2013) · The ISME Journal · doi:10.1038/ismej.2012.141 · Cited by 24

Acoustic stress induces long term severe intestinal inflammation in the mouse

Miranda, S., & Roux, M. E. (2017) · Toxicology Letters · doi:10.1016/j.toxlet.2017.07.898 · Cited by 16