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Research Host-microbe Interactions



Garcia-Morena, D., Fernandez-Cantos, M. V., Escalera, S. L., Lok, J., Iannone, V., Cancellieri, P., Maathuis, W., Panagiotou, G., Aranzamendi, C., Aidy, S. E., Kolehmainen, M., El-Nezami, H., Wellejus, A., & Kuipers, O. P. (2024). In Vitro Influence of Specific Bacteroidales Strains on Gut and Liver Health Related to Metabolic Dysfunction-Associated Fatty Liver Disease. Probiotics and Antimicrobial Proteins. Advance online publication.


Scheurink, T. A. W., Borkent, J., Gangadin, S. S., El Aidy, S., Mandl, R., & Sommer, I. E. C. (2023). Association between gut permeability, brain volume, and cognition in healthy participants and patients with schizophrenia spectrum disorder. Brain and Behavior, 13(6), Article e3011.
Jansma, J., Thome, N. U., Schwalbe, M., Chatziioannou, A. C., Elsayed, S. S., van Wezel, G. P., van den Abbeele, P., van Hemert, S., & El Aidy, S. (2023). Dynamic effects of probiotic formula ecologic®825 on human small intestinal ileostoma microbiota: A network theory approach. Gut Microbes, 15(1), Article 2232506.
Mahdy, M. S., Azmy, A. F., Dishisha, T., Mohamed, W. R., Ahmed, K. A., Hassan, A., Aidy, S. E., & El-Gendy, A. O. (2023). Irinotecan-gut microbiota interactions and the capability of probiotics to mitigate Irinotecan-associated toxicity. BMC Microbiology, 23(1), Article 53.
Jansma, J., Chatziioannou, A. C., Castricum, K., van Hemert, S., & El Aidy, S. (2023). Metabolic network construction reveals probiotic-specific alterations in the metabolic activity of a synthetic small intestinal community. Msystems, 8(5), Article 00332-23.
Waclawiková, B., Cesar Telles de Souza, P., Schwalbe, M., Neochoritis, C. G., Hoornenborg, W., Nelemans, S. A., Marrink, S. J., & El Aidy, S. (2023). Potential binding modes of the gut bacterial metabolite, 5-hydroxyindole, to the intestinal L-type calcium channels and its impact on the microbiota in rats. Gut Microbes, 15(1), Article 2154544.


Bunt, D. V., Aidy, S. E., & Minnaard, A. J. (2023). Divergent Total Synthesis of Fornicin A, Fornicin D, and Ganodercin D, Meroterpenoids from Ganoderma Mushrooms. European Journal of Organic Chemistry, 26(6), Article e202201446.
El Aidy, S., & Waclawiková, B. (2022). 5-hydroxyindole and analogs thereof as stimulants of gut motility. (Patent No. WO2022010352).
González-Dávila, P., Schwalbe, M., Danewalia, A., Dalile, B., Verbeke, K., Mahata, S. K., & El Aidy, S. (2022). Catestatin selects for colonization of antimicrobial-resistant gut bacterial communities. The ISME journal, 16, 1873–1882.
Krieg, C., Weber, L. M., Fosso, B., Marzano, M., Hardiman, G., Olcina, M. M., Domingo, E., El Aidy, S., Mallah, K., Robinson, M. D., & Guglietta, S. (2022). Complement downregulation promotes an inflammatory signature that renders colorectal cancer susceptible to immunotherapy. Journal for immunotherapy of cancer, 10(9), Article e004717.
Waclawiková, B., Codutti, A., Alim, K., & El Aidy, S. (2022). Gut microbiota-motility interregulation: Insights from in vivo, ex vivo and in silico studies. Gut Microbes, 14(1), Article 1997296.
González-Dávila, P., Schwalbe, M., Danewalia, A., Wardenaar, R., Dalile, B., Verbeke, K., Mahata, S. K., & El Aidy, S. (2022). Gut microbiota transplantation drives the adoptive transfer of colonic genotype-phenotype characteristics between mice lacking catestatin and their wild type counterparts. Gut Microbes, 14(1), Article e2081476.
Jansma, J., van Essen, R., Haarman, B. C. M., Chatziioannou, A. C., Borkent, J., Ioannou, M., van Hemert, S., Sommer, I. E. C., & El Aidy, S. (2022). Metabolic phenotyping reveals a potential link between elevated faecal amino acids, diet and symptom severity in individuals with severe mental illness. Journal of Psychiatric Research, 151, 507-515.
Maassen, S., Warner, H., Ioannidis, M., Jansma, J., Markus, H., El Aidy, S., Chiara, M.-D., Chiara, J. L., Maierhofer, L., Weavers, H., & van den Bogaart, G. (2022). Mitochondrial interaction of fibrosis-protective 5-methoxy tryptophan enhances collagen uptake by macrophages. Free Radical Biology and Medicine, 188, 287-297. Article 202206235.
van Kessel, S. P., Bullock, A., van Dijk, G., & El Aidy, S. (2022). Parkinson's disease medication alters small intestinal motility and microbiota composition in healthy rats. Msystems, 7(1), Article e0119121.


Muntjewerff, E. M., Tang, K., Lutter, L., Christoffersson, G., Nicolasen, M. J. T., Gao, H., Katkar, G. D., Das, S., Ter Beest, M., Ying, W., Ghosh, P., Aidy, S. E., Oldenburg, B., van den Bogaart, G., & Mahata, S. K. (2021). Chromogranin A regulates gut permeability via the antagonistic actions of its proteolytic peptides. Acta physiologica, 232(2), Article e13655.
Waclawiková, B., Bullock, A., Schwalbe, M., Aranzamendi, C., Nelemans, S. A., van Dijk, G., & El Aidy, S. (2021). Gut bacteria-derived 5-hydroxyindole is a potent stimulant of intestinal motility via its action on L-type calcium channels. PLOS BIOLOGY, 19(1), Article e3001070.
van Kessel, S. P., Auvinen, P., Scheperjans, F., & El Aidy, S. (2021). Gut bacterial tyrosine decarboxylase associates with clinical variables in a longitudinal cohort study of Parkinsons disease. NPJ Parkinson's disease, 7(1), Article 115.
Bunt, D. V., Minnaard, A. J., & El Aidy, S. (2021). Potential Modulatory Microbiome Therapies for Prevention or Treatment of Inflammatory Bowel Diseases. Pharmaceuticals, 14(6), Article 506.
Aresti-Sanz, J., Schwalbe, M., Pereira, R. R., Permentier, H., & El Aidy, S. (2021). Stability of methylphenidate under various ph conditions in the presence or absence of gut microbiota. Pharmaceuticals, 14(8), Article 733.
Jansma, J., & El Aidy, S. (2021). Understanding the host-microbe interactions using metabolic modeling. Microbiome, 9(1), Article 16.


Kiewiet, M. B. G., Elderman, M. E., Aidy, S. E., Burgerhof, J. G. M., Visser, H., Vaughan, E. E., Faas, M. M., & de Vos, P. (2021). Flexibility of Gut Microbiota in Ageing Individuals during Dietary Fiber Long-Chain Inulin Intake. Molecular Nutrition & Food Research, Article e2000390.
Jansma, J., Brinkman, F., van Hemert, S., & El Aidy, S. (2021). Targeting the endocannabinoid system with microbial interventions to improve gut integrity. Progress in Neuro-Psychopharmacology and Biological Psychiatry, 106, Article 110169.
Morais, L. H., Golubeva, A. V., Moloney, G. M., Moya-Pérez, A., Ventura-Silva, A. P., Arboleya, S., Bastiaanssen, T. F. S., O'Sullivan, O., Rea, K., Borre, Y., Scott, K. A., Patterson, E., Cherry, P., Stilling, R., Hoban, A. E., El Aidy, S., Sequeira, A. M., Beers, S., Moloney, R. D., ... Cryan, J. F. (2020). Enduring Behavioral Effects Induced by Birth by Caesarean Section in the Mouse. Current Biology, 30(19), 3761-3774.
van Kessel, S. P., de Jong, H. R., Winkel, S. L., van Leeuwen, S. S., Nelemans, S. A., Permentier, H., Keshavarzian, A., & El Aidy, S. (2020). Gut bacterial deamination of residual levodopa medication for Parkinson's disease. BMC Biology, 18(1), Article 137.
Haarman, B., El Aidy, S., van Hemert, S., Fu, J., Festen, N., & Sommer, I. E. C. (2020). The gut-brain axis in bipolar disorder and schizophrenia – a target for precision psychiatry?. Abstract from Digitaal NVVP voorjaarscongres , Netherlands.
Haarman, B., Ioannou, M., Borkent, J., Doorduin, J., Fu, J., El Aidy, S., & Sommer, I. E. C. (2020). The impact of intestinal permeability and intestinal microbiome on cerebral immunological activity and myelination in bipolar disorder. Poster session presented at 22nd Annual Conference of the International Society for Bipolar Disorders.
Haarman, B. C. M., Ioannou, M., Borkent, J., Doorduin, J., Fu, J., El Aidy, S., & Sommer, I. E. C. (2020). The impact of intestinal permeability and intestinal microbiome on cerebral immunological activity and myelination in bipolar disorder. Bipolar Disorders, 22, 84-85.


El Aidy, S., Bolsius, Y. G., Raven, F., & Havekes, R. (2020). A brief period of sleep deprivation leads to subtle changes in mouse gut microbiota. Journal of Sleep Research, 29(6), Article e12920.
Bugda Gwilt, K., González, D. P., Olliffe, N., Oller, H., Hoffing, R., Puzan, M., El Aidy, S., & Miller, G. M. (2020). Actions of Trace Amines in the Brain-Gut-Microbiome Axis via Trace Amine-Associated Receptor-1 (TAAR1). Cellular and molecular neurobiology, 40(2), 191-201.
van Kessel, S. P., & El Aidy, S. (2019). Bacterial Metabolites Mirror Altered Gut Microbiota Composition in Patients with Parkinson's Disease. Journal of Parkinson's Disease, 9(2), S359-S370.
van Kessel, S. P., & El Aidy, S. (2019). Contributions of Gut Bacteria and Diet to Drug Pharmacokinetics in the Treatment of Parkinson's Disease. Frontiers in Neurology, 10, Article 1087.
van Kessel, S. P., Frye, A. K., El-Gendy, A. O., Castejon, M., Keshavarzian, A., van Dijk, G., & El Aidy, S. (2019). Gut bacterial tyrosine decarboxylases restrict levels of levodopa in the treatment of Parkinson's disease. Nature Communications, 10(1), Article 310.
Aarts, E., & El Aidy, S. (2019). Increasing reproducibility and interpretability of microbiota-gut-brain studies on human neurocognition and intermediary microbial metabolites. Behavioral and Brain Sciences, 42, Article e61.
Sanz, J. A., & El Aidy, S. (2019). Microbiota and gut neuropeptides: a dual action of antimicrobial activity and neuroimmune response. Psychopharmacology, 236(5), 1597-1609.
Torres-Fuentes, C., Golubeva, A. V., Zhdanov, A. V., Wallace, S., Arboleya, S., Papkovsky, D. B., El Aidy, S., Ross, P., Roy, B. L., Stanton, C., Dinan, T. G., Cryan, J. F., & Schellekens, H. (2019). Short-chain fatty acids and microbiota metabolites attenuate ghrelin receptor signaling. The FASEB Journal, 33(12), 13546-13559.


Waclawikova, B., & El Aidy, S. (2018). Role of Microbiota and Tryptophan Metabolites in the Remote Effect of Intestinal Inflammation on Brain and Depression. Pharmaceuticals, 11(3), Article 63.
Bears, A., Oosting, A., Lohuis, M., Koehorse, M., El Aidy, S., Hugenholtz, F., Smidt, H., Mischke, M., Boekschoten, M. V., Verkade, H. J., Garssen, J., van der Beek, E. M., Knol, J., de Vos, P., van Bergenhenegouwen, J., & Fransen, F. (2018). Sex differences in lipid metabolism are affected by presence of the gut microbiota. Scientific Reports, 8, Article 13426.


Fransen, F., van Beek, A. A., Borghuis, T., El Aidy, S., Hugenholtz, F., van der Gaast-de Jongh, C., Savelkoul, H. F. J., De Jonge, M. I., Boekschoten, M. V., Smidt, H., Faas, M. M., & de Vos, P. (2017). Aged Gut Microbiota Contributes to Systemical Inflammaging after Transfer to Germ-Free Mice. Frontiers in Immunology, 8, Article 1385.
Koopman, M., El Aidy, S., & MIDtrauma Consortium (2017). Depressed gut? The microbiota-diet-inflammation trialogue in depression. Current opinion in psychiatry, 30(5), 369-377.
El Aidy, S., Ramsteijn, A. S., Dini-Andreote, F., van Eijk, R., Houwing, D. J., Salles, J. F., & Olivier, J. D. A. (2017). Serotonin transporter genotype modulates the gut microbiota composition in young rats, an effect augmented by early life stress. Frontiers in cellular neuroscience, 11, Article 222.
Fransen, F., van Beek, A. A., Borghuis, T., Meijer, B., Hugenholtz, F., van der Gaast-de Jongh, C., Savelkoul, H. F., de Jonge, M. I., Faas, M. M., Boekschoten, M. V., Smidt, H., El Aidy, S., & de Vos, P. (2017). The Impact of Gut Microbiota on Gender-Specific Differences in Immunity. Frontiers in Immunology, 8, Article 754.
Vinke, P. C., El Aidy, S., & van Dijk, G. (2017). The role of supplemental complex dietary carbohydrates and gut microbiota in promoting cardiometabolic and immunological health in obesity: Lessons from healthy non-obese individuals. Frontiers in nutrition, 4, Article 34.
Fransen, F., Sahasrabudhe, N. M., Elderman, M., Bosveld, M., El Aidy, S., Hugenholtz, F., Borghuis, T., Kousemaker, B., Winkel, S., Gaast-de Jongh, C. E., Jonge, M. I. D., Boekschoten, M. V., Smidt, H., Schols, H. A., & de Vos, P. (2017). β2→ 1-fructans modulate the immune system in vivo by direct interaction with the mucosa in a microbiota-independent fashion. Frontiers in Immunology, 8, Article 154.


El Aidy, S. (2016). De invloed op ons brein. In M. Kleerebezem, W. Hoekstra, & A. van de Graaf (Eds.), Ons microbioom: Wat betekenen bacteriën voor onze gezondheid? (4 ed., Vol. 35, pp. 54-57). (Cahier Biowetenschappen en Maatschappij). Stichting Biowetenschappen en Maatschappij.
El Aidy, S., Stilling, R., Dinan, T. G., & Cryan, J. F. (2016). Microbiome to Brain: Unravelling the Multidirectional Axes of Communication. In M. Lyte (Ed.), Microbial Endocrinology: Interkingdom Signalling in Infectious Diseases and Health (2 ed., Vol. 874, pp. 301-336). (Advances in Experimental Medicine and Biology; Vol. 874). Springer International Publishing AG.
Sarker, S. A., Sultana, S., Reuteler, G., Moine, D., Descombes, P., Charton, F., Bourdin, G., Mccallin, S., Ngom-bru, C., Neville, T., Akter, M., Huq, S., Qadri, F., Talukdar, K., Kassam, M., Delley, M., Loiseau, C., Deng, Y., El Aidy, S., ... Brüssow, H. (2016). Oral Phage Therapy of Acute Bacterial Diarrhea With Two Coliphage Preparations: A Randomized Trial in Children From Bangladesh. EBioMedicine, 124-137.
Kelly, J. R., Borre, Y., O' Brien, C., Patterson, E., El Aidy, S., Deane, J., Kennedy, P. J., Beers, S., Scott, K., Moloney, G., Hoban, A. E., Scott, L., Fitzgerald, P., Ross, P., Stanton, C., Clarke, G., Cryan, J. F., & Dinan, T. G. (2016). Transferring the blues: Depression-associated gut microbiota induces neurobehavioural changes in the rat. Journal of Psychiatric Research, 82, 109-118.


Fransen, F., Zagato, E., Mazzini, E., Fosso, B., Manzari, C., El Aidy, S., Chiavelli, A., D'Erchia, A. M., Sethi, M. K., Pabst, O., Marzano, M., Moretti, S., Romani, L., Penna, G., Pesole, G., & Rescigno, M. (2015). BALB/c and C57BL/6 Mice Differ in Polyreactive IgA Abundance, which Impacts the Generation of Antigen-Specific IgA and Microbiota Diversity. Immunity, 43(3), 527-540.
Pusceddu, M. M., El Aidy, S., Crispie, F., O'Sullivan, O., Cotter, P., Stanton, C., Kelly, P., Cryan, J. F., & Dinan, T. G. (2015). Correction: N-3 Polyunsaturated Fatty Acids (PUFAs) Reverse the Impact of Early-Life Stress on the Gut Microbiota. PLoS ONE, 10(10), Article e0142228.
El Aidy, S., Dinan, T. G., & Cryan, J. F. (2015). Gut Microbiota: The conductor in the Orchestra of immune-neuroendocrine communication. Clinical Therapeutics, 37(5), 954-967.
Menckeberg, C. L., Hol, J., Simons-Oosterhuis, Y., Raatgeep, H. R. C., de Ruiter, L. F., Lindenbergh-Kortleve, D. J., Korteland-van Male, A. M., El Aidy, S., van Lierop, P. P. E., Kleerebezem, M., Groeneweg, M., Kraal, G., Elink-Schuurman, B. E., de Jongste, J. C., Nieuwenhuis, E. E. S., & Samsom, J. N. (2015). Human buccal epithelium acquires microbial hyporesponsiveness at birth, a role for secretory leukocyte protease inhibitor. Gut, 64(6), 884-893.
Pusceddu, M. M., El Aidy, S., Crispie, F., O'Sullivan, O., Cotter, P., Stanton, C., Kelly, P., Cryan, J. F., & Dinan, T. G. (2015). N-3 Polyunsaturated Fatty Acids (PUFAs) Reverse the Impact of Early-Life Stress on the Gut Microbiota. PLoS ONE, 10(10), Article e0139721.
El Aidy, S., van den Bogert, B., & Kleerebezem, M. (2015). The small intestine microbiota, nutritional modulation and relevance for health. Current Opinion in Biotechnology, 32, 14-20.


El Aidy, S., Dinan, T. G., & Cryan, J. F. (2014). Immune modulation of the brain-gut-microbe axis. Frontiers in Microbiology, 5, Article 146.
El Aidy, S., Derrien, M., Aardema, R., Hooiveld, G., Richards, S. E., Dane, A., Dekker, J., Vreeken, R., Levenez, F., Doré, J., Zoetendal, E. G., van Baarlen, P., & Kleerebezem, M. (2014). Transient inflammatory-like state and microbial dysbiosis are pivotal in establishment of mucosal homeostasis during colonisation of germ-free mice. Beneficial microbes, 5(1), 67-77.


El Aidy, S., Derrien, M., Merrifield, C. A., Levenez, F., Doré, J., Boekschoten, M. V., Dekker, J., Holmes, E., Zoetendal, E. G., van Baarlen, P., Claus, S. P., & Kleerebezem, M. (2013). Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon. The ISME journal, 7(4), 743-755.
El Aidy, S., Van den Abbeele, P., Van de Wiele, T., Louis, P., & Kleerebezem, M. (2013). Intestinal colonization: how key microbial players become established in this dynamic process: microbial metabolic activities and the interplay between the host and microbes. BioEssays, 35(10), 913-923.
El Aidy, S., & Kleerebezem, M. (2013). Molecular signatures for the dynamic process of establishing intestinal host-microbial homeostasis: potential for disease diagnostics? Current opinion in gastroenterology, 29(6), 621-627.
Van den Abbeele, P., Verstraete, W., El Aidy, S., Geirnaert, A., & Van de Wiele, T. (2013). Prebiotics, faecal transplants and microbial network units to stimulate biodiversity of the human gut microbiome. Microbial Biotechnology, 6(4), 335-340.
El Aidy, S., Hooiveld, G., Tremaroli, V., Bäckhed, F., & Kleerebezem, M. (2013). The gut microbiota and mucosal homeostasis: colonized at birth or at adulthood, does it matter? Gut Microbes, 4(2), 118-124.
El Aidy, S., Merrifield, C. A., Derrien, M., van Baarlen, P., Hooiveld, G., Levenez, F., Dore, J., Dekker, J., Holmes, E., Claus, S. P., Reijngoud, D.-J., & Kleerebezem, M. (2013). The gut microbiota elicits a profound metabolic reorientation in the mouse jejunal mucosa during conventionalisation. Gut, 62(9), 1306-1314.


El Aidy, S., van Baarlen, P., Derrien, M., Lindenbergh-Kortleve, D. J., Hooiveld, G., Levenez, F., Dore, J., Dekker, J., Samsom, J. N., Nieuwenhuis, E. E. S., & Kleerebezem, M. (2012). Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice. Mucosal immunology, 5(5), 567-579.
El Aidy, S., Kunze, W., Bienenstock, J., & Kleerebezem, M. (2012). The microbiota and the gut-brain axis: insights from the temporal and spatial mucosal alterations during colonisation of the germfree mouse intestine. Beneficial microbes, 3(4), 251-259.


Van den Abbeele, P., Gérard, P., Rabot, S., Bruneau, A., El Aidy, S., Derrien, M., Kleerebezem, M., Zoetendal, E. G., Smidt, H., Verstraete, W., Van de Wiele, T., & Possemiers, S. (2011). Arabinoxylans and inulin differentially modulate the mucosal and luminal gut microbiota and mucin-degradation in humanized rats. Environmental Microbiology, 13(10), 2667-2680.


Booijink, C. C. G. M., El-Aidy, S., Rajilić-Stojanović, M., Heilig, H. G. H. J., Troost, F. J., Smidt, H., Kleerebezem, M., De Vos, W. M., & Zoetendal, E. G. (2010). High temporal and inter-individual variation detected in the human ileal microbiota. Environmental Microbiology, 12(12), 3213-3227.
Van den Abbeele, P., Grootaert, C., Marzorati, M., Possemiers, S., Verstraete, W., Gerard, P., Rabot, S., Bruneau, A., El Aidy, S., Derrien, M., Zoetendal, E., Kleerebezem, M., Smidt, H., & Van de Wiele, T. (2010). Microbial Community Development in a Dynamic Gut Model Is Reproducible, Colon Region Specific, and Selective for Bacteroidetes and Clostridium Cluster IX. Applied and environmental microbiology, 76(15), 5237-5246.
Last modified:09 June 2023 8.36 p.m.