Publications

Here is a list of all our publications, including both pre-prints and peer-reviewed articles. If you have any questions or need access to any of our work, please contact us!

2024

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. https://doi.org/10.1007/s12602-024-10219-1

2023

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. https://doi.org/10.1002/ejoc.202201446
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), e0033223. https://doi.org/10.1128/msystems.00332-23 Download
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), 2232506. https://doi.org/10.1080/19490976.2023.2232506 Download
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), 53. https://doi.org/10.1186/s12866-023-02791-3
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), e3011. https://doi.org/10.1002/brb3.3011
Waclawiková, B., Telles de Souza, P. C., 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), 2154544. https://doi.org/10.1080/19490976.2022.2154544

2022

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(8), 1873-1882. https://doi.org/10.1038/s41396-022-01240-9
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), 2081476. https://doi.org/10.1080/19490976.2022.2081476
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. https://doi.org/10.1016/j.jpsychires.2022.05.011
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). https://doi.org/10.1136/jitc-2022-004717
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 & medicine, 188, 287-297. https://doi.org/10.1016/j.freeradbiomed.2022.06.235
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), 1997296. https://doi.org/10.1080/19490976.2021.1997296
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), e0119121. https://doi.org/10.1128/msystems.01191-21

2021

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 (Basel, Switzerland), 14(8). https://doi.org/10.3390/ph14080733
Bunt, D. V., Minnaard, A. J., & El Aidy, S. (2021). Potential Modulatory Microbiome Therapies for Prevention or Treatment of Inflammatory Bowel Diseases. Pharmaceuticals (Basel, Switzerland), 14(6). https://doi.org/10.3390/ph14060506
Jansma, J., & El Aidy, S. (2021). Understanding the host-microbe interactions using metabolic modeling. Microbiome, 9(1), 16. https://doi.org/10.1186/s40168-020-00955-1
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 & Biological Psychiatry, 106, 110169. https://doi.org/10.1016/j.pnpbp.2020.110169
Kiewiet, M. B. G., Elderman, M. E., El Aidy, S., 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, 65(4), e2000390. https://doi.org/10.1002/mnfr.202000390
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., El Aidy, S., 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), e13655. https://doi.org/10.1111/apha.13655
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. https://doi.org/10.1371/journal.pbio.3001070
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), 115. https://doi.org/10.1038/s41531-021-00260-0

2020

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. https://doi.org/10.1007/s10571-019-00772-7
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), e12920. https://doi.org/10.1111/jsr.12920
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.e6. https://doi.org/10.1016/j.cub.2020.07.044
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), 137. https://doi.org/10.1186/s12915-020-00876-3

2019

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. https://doi.org/10.1017/S0140525X18002777
Aresti Sanz, J., & El Aidy, S. (2019). Microbiota and gut neuropeptides: a dual action of antimicrobial activity and neuroimmune response. Psychopharmacology, 236(5), 1597-1609. https://doi.org/10.1007/s00213-019-05224-0
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. https://doi.org/10.1096/fj.201901433R
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(s2), S359-S370. https://doi.org/10.3233/JPD-191780
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, 1087. https://doi.org/10.3389/fneur.2019.01087
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), 310. https://doi.org/10.1038/s41467-019-08294-y

2018

Baars, A., Oosting, A., Lohuis, M., Koehorst, 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(1), 13426. https://doi.org/10.1038/s41598-018-31695-w
Waclawiková, B., & El Aidy, S. (2018). Role of Microbiota and Tryptophan Metabolites in the Remote Effect of Intestinal Inflammation on Brain and Depression. Pharmaceuticals (Basel, Switzerland), 11(3). https://doi.org/10.3390/ph11030063

2017

Fransen, F., Sahasrabudhe, N. M., Elderman, M., Bosveld, M., El Aidy, S., Hugenholtz, F., Borghuis, T., Kousemaker, B., Winkel, S., van der Gaast-de Jongh, C., de Jonge, M. I., Boekschoten, M. V., Smidt, H., Schols, H. A., & de Vos, P. (2017). β2→1-Fructans Modulate the Immune System In Vivo in a Microbiota-Dependent and -Independent Fashion. Frontiers in Immunology, 8, 154. https://doi.org/10.3389/fimmu.2017.00154
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. https://doi.org/10.3389/fimmu.2017.01385
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, 754. https://doi.org/10.3389/fimmu.2017.00754
Koopman, M., MIDtrauma consortium, & El Aidy, S. (2017). Depressed gut? The microbiota-diet-inflammation trialogue in depression. Current Opinion in Psychiatry, 30(5), 369-377. https://doi.org/10.1097/YCO.0000000000000350
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, 34. https://doi.org/10.3389/fnut.2017.00034

2016

El Aidy, S., Stilling, R., Dinan, T. G., & Cryan, J. F. (2016). Microbiome to Brain: Unravelling the Multidirectional Axes of Communication. Advances in experimental medicine and biology, 874, 301-36. https://doi.org/10.1007/978-3-319-20215-0_15
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, 109-18. https://doi.org/10.1016/j.jpsychires.2016.07.019
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, 4, 124-37. https://doi.org/10.1016/j.ebiom.2015.12.023

2015

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), 954-67. https://doi.org/10.1016/j.clinthera.2015.03.002
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. https://doi.org/10.1016/j.copbio.2014.09.005
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), 527-40. https://doi.org/10.1016/j.immuni.2015.08.011
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), 884-93. https://doi.org/10.1136/gutjnl-2013-306149
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. https://doi.org/10.1371/journal.pone.0142228
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. https://doi.org/10.1371/journal.pone.0139721

2014

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. https://doi.org/10.3920/BM2013.0018
El Aidy, S., Dinan, T. G., & Cryan, J. F. (2014). Immune modulation of the brain-gut-microbe axis. Frontiers in Microbiology, 5, Article 146. https://doi.org/10.3389/fmicb.2014.00146

2013

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), 621-7. https://doi.org/10.1097/MOG.0b013e328365d365
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. https://doi.org/10.1038/ismej.2012.142
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), 118-24. https://doi.org/10.4161/gmic.23362
El Aidy, S., Merrifield, C. A., Derrien, M., van Baarlen, P., Hooiveld, G., Levenez, F., Doré, 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. https://doi.org/10.1136/gutjnl-2011-301955
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), 913-23. https://doi.org/10.1002/bies.201300073
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), 335-40. https://doi.org/10.1111/1751-7915.12049

2012

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), 251-9. https://doi.org/10.3920/BM2012.0042
El Aidy, S., van Baarlen, P., Derrien, M., Lindenbergh-Kortleve, D. J., Hooiveld, G., Levenez, F., Doré, 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), 567-79. https://doi.org/10.1038/mi.2012.32

2011

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), 2667-80. https://doi.org/10.1111/j.1462-2920.2011.02533.x

2010

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), 3213-27. https://doi.org/10.1111/j.1462-2920.2010.02294.x
Van den Abbeele, P., Grootaert, C., Marzorati, M., Possemiers, S., Verstraete, W., Gérard, 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), 5237-46. https://doi.org/10.1128/AEM.00759-10

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