Department for BioMedical Research (DBMR)

Systems biomedicine of cellular development and signaling in health and disease - SBM

Yilmaz Lab

Publications

2023

  1. Marchukov D, Li J, Juillerat P, Misselwitz B, Yilmaz B. (2023). Benchmarking microbial DNA enrichment protocols from human intestinal biopsies. Frontiers in Genetics, 14:1184473.
  2. Jakob, M. O., D. Spari, D. Sanchez Taltavull, L. Salm, B. Yilmaz, R. Doucet Ladeveze, C. Mooser, D. Pereyra, Y. Ouyang, T. Schmidt, I. Mattiola, P. Starlinger, D. Stroka, F. Tschan, D. Candinas, G. Gasteiger, C. S. N. Klose, A. Diefenbach, M. Gomez de Aguero and G. Beldi (2023). ILC3s restrict the dissemination of intestinal bacteria to safeguard liver regeneration after surgery. Cell Report 42(3): 112269.
  3. Spari, D., Zwicky, S.N., Yilmaz, B., Salm, L., Candinas, D., and Beldi, G. (2023). Intestinal dysbiosis as an intraoperative predictor of septic complications: evidence from human surgical cohorts and preclinical models of peritoneal sepsis. Scientific Reports, 13, 22921. 10.1038/s41598-023-49034-z.
  4. Cecchini, L., Barmaz, C., Cea, M.J.C., Baeschlin, H., Etter, J., Netzer, S., Bregy, L., Marchukov, D., Trigo, N.F., Meier, R., et al. (2023). The Bern Birth Cohort (BeBiCo) to study the development of the infant intestinal microbiota in a high-resource setting in Switzerland: rationale, design, and methods. BMC Pediatr 23, 560.
  5. Munjoma, P.T., Chandiwana, P., Wyss, J., Mazhandu, A.J., Jordi, S.B.U., Gutsire, R., Katsidzira, L., Yilmaz, B*., Misselwitz, B., and Duri, K. (2023). Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance. Frontiers in immunology 14, 1280262
  6. Remund B, Yilmaz B, Sokollik C. (2023), D-Lactate: Implications for Gastrointestinal Diseases. Children (Basel) 10(6).
  7. Birchenough, G.M.H., Schroeder, B.O., Sharba, S., Arike, L., Recktenwald, C.V., Puertolas-Balint, F., Subramani, M.V., Hansson, K.T., Yilmaz, B., Linden, S.K., et al. (2023). Muc2-dependent microbial colonization of the jejunal mucus layer is diet sensitive and confers local resistance to enteric pathogen infection. Cell Report 42, 112084.
  8. Papotto, P.H., Yilmaz, B., Pimenta, G., Mensurado, S., Cunha, C., Fiala, G., da Costa, D.G., Gonçalves-Sousa, N., Chan, B.H.K., Blankenhaus, B., Carvalho, T., Macpherson, A.J., Allen, J.E., Silva-Santos, B., (2023). Maternal γδ T cells shape offspring pulmonary type-2 immunity in a microbiota-dependent manner. Cell Report 112074.
  9. Chandiwana, P., Munjoma, P.T., Mazhandu, A.J., Li, J., Baertschi, I., Wyss, J., Jordi, S.B.U., Mazengera, L.R., Yilmaz, B., Misselwitz, B., et al. (2023). Antenatal gut microbiome profiles and effect on pregnancy outcome in HIV infected and HIV uninfected women in a resource limited setting. Bmc Microbiol 23, 4.

2022

  1. Yilmaz, B.*, T. Fuhrer, D. Morgenthaler, N. Krupka, D. Wang, D. Spari, D. Candinas, B. Misselwitz, G. Beldi, U. Sauer and A. J. Macpherson (2022). Plasticity of the adult human small intestinal stoma microbiota. Cell host & microbe 30, 1773-1787 e1776.
  2. Macpherson, A. J. and Yilmaz, B. (2022). Microbial drivers of DSS variability. Nature Microbiology, 7(4): 478-479.
  3. Kocaefe-Ozsen, N.*, Yilmaz, B.*, Alkim, C., Arslan, M., Topaloglu, A., Kisakesen, H.L.B., Gulsev, E., and Cakar, Z.P. (2022). Physiological and Molecular Characterization of an Oxidative Stress-Resistant Saccharomyces cerevisiae Strain Obtained by Evolutionary Engineering. Front Microbiol 13, 822864. * co-first author
  4. Rohm, T. V., L. Keller, A. J. T. Bosch, S. AlAsfoor, Z. Baumann, A. Thomas, S. J. Wiedemann, L. Steiger, E. Dalmas, J. Wehner, L. Rachid, C. Mooser, Yilmaz, B. N. Fernandez Trigo, A. J. Jauch, S. Wueest, D. Konrad, S. Henri, J. H. Niess, P. Hruz, S. C. Ganal-Vonarburg, J. Roux, D. T. Meier and C. Cavelti-Weder (2022). Targeting colonic macrophages improves glycemic control in high-fat diet-induced obesity. Communications Biology (Nature) 5(1): 370.
  5. Mossad, O., B. Batut, Yilmaz, B., N. Dokalis, C. Mezo, E. Nent, L. S. Nabavi, M. Mayer, F. J. M. Maron, J. M. Buescher, M. G. de Aguero, A. Szalay, T. Lammermann, A. J. Macpherson, S. C. Ganal-Vonarburg, R. Backofen, D. Erny, M. Prinz and T. Blank (2022). "Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N(6)-carboxymethyllysine." Nat Neuroscience 25(3): 295-305.
  6. Chandiwana, P., P. T. Munjoma, A. J. Mazhandu, L. R. Mazengera, B. Misselwitz, S. B. U. Jordi, Yilmaz, B., and K. Duri (2022). "Antenatal and postpartum immunological markers levels in women with HIV infection and malnutrition in a low resource setting: A pilot study. European Journal of Inflammation 20: 1721727X221139261.
  7. Sudworth, A., Segers, F.M., Yilmaz, B., Guslund, N.C., Macpherson, A.J., Dissen, E., Qiao, S.W., and Inngjerdingen, M. (2022). Innate lymphoid cell characterization in the rat and their correlation to gut commensal microbes. Eur J Immunol
  8. Romano Schneider, Marko Kraljević, Ralph Peterli, Theresa V. Rohm, Angela J.T. Bosch, Andy J.Y. Low, Lena Keller, Shefaa AlAsfoor, Simon Häfliger, Yilmaz, B., Caspar J. Peterson, Ioannis I. Lazaridis, Pascale Vonaesch, Tarik Delko, Claudia Cavelti-Weder, (2022) Roux-en-Y gastric bypass with a long compared to a short biliopancreatic limb improves weight loss and glycemic control in obese mice: Long vs. short biliopancreatic limb gastric bypass in mice, Surgery for Obesity and Related Diseases, 18(11):1286-1297
  9. Jordi, S. B. U., B. M. Lang, J. Wyss, B. Auschra, Yilmaz, B., N. Krupka, T. Greuter, P. Schreiner, L. Biedermann, M. Preisig, R. von Kanel, G. Rogler, S. Begre, B. Misselwitz and I. B. D. c. s. g. Swiss (2022). The personality traits activity, self-reproach, and negative affect jointly predict clinical recurrence, depressive symptoms, and low quality of life in inflammatory bowel disease patients. Journal of Gastroenterology 57(11): 848-866.
  10. Fregolente, L. G., J. D. Warncke, J. Van der Meer, M. Schmidt, R. Khatami, A. J. Macpherson, Yilmaz, B., C. L. A. Bassetti and S. Investigators (2022). Sphyncs: Gut Microbiota Composition Is Different in Narcolepsy Type 1 and Narcolepsy Borderland. Sleep Medicine 100: S167-S167.

2021

  1. *Papotto, P.H., *Yilmaz, B. & Silva-Santos, (2021), B. Crosstalk between γδ T cells and the microbiota. Nature Microbiology https://doi.org/10.1038/s41564-021-00948-2, *Co-first author (Perspective)
  2. *Yilmaz, B., *Mooser, C., *Keller, I., et al. (2021), Long-term evolution and short-term adaptation of microbiota strains and sub-strains Cell Host and Microbe, 29, 650–663 (peer-reviewed original research papers)
  3. Singh, S., Thompson, J., Yilmaz, B., et al., (2021) Loss of α-gal during primate evolution enhanced antibody-effector function and resistance to bacterial sepsis. Cell Host Microbe, 29, 347–36 (peer-reviewed original research papers)
  4. Singh, S., Bastos-Amador, P., Thompson, J., Truglio, M., Yilmaz, B., et al., (2021) Glycan-based shaping of the microbiota during primate evolution. eLife 2021;10:e67450 (peer-reviewed original research papers)
  5. Sanchez-Taltavull D, Castelo-Szekely V, Murugan S, Hamley JID, Rollenske T, Ganal-Vonarburg SC, Büchi I, Keogh A, Li H, Salm L, Spari D, Yilmaz B, Zimmermann J, Gerfin M, Roldan E, Beldi G; UVCM-COVID researchers. (2021), Regular testing of asymptomatic healthcare workers identifies cost-efficient SARS-CoV-2 preventive measures. PLoS One. 5;16(11):e0258700. (peer-reviewed original research papers)
  6. Denoth, L., Juillerat, P., Kremer, A.E., Rogler, G., Scharl, M., Yilmaz, B. *, Bluemel, S.*, and Study, o.b.o.t.S.I.C. (2021). Modulation of the Mucosa-Associated Microbiome Linked to the PTPN2 Risk Gene in Patients with Primary Sclerosing Cholangitis and Ulcerative Colitis. Microorganisms 9, 1752., *Senior co-last author (peer-reviewed original research papers)
  7. Juanola, O., Hassan, M., Kumar, P., Yilmaz, B., et al. (2021). Intestinal microbiota drives cholestasis-induced specific hepatic gene expression patterns. Gut Microbes 13, 1–20.  (peer-reviewed original research papers)
  8. *Yilmaz, B., et al., (2021). Pilot Sub-Study of the Effect of Hepatitis C Cure by Glecaprevir and Pibrentasvir on the Gut Microbiome of Patients with Chronic Hepatitis C Genotypes 1 to 6 in the Mythen Study, Pharmaceuticals, 16;14(9):931, *Corresponding author (peer-reviewed original research papers)
  9. Caparrós E, Wiest R, Scharl M, Rogler G, Gutiérrez Casbas A, Yilmaz B, Wawrzyniak M, Francés R. (2021), Dysbiotic microbiota interactions in Crohn's disease. Gut Microbes. 13(1):1949096. (review)
  10. Dietmann A, Wenz E, Meer J, Ringli M, Warncke JD, Edwards E, Schmidt MH, Bernasconi CA, Nirkko A, Strub M, Miano S, Manconi M, Acker J, Manitius, S., Baumann, C., Valko, P.O., Yilmaz, B., et al., (2021), The Swiss Primary Hypersomnolence and Narcolepsy Cohort study (SPHYNCS): Study protocol for a prospective, multicentre cohort observational study. J Sleep Res, 2021;00:e13296.
  11. Zhang, Y., Feng, L., Wang, X., Fox, M., Luo, L., Du, L., Chen, B., Chen, X., He, H., Zhu, S., Hu, Z., Chen, S., Long, Y., Zhu, Y. Xu, L., Deng, Y., Misselwitz, B., Lang, B.M., Yilmaz, B., Kim, J.J., Owyang, C., Dai, N., (2021), Low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols diet compared with traditional dietary advice for diarrhea-predominant irritable bowel syndrome: a parallel-group, randomized controlled trial with analysis of clinical and microbiological factors associated with patient outcomes. Am J Clin Nutrition doi:10.1093/ajcn/nqab005 (peer-reviewed original research papers)
  12. Rogler, G., Scharl, M., Spalinger, M., Yilmaz, B., et al., (2021), Diet and Inflammatory Bowel Disease: What Quality Standards Should Be Applied in Clinical and Laboratory Studies? Mol Nutr Food Res 2000514 (review)
  13. Obata, Y., Boeing, S., Castaño, A., Bon-Frauches, A.C., Gomez de Agüero, M., Boesmans, W., Yilmaz, B., et al, (2020), Neuronal programming by microbiota enables environmental regulation of intestinal motility, Nature, 578 (7794), 284-289 (peer-reviewed original research papers)

2020

  1. Li, H., Limenitakis, J.P., Greiff, V. Yilmaz, B., et al., (2020), Mucosal or systemic microbiota exposures shape the B cell repertoire. Nature, 584, 274–278 (peer-reviewed original research papers)
  2. Humbel, F., J. H. Rieder, Y. Franc, P. Juillerat, M. Scharl, B. Misselwitz, P. Schreiner, S. Begre, G. Rogler, R. von Kanel, Yilmaz, B*., Biedermann, L.* (2020), Association of Alterations in Intestinal Microbiota with Impaired Psychological Function in Patients with IBD in Remission. Clin Gastroenterol Hepatol., *Authors share co-senior and corresponding authorship. (peer-reviewed original research papers)
  3. Mezo, C., N. Dokalis, O. Mossad, O. Staszewski, J. Neuber, Yilmaz, B., et al., (2020), Different effects of constitutive and induced microbiota modulation on microglia in a mouse model of Alzheimer's disease. Acta Neuropat Commun 8(1): 119. (peer-reviewed original research papers)
  4. Katsidzira, L., Mudombi, W.F., Makunike-Mutasa, R., Yilmaz, B., Blank, A., Rogler, G., Macpherson, A., Vavricka, S., Gangaidzo, I., and Misselwitz, B. (2020), Inflammatory bowel disease in sub-Saharan Africa: a protocol of a prospective registry with a nested case-control study. BMJ Open 10, e039456.
  5. Schreiner P, Rossel J, Biedermann L, Valko PO, Baumann CR, Greuter T, Scharl M, Vavricka SR, Pittet V, Juillerat P, Rogler G, Känel R von, Misselwitz B., et al., (2020), Fatigue in inflammatory bowel disease and its impact on daily activities. Aliment Pharm Therap. 2020:00:1-12 (peer-reviewed original research papers)

2019

  1. Yilmaz, B., et al. (2019), Microbial network disturbances in relapsing refractory Crohn’s disease, Nature Medicine, 25, 323–336 (peer-reviewed original research papers)
  2. Yilmaz, B., et al., (2019), The Intestinal Universe—Full of Gut Heroes Who Need Sidekicks, Frontiers for Young Minds, 7(111), 1-8 *Corresponding author (review)
  3. Sorribas, M., Jakob, M.O., Yilmaz, B., et al., (2019), FxR-modulates the gut-vascular barrier by regulating the entry sites for bacterial translocation in experimental cirrhosis, Journal of Hepatology, 2019 Dec;71(6):1126-1140 (peer-reviewed original research papers)
  4. Schreiner, P., Yilmaz, B., et al., (2019), Vegetarian or gluten-free diets in patients with inflammatory bowel disease are associated with lower psychological well-being and a different gut microbiota, but no beneficial effects on the course of the disease, United European Gastroenterology Journal, 0(0) 1–15.  (peer-reviewed original research papers)

2018 and earlier

  1. Yilmaz, B., Schibli, S., Macpherson, A. J., Sokollik, C., (2018), Suppression of D-Lactic acidosis crisis via administration of probiotics, Pediatrics, 42 (3): e20180337 (peer-reviewed original research papers)
  2. Yilmaz, B., et al., (2018), The presence of genetic risk variants within PTPN2 and PTPN22 shape intestinal microbiota composition and disease severity in IBD patients, PLoSOne, 13(7): e0199664. (peer-reviewed original research papers)
  3. Yilmaz, B.*, Hai, L., (2018) Gut microbiota and Iron: The crucial actors in health and disease, Pharmaceuticals, 11(4), 98 *Corresponding author (review)
  4. Macpherson, A. J., Yilmaz, B., et al., (2018), IgA Function in Relation to the Intestinal Microbiota. Annual Reviews in Immunology 36, 359–381 (review)
  5. Macpherson, A. J. & Yilmaz, B. (2018). Antibodies that lIgAte our intestinal microbes, Science Immunology 3, eaat4037 (commentaries)
  6. Arslan, M., Yildiz, B., Yilmaz, B., et al. (2018), An improved semi-quantitative spot assay to analyse chronological lifespan in yeast, Romanian Biotechnological Letters, 23 (3). (peer-reviewed original research papers)
  7. Uchimura, Y., Fuhrer, T., Li, H., Lawson, M.A., M. Zimmermann, Yilmaz, B., et al., (2018), Antibodies set boundaries limiting microbial metabolite penetration and the resultant mammalian host response, Immunity, 49, 1–15 (peer-reviewed original research papers)
  8. Soares, M.P. & Yilmaz, B*. Microbiota Control of Malaria Transmission, (2015), Trends in Parasitology. 32(2):120-30. *Corresponding author
  9. Yilmaz, B., Bergerson, R., Galson, J., Leventhal, D., RPA. Barbosa, X. Cai (2015), What drives you? Trends in Immunology. 36 (5), 278-279 (commentaries)
  10. Yilmaz, B. Portugal, S., Tran T.M., Gozzelino R., Ramos, S., Gomes, J., Regalado, A., Cowan P.J., d’Apice A.J.F., A.S. Chong, Doumbo O.K., Traore B., Crompton, P.D., Silveira, H., Soares, M.P., (2014), Gut Microbiota Elicits a Protective Immune Response Against Malaria Transmission, Cell. 159; 1277 - 1289.
  11. Vata, C., K., Yilmaz, B., Altintas, A., Sachs, M., Akcetin, Z., Cakar, Z., P., (2008), Combinatorial Data-Mining Using Pdq_Med and Treeview: A Gene-Disease Story, HIBIT 2008: Proceedings of International Symposium on Health Informatics and Bioinformatics, Istanbul, Turkey (conference paper)