Publications
_{Microbiome Science}

Klag, K.; Ott, D.; Tippetts, S.; Nicolson, R.; Tatum, S.; Bauer, K.; Stephen-Victor, E.; Weis, A.; Bell, R.; Weagley, J. et al.; Maschek, A.; Vu, D.; Heaver, S.; Ley, R.; O'Connell, R.; Holland, W.; Summers, S.; Stephens, W.; Round, J.: Dietary fat disrupts a commensal-host lipid network that promotes metabolic health. Cell Metabolism 38 (1), pp. 157 - 173 (2026)

Liu, Y.; Kiesser, A.; Vadlamani, A.; Kouris, A.; Strous, M.: Exceptionally high carbon fixation and nitrogen assimilation rates in microbial mats of an alkaline soda lake. The ISME Journal 19 (1), wraf226 (2026)

Varvara, R.-A.; Budde, H.; Ley, R.; Vodnar, D.: Optimizing Magnesium Uptake in Lacticaseibacillus Rhamnosus To Advance Nutribiotic Strategies. Current Microbiology 83 (2), 132 (2026)

Lucas, T.; Biehain, U.; Gautam, A.; Gemeinhardt, K.; Lass, T.; Konzalla, S.; Ley, R.; Angenent, L.; Huson, D.: MMonitor: Software for Real-Time Monitoring of Microbial Communities Using Long Reads. Cell Reports Methods Epub ahead (2025)

Ngwese, M.; Adegbite, B.; Zinsou, J.; Fitzstevens, J.; Schmidt, V.; Moure, A.; Maloum, M.; Tyakht, A.; Huus, K.; Youngblut, N. et al.; Kremsner, P.; Adegnika, A.; Ley, R.: Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa. Gut Microbes 17 (1), 2587966 (2025)

Geibel, C.; Schubert, J.; Knoblauch, S.; Hernandez, A.; Boldt, L.; Schneider, D.; Papadopoulos Lambidis, S.; Vitale, G.; Fleischer, J.; Haussmann, M. et al.; Wang, M.; Brötz-Oesterhelt, H.; Petras, D.: High-Frequency Microfluidic Fractionation for Compound-Resolved Bioactivity-Based Metabolomics. Analytical Chemistry 97 (43), pp. 24093 - 24104 (2025)

Fuentes, J.; Singh, S.; Pudlo, N.; Heaver, S.; Ley, R.; Martens, E.: Carbohydrates and the oxidative branch of the pentose phosphate pathway modify Bacteroides thetaiotaomicron phage resistance by phase variable S-layers. Journal of Bacteriology 207 (10), e0017825 (2025)

Siebner, A.; Griesbaum, J.; Huus, K.; Flügge, J.; Hopfensperger, K.; Michel, T.; Schneiderhan-Marra, N.; Sauter, D.; Kremsner, P.; Ley, R. et al.; Dulovic, A.; Esen, M.: Class switch toward IgG2 and IgG4 is more pronounced in BNT162b2 compared to mRNA-1273 COVID-19 vaccinees. International Journal of Infectious Diseases 159, 107990 (2025)

Suzuki, T.; Akbuğa-Schön, T.; Waters, J.; Jakob, D.; Vu, D.; Ballinger, M.; Di Rienzi, S.; Chang, H.; de Araujo, I.; Tyakht, A. et al.; Ley, R.: Selection and transmission of the gut microbiome alone can shift mammalian behavior. Nature Communications 16, 9482 (2025)

Dimore, A.; Kuplicki, R.; McDonald, D.; Kumar, M.; Estaki, M.; Youngblut, N.; Tyakht, A.; Ackermann, G.; Blach, C.; MahmoudianDehkordi, S. et al.; Dunlop, B.; Bhattacharyya, S.; Guinjoan, S.; Mandaviya, P.; Ley, R.; Kaddaruh-Dauok, R.; Paulus, M.; Knight, R.; Alzheimer Gut Microbiome Project Consortium: Medication Use is Associated with Distinct Microbial Features in Anxiety and Depression. Molecular Psychiatry 30 (6), pp. 2545 - 2557 (2025)

Enav, H.; Ley, R.: Tracking gene order provides a new perspective on intraspecific evolution in microbiotas. Nature Biotechnology 43 (5), pp. 698 - 699 (2025)

Enav, H.; Paz, I.; Ley, R.: Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution. Nature Biotechnology 43 (5), pp. 773 - 783 (2025)

Gilbert, J.; Azad, M.; Bäckhed, F.; Blaser, M.; Byndloss, M.; Chiu, C.; Chu, H.; Dugas, L.; Elinav, E.; Gibbons, S. et al.; Gilbert, K.; Henn, M.; Ishaq, A.; Ley, R.; Lynch, S.; Segal, E.; Spector, T.; Strandwitz, P.; Suez, J.; Tropini, C.; Whiteson, K.; Knight, R.: Clinical translation of microbiome research. Nature Medicine 31 (4), pp. 1099 - 1113 (2025)

Kim, S.-G.; Ott, R.; Bretin, A.; Abo, H.; Wang, Y.; Wang, Y.; Winer, S.; Winer, D.; Reddivari, L.; Heaver, S. et al.; Ley, R.; Pellizzon, M.; Ngo, V.; Gewirtz, A.: Wheat Fiber Suppresses Development of Colitis via Microbiota-Mediated Fermentation-Independent Metabolites that Reprogram Intestinal Macrophages. Cell Host & Microbe (accepted)

Rytter, H.; Naimi, S.; Wu, G.; Lewis, J.; Duquesnoy, M.; Vigué, L.; Tenaillon, O.; Belda, E.; Vazquez-Gomez, M.; Touly, N. et al.; Arnone, D.; Hao, F.; Ley, R.; Clément, K.; Peyrin-Biroulet, L.; Patterson, A.; Gewirtz, A.; Chassaing, B.: In vitro microbiota model recapitulates and predicts individualised sensitivity to dietary emulsifier. Gut 74 (5), pp. 761 - 774 (2025)

Winsor, N.; Bayer, G.; Singh, O.; Chan, J.; Li, L.; Lieng, B.; Foerster, E.; Popovic, A.; Tsankov, B.; Maughan, H. et al.; Lemire, P.; Tam, E.; Streutker, C.; Chen, L.; Heaver, S.; Ley, R.; Parkinson, J.; Montenegro-Burke, J.; Birchenough, G.; Philpott, D.; Girardin, S.: Cross-kingdom-mediated detection of intestinal protozoa through NLRP6. Cell Host & Microbe 33 (3), pp. 388 - 407 (2025)

Huus, K.; Ley, R.: Gut bacterial metabolism produces neuroactive steroids in pregnant women. Life Metabolism 3 (6), loae030 (2024)

Noriega Tejada, J.; Walters, W.; Wang, Y.; Kordahi, M.; Chassaing, B.; Pickard, J.; Nunez, G.; Ley, R.; Gewirtz, A.: Prevention and cure of murine C. difficile infection by a Lachnospiraceae strain. Gut Microbes 16 (1), 2392872 (2024)

Chang, H.; Perkins, M.; Novaes, L.; Qian, F.; Zhang, T.; Neckel, P.; Ley, R.; Han, W.; De Araújo, I.: Stress-sensitive neural circuits change the gut microbiome via duodenal glands. Cell 187 (19), pp. 5393 - 5412 (2024)

Maier, L.; Stein-Thoeringer, C.; Ley, R.; Brötz-Oesterhelt, H.; Link, H.; Ziemert, N.; Wagner, S.; Peschel, A.: Integrating research on bacterial pathogens and commensals to fight infections-an ecological perspective. The Lancet Microbe 5 (8), 100843 (2024)