Publications of RE Ley

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 Epub ahead (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 Epub ahead (2025)

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 Epub ahead (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)

Salazar-Jaramillo, L.; de la Cuesta-Zuluaga, J.; Chica, L.; Cadavid , M.; Ley, R.; Reyes, A.; Escobar, J.: Gut microbiome diversity within Clostridia is negatively associated with human obesity. mSystems 9 (8), e0062724 (2024)

Enav, H.; Ley, R.: Tracking gene order provides a new perspective on intraspecific evolution in microbiotas. Nature Biotechnology Epub ahead (2024)

Enav, H.; Paz, I.; Ley, R.: Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution. Nature Biotechnology Epub ahead (2024)

Mirretta Barone, C.; Heaver, S.; Gruber, L.; Zundel, F.; Vu, D.; Ley, R.: Spatially resolved lipidomics shows conditional transfer of lipids produced by Bacteroides thetaiotaomicron into the mouse gut. Cell Host & Microbe 32 (6), pp. 1025 - 1036 (2024)

Akbuğa-Schön, T.; Suzuki, T.; Jakob, D.; Vu, D.; Waters, J.; Ley, R.: The keystone gut species Christensenella minuta boosts gut microbial biomass and voluntary physical activity in mice. mBio 15 (2), e0283623 (2024)

Walters, W.; Ley, C.; Hastie, T.; Ley, R.; Parsonnet, J.: A modified Michaelis-Menten equation estimates growth from birth to 3 years in healthy babies in the USA. BMC Medical Research Methodology 24 (1), 27 (2024)

Daniel, N.; Wu, G.; Walters, W.; Compher , C.; Ni, J.; Delaroque, C.; Albenberg, L.; Ley, R.; Patterson, A.; Lewis, J. et al.; Gewirtz, A.; Chassaing, B.: Human intestinal microbiome determines individualized inflammatory response to dietary emulsifier carboxymethylcellulose consumption. Cellular and Molecular Gastroenterology and Hepatology 17 (2), pp. 315 - 318 (2024)

de la Cuesta Zuluaga, J.; Huus, K.; Youngblut, N.; Escobar, J.; Ley, R.: Obesity is the main driver of altered gut microbiome functions in the metabolically unhealthy. Gut Microbes 15 (2), 2246634 (2023)

Casini, I.; McCubbin, T.; Esquivel-Elizondo, S.; Luque, G.; Evseeva, D.; Fink, C.; Beblawy, S.; Youngblut, N.; Aristilde, L.; Huson, D. et al.; Dräger, A.; Ley, R.; Marcellin, E.; Angenent, L.; Molitor, B.: An integrated systems-biology approach reveals differences in formate metabolism in the genus Methanothermobacter. iScience 26 (10), 108016 (2023)

Clasen, S.; Ley, R.: Wie der Toll-like-Rezeptor 5 die Immunantwort umgeht. Biospektrum 29 (6), pp. 637 - 639 (2023)

Marsh, J.; Kirk, C.; Ley, R.: Toward Microbiome Engineering: Expanding the Repertoire of Genetically Tractable Members of the Human Gut Microbiome. Annual Review of Microbiology 77, pp. 427 - 449 (2023)

Bretin, A.; Zou, J.; Yeoh, V.; Ngo, V.; Winer, S.; Winer, D.; Reddivari, L.; Pellizzon, M.; Walters, W.; Patterson, A. et al.; Ley, R.; Chassaing, B.; Vijay-Kumar, M.; Gewirtz, A.: Psyllium Fiber Protects Against Colitis Via Activation of Bile Acid Sensor Farnesoid X Receptor. Cellular and Molecular Gastroenterology and Hepatology 15 (6), pp. 1421 - 1442 (2023)

Mineeva, O.; Danciu, D.; Schölkopf, B.; Ley, R.; Rätsch, G.; Youngblut, N.: ResMiCo: increasing the quality of metagenome-assembled genomes with deep learning. PLoS Computational Biology 19 (5), e1011001 (2023)