Publications
_{Microbiome Science}

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.; 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)

Bryson, A.; Chatterjee, M.; Holdermann, I.; Kirk, C.; Kisker, J.; Simic, I.; Ley, R.; Marsh, J.: Human Gut Microbiome Engineering: Unlocking the Genetic Vault. In SeaWheat COST Action Workshop: Advances in Biome Research of Ulva, p. 32. SeaWheat COST Action Workshop: Advances in Biome Research of Ulva, Faro, Portugal, March 18, 2025 - March 19, 2025. (2025)

Enav, H.: Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution. 5th Ghent Gut Inflammation Group Meeting, Ghent, Belgium (2025)

Huus, K.: Flagellin in the Gut Microbiome is a Diet-Adjustable Adjuvant for Vaccination. BioConnect Seminar: Max Planck Institute for Biology, Tübingen, Germany (2025)

Mbong Ngwese, M.: Expanding the diversity and functional insights of human gut methanogens through cultivation and genomics. BioConnect Seminar: Max Planck Institute for Biology, Tübingen, Germany (2025)

Boudrioua , A.; Coyle, T.; Piselli, C.; Pitotti, G.; Pietsch, M.; Kronenberger, T.; Korotkov, V.; Maier, L.; Flieger, A.; Hartmann, M. et al.; Brönstrup, M.; Wagner, S.: An anti-virulence strategy to treat Salmonella infections: Development of lead compounds targeting the transcriptional regulator HilD. Gemeinsame DGI/DZIF-Tagung 2025, München, Germany (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. (submitted)

Schlaiß, C.; Baur, S.; Marsh, J.; Gemeinhardt, K.; Angenent, L.: Genetic modification of Clostridium kluyveri for heterologous n-butanol and n-hexanol production. (submitted)

Huus, K.; μHEAT Clinical Study Group; Tan, Y.; Abo, H.; Keller, R.; Atay, E.; Vu, D.; Dauser, S.; Prokipchuk, A.; Tyakht, A. et al.; Youngblut, N.; Chassaing, B.; Kang, S.-M.; Parsonnet, J.; Kremsner, P.; Maier, L.; Gewirtz, A.; Esen, M.; Ley, R.: Flagellin in the human gut microbiome is a diet-adjustable adjuvant for vaccination. (submitted)

Makki, K.; Martino, M.; Alberdi, A.; Aizpurua, O.; Quagliariello, A.; Olsson, A.; Clasen, S.; Jonsson, J.; Brolin, H.; Dwibedi, C. et al.; Yang, G.; Favero, C.; Bergh, P.-O.; Schnupf, M.; Ley, R.; Khan, M.-T.; Tremaroli, V.; Backhed, F.: Characterization and description of Clostridium filamentum ETTB, a novel gut bacterium with TLR5 modulating properties. (submitted)

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. (submitted)

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 shifts mammalian behavior. (submitted)