Publications
^{_{Microbiome Science}}

Ruaud, A.; Pfister, N.; Ley, R.; Youngblut, N.: Interpreting tree ensemble machine learning models with endoR. PLoS Computational Biology 18 (12), e1010714 (2022)

Barnett, S.; Youngblut, N.; Buckley, D.: Bacterial community dynamics explain carbon mineralization and assimilation in soils of different land-use history. Environmental Microbiology 24 (11), pp. 5230 - 5247 (2022)

Wilhelm, R.; Barnett, S.; Swenson, T.; Youngblut, N.; Koechli, C.; Bowen, P.; Northen, T.; Buckley, D.: Tracing carbon metabolism with stable isotope metabolomics reveals the legacy of diverse carbon sources in soil. Applied and Environmental Microbiology 88 (22), e0083922 (2022)

Welter, D.; Ruaud, A.; Henseler, Z.; De Jong, H.; van Coeverden de Groot, P.; Michaux, J.; Gormezano, L.; Waters, J.; Youngblut, N.; Ley, R.: Free-living psychrophilic bacteria of the genus Psychrobacter are descendants of pathobionts. mSystems (accepted)

Suzuki, T.; Fitzstevens, J.; Schmidt, V.; Enav, H.; Huus, K.; Mbong Ngwese, M.; Grießhammer, A.; Pfleiderer, A.; Adegbite, B.; Zinsou, J. et al.; Esen, M.; Velavan, T.; Adegnika, A.; Song, L.; Spector, T.; Muehlbauer, A.; Marchi, N.; Kang, H.; Maier, L.; Blekhman, R.; Ségurel, L.; Ko, G.; Youngblut, N.; Kremsner, P.; Ley, R.: Codiversification of gut microbiota with humans. Science 377 (6612), pp. 1328 - 1332 (2022)

Youngblut, N.; de la Cuesta-Zuluaga, J.; Ley, R.: Incorporating genome-based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes. Environmental Microbiology 24 (9), pp. 3966 - 3984 (2022)

Heaver, S.; He, H.; Tang, P.; Baslé, A.; Barone, C.; Vu, D.; Waters, J.; Marles-Wright, J.; Johnson, E.; Campopiano, D. et al.; Ley, R.: Characterization of inositol lipid metabolism in gut-associated Bacteroidetes. Nature Microbiology 7 (7), pp. 986 - 1000 (2022)

Andrade-Martínez, J.; Camelo Valera, L.; Chica Cárdenas , L.; Forero-Junco, L.; López-Leal, G.; Moreno-Gallego, J.; Rangel-Pineros, G.; Reyes, A.: Computational Tools for the Analysis of Uncultivated Phage Genomes. Microbiology and Molecular Biology Reviews 86 (2), e0000421 (2022)

Enav, H.; Bäckhed, F.; Ley, R.: The developing infant gut microbiome: A strain-level view. Cell Host & Microbe 30 (5), pp. 627 - 638 (2022)

Laloum, E.; Cattan-Tsaushu, E.; Schwartz, D.; Shaalan, H.; Enav, H.; Kolan, D.; Avrani, S.: Isolation and characterization of a novel Lambda-like phage infecting the bloom-forming cyanobacteria Cylindrospermopsis raciborskii. Environmental Microbiology 24 (5), pp. 2435 - 2448 (2022)

Chassaing, B.; Compher, C.; Bonhomme, B.; Liu, Q.; Tian, Y.; Walters, W.; Nessel, L.; Delaroque, C.; Hao, F.; Gershuni, V. et al.; Chau, L.; Ni, J.; Bewtra, M.; Albenberg, L.; Bretin, A.; McKeever, L.; Ley, R.; Patterson, A.; Wu, G.; Gewirtz, A.; Lewis, J.: Randomized Controlled-Feeding Study of Dietary Emulsifier Carboxymethylcellulose Reveals Detrimental Impacts on the Gut Microbiota and Metabolome. Gastroenterology 162 (3), pp. 743 - 756 (2022)

Ataeian, M.; Liu, Y.; Kouris, A.; Hawley, A.; Strous, M.: Ecological Interactions of Cyanobacteria and Heterotrophs Enhances the Robustness of Cyanobacterial Consortium for Carbon Sequestration. Frontiers in Microbiology 13, 780346 (2022)

Beckman, E.; Martins, F.; Suzuki, T.; Bi, K.; Keeble, S.; Keeble, J.; Chavez, A.; Ballinger, M.; Agwamba, K.; Nachman, M.: The genomic basis of high-elevation adaptation in wild house mice (Mus musculus domesticus) from South America. Genetics 220 (2), iyab226 (2022)

Marsh, J.; Ley, R.: Microbiome engineering: Taming the untractable. Cell 185 (3), pp. 416 - 418 (2022)

Suzuki, T.; Ley, R.: Microbes set the (woodrat) menu: Host genetics control diet-specific gut microbes. Proceedings of the National Academy of Sciences of the United States of America 119 (2), e2120125118 (2022)

Wang, S.; Sun, P.; Zhang, G.; Grey, N.; Dolfing, J.; Esquivel-Elizondo, S.; Peñuelas, J.; Wu, Y.: Contribution of periphytic biofilm of paddy soils to carbon dioxide fixation and methane emissions. The Innovation 3 (1), 100192 (2022)

Clasen, S.: Silent Recognition of Flagellins from Human Gut Commensal Bacteria by Toll-like Receptor 5. In 8th Conference on Beneficial Mirobes. 8th Conference on Beneficial Mirobes, Madison, WI, USA, July 10, 2022 - July 14, 2022. (2022)

Huus, K.: From famine to fever: immunity, diet, and the microbiome. University of Ottawa: Special Seminar Series on Microbiomes, Ottawa, Canada (2022)

Ley, R.: Silent Recognition of Flagellins from Human Gut Commensal Bacteria by Toll-Like Receptor 5. Keystone Symposia: Novel Approaches Against Emerging Antimicrobial Resistance (RQ4), Banff, AB, Canada (2022)

Suzuki, T.: Codiversification of gut microbiota with humans. Keystone Symposia: Novel Approaches Against Emerging Antimicrobial Resistance (RQ4), Banff, AB, Canada (2022)