Publications of ND Youngblut

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)

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)

Clasen, S.; Bell, M.; Borbón, A.; Lee, D.-H.; Henseler, Z.; de la Cuesta-Zuluaga, J.; Parys, K.; Zou, J.; Wang, Y.; Altmannova, V. et al.; Youngblut, N.; Weir, J.; Gewirtz, A.; Belkhadir, Y.; Ley, R.: Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5. Science Immunology 8 (79), eabq7001 (2023)

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)

Barnett, S.; Youngblut, N.; Koechli, C.; Buckley, D.: Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling. Proceedings of the National Academy of Sciences of the United States of America 118 (47), e2115292118 (2021)

Youngblut, N.; Reischer, G.; Dauser, S.; Maisch, S.; Walzer, C.; Stalder, G.; Farnleitner, A.; Ley, R.: Vertebrate host phylogeny influences gut archaeal diversity. Nature Microbiology 6 (11), pp. 1443 - 1454 (2021)

Youngblut, N.; Ley, R.: Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets. PeerJ 9, e12198 (2021)

Liu, X.; Sutter, J.; de la Cuesta-Zuluaga, J.; Waters, J.; Youngblut, N.; Ley, R.: Reclassification of Catabacter hongkongensis as Christensenella hongkongensis comb. nov. based on whole genome analysis. International Journal of Systematic and Evolutionary Microbiology 71 (4), 004774 (2021)

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, Psychrotrophic Bacteria of the Genus Psychrobacter Are Descendants of Pathobionts. mSystems 6 (2), e00258-21 (2021)

de la Cuesta-Zuluaga, J.; Spector, T.; Youngblut, N.; Ley, R.: Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut. mSystems 6 (1), e00939-20 (2021)

Youngblut, N.; de la Cuesta-Zuluaga, J.; Reischer, G.; Dauser, S.; Schuster, N.; Walzer, C.; Stalder, G.; Farnleitner, A.; Ley, R.: Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity. mSystems 5 (6), e01045-20 (2020)

Schmidt, V.; Enav, H.; Enav, H.; Spector, T.; Youngblut, N.; Ley, R.: Strain-Level Analysis of Bifidobacterium spp. from Gut Microbiomes of Adults with Differing Lactase Persistence Genotypes. mSystems 5 (5), e00911-20 (2020)

Mineeva, O.; Rojas-Carulla, M.; Ley, R.; Schölkopf, B.; Youngblut, N.: DeepMAsED: evaluating the quality of metagenomic assemblies. Bioinformatics 36 (10), pp. 3011 - 3017 (2020)

de la Cuesta-Zuluaga, J.; Ley, R.; Youngblut, N.: Struo: a pipeline for building custom databases for common metagenome profilers. Bioinformatics 36 (7), pp. 2314 - 2315 (2020)