Microbial ecology and evolution of human gut methanogens
Max Planck Insitute for Biology
Faculty in: TIPP
- B.Sc. Biology, Western Illinois University; Macomb, IL, USA, 2004-2008
- Ph.D. Microbiology, The University of Illinois; Urbana-Champaign, IL, USA, 2008-2013
- Post-Doc, Cornell University, NY, USA, 2014-2016
- Group/Project Leader in the Department of Microbiome Sciences since 2016
The overarching goal of our group is to understanding how microbes have adapted to the gut environment and the implications for host health. The taxonomic scope of our work ranges from assessing total microbial community diversity to targeted investigations of particular species. We are particularly focused on Methanobrevibacter smithii, the most prominent archaeon in the human gut. Multiple studies have shown that M. smithii is heritable in humans, suggesting a role for host genetics in the ecology and evolution of the microbe. At a broader taxonomic scale, our group is assessing how vertebrate evolutionary history and ecology explains gut microbial community variation. In the pursuit of our biological goals, we have developed a number of bioinformatic approaches to more efficiently gain insight from next generation sequencing data.
Available PhD Projects in the IMPRS
- Effect of methanogenesis on the metabolic output of microbial communities. In this project, you will design synthetic bacterial communities and test how the addition of methanogenesis impacts their metabolic outputs with comparisons of metabolic models and metabolite measurements. This work will be carried out using bioreactors systems.
- Youngblut, N., J, Reischer, G., Dauser, S., Maisch, S., Walzer, C., Stalder, G., Farnleitner, A., Ley, R. (2020) Vertebrate host phylogeny influences gut archaeal diversity. Nature Microbiology, in press.
- Youngblut, N., Cuesta-Zuluaga, J, Reischer, G., Dauser, S., Schuster, N., Walzer, C., Stalder, G., Farnleitner, A., Ley, R. (2020) Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity. mSystems 5 (6). doi: https://doi.org/10.1128/mSystems.01045-20
- Youngblut, N., Reischer, G., Walters, W., Schuster, N., Walzer, C., Stalder, G., Ley, R., Farnleitner A. (2019) Host Diet and Evolutionary History Explain Different Aspects of Gut Microbiome Diversity among Vertebrate Clades. Nature Communications 10 (1): 2200. doi: https://doi.org/10.1038/s41467-019-10191-3
- Mineeva, O., Rojas-Carulla, M., Ley R., Schölkopf, B., Youngblut, N. (2020). DeepMAsED: Evaluating the Quality of Metagenomic Assemblies. Bioinformatics 36 (10): 3011–17.doi: https://doi.org/10.1093/bioinformatics/btaa124
- Cuesta-Zuluaga, J, Spector, T, Youngblut, N., and Ley, R. (2021) Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut. mSystems 6 (1). doi: https://doi.org/10.1128/mSystems.00939-20