Computational Microbiology

Quick Guide

• Topic: Human microbiome
• Analyzing previously-collected metagenomics data for new insights
• Requires previous command-line (terminal) coding experience

Introduction to the Human Microbiome and Computational Microbiology

In this research area, you will be studying the human microbiome, the collection of microbes that live on and in the human body. These microbes include bacteria, archaea, fungi, protists, and viruses. The human microbiome is the subject of intense study because disruption of the microbiome has been linked to several diseases and medical conditions, including obesity, anxiety, pathogen infections, immune diseases, and cancer. However, researchers and clinicians are only just beginning to understand the mechanisms underlying those links and are still discovering new relationships between the microbiome and human health. In fact, there are several research labs here on campus at the University of Minnesota actively researching this topic: the Knights Lab, the Blekhman Lab, the Gomez Lab are among them.

In the computational microbiology area of this course you will use your own computer and the supercomputers at the Minnesota Supercomputing Institute (MSI) to analyze microbiome data. Many microbiome research projects, such as the Human Microbiome Project, collect enormous amounts of data about individuals' microbiomes and other information relevant information about the study individuals, such as health status and life history. Students use those published data sets to ask new questions and find unexplored associations between the microbiome and health, geography, physiology, diet, and more. To accomplish this goal, students use advanced data analysis, statistical, and data visualization techniques via the R software environment for statistical computing and graphics. This work involves writing computer code and scripts.

Suggested Background Reading

• Summary of available datasets and the papers that describe them

References for Dataset Papers

• HMP. Structure, function and diversity of the healthy human microbiome. Nature. 2012. 486:207-214.
• Vangay, P. et al. “US Immigration Westernizes the Human Gut Microbiome” Cell, 2018. https://doi.org/10.1016/j.cell.2018.10.029
• Smits SA, et al. Seasonal cycling in the gut microbiome of the Hadza hunter gatherers of Tanzania. Science. 2017. 10.1126
• Charlson ES, et al. Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS ONE. 2010. 5:e15216.
• Gevers D, et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host & Microbe. 2014. 15: 382–392.
• Wu GD, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011. 334: 105-108.
• Yatsunenko T, et al. Human gut microbiome viewed across age and geography. Nature. 2012. 486: 222-228.