Dan Knights, PhD

Assistant Professor, College of Biological Sciences

Dan Knights

Contact Info


Office Phone 612-564-2762

Lab Phone 612-564-2762

Assistant Professor, College of Biological Sciences

Department of Computer Science and Engineering

Microbiology, Immunology and Cancer Biology (MICaB) Ph.D. Graduate Program

PhD, University of Colorado, Boulder, 2012


Research Summary/Interests

Host-microbiome interactions and computational metagenomics
Our lab finds patterns in microbial community genomics that link to human health. Humans have co-evolved with communities of microbes that protect us from infection by pathogens, aid in the education of our immune systems, and help us extract nutrients from food; yet only through recent advances in DNA sequencing technology have we begun to understand the vast complexity of these communities. The genetics of our microbes are unique to each of us, and yet the mixture of our microbial genes—our microbiome—has been linked to a surprising number of diseases. Human microbiomes are so important to our health that they are sometimes called our “second genome”. Our lab's work applies tools from machine learning to predict health outcomes in multi-omics assays of large patient cohorts and animal models. The methods we are developing will help lay the foundation for developing microbiome-based diagnostics and therapeutics for microbiome-related human diseases.


  • Knights D, Lassen KG, Xavier RJ. 2013. Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome. Gut, 62 (10), 1505-1510.
  • Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, Kau AL, Rich SS, Concannon P, Mychaleckyj JC, Liu J, Houpt E, Li JV, Holmes E, Nicholson J, Knights D, Ursell LK, Knight R, Gordon JI. 2013. Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor. Science, 548-54.
  • Huttenhower C, Gevers D, Knight R, et al. 2012. Structure, Function and Diversity of the Healthy Human Microbiome. Nature 486, 207--214.
  • 2012. The Human Microbiome Consortium. A framework for microbiome research. Nature 486, 215--221.
  • Yatsunenko T, Rey F, Manary M, Trehan I, Dominguez-Bello MG, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Lozupone C, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI. 2012. Human gut microbiome differentiation viewed across age and geography. Nature 486 (7402), 222-227.
  • Wu GD, Chen J, Hoffmann C, Bittinger K, Chen Y, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD. 2011. Linking long-term dietary patterns with gut microbial enterotypes. Science Oct 7;334(6052):105c8.
  • Knights D, Parfrey LW, Zaneveld J, Lozupone C, Knight R. 2011. Human-associated microbial signatures: examining their predictive value. Cell Host & Microbe. Oct 4;10(4):292-6.
  • Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST. 2011. Bayesian community-wide culture-independent microbial source tracking. Nature Methods Jul 17;8(9):761-3.
  • Muegge BD, Kuczynski J, Knights D, Clemente JC, Peña AG, Fontana L, Henrissat B, Knight R, Gordon JI. 2011. Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans. Science May 20; 332(6032):970-974.
  • Werner JJ, Knights D, Garcia ML, Scalfone NB, Smith S, Yarasheski K, Cummings TA, Beers AR, Knight R, Angenent LT. 2011. Bacterial Community Structures are Unique and Resilient in Full-Scale Bioenergy Systems. PNAS 108, 4158-4163.