Hacking the microbiome


Hack·ing [HAK-ing]


1. Writing or refining computer programs skillfully.


2. Seeking and exploiting weaknesses in a complex system in order to change its behavior for one's benefit.


Our computational microbiology lab develops methods that bring precision medicine to the microbiome. We apply those methods to find patterns in microbial communities that predict and diagnose human diseases.


Lab News

Carbon statement


The Knights Lab offsets all carbon emissions for all work-related flights. 

Offsetting your flight's carbon footprint is easy:

  1. Calculate the emissions of your flight per passenger using the ICAO calculator, or use this rule of thumb: a typical round-trip domestic flight emits around 1,000 lbs or less of carbon per passenger; a typical international flight emits around 2,000 lbs or less of carbon per passenger. 

  2. Purchase audited carbon offsets at terrapass.com. Currently this will cost $5 per 1,000 pounds, so $5 for a domestic flight and $10 for an international flight. Make your flight carbon-negative by doubling the amount.

  3. Don't forget to spread the word after you make your purchase!

Dan Knights


Dr. Dan Knights is an Associate Professor in the Department of Computer Science and Engineering and the BioTechnology Institute at the University of Minnesota. He obtained his Ph.D. in Computer Science under Rob Knight and Mike Mozer at the University of Colorado at Boulder, with a certificate in Interdisciplinary Quantitative Biology from the University of Colorado's BioFrontiers Institute. He came to the University of Minnesota from a post-doctoral fellowship in the lab of Ramnik Xavier at Harvard Medical School and the Broad Institute of MIT and Harvard.


Selected publications

Ward TL, Dominguez-Bello MG, Heisel T, Al-Ghalith G, Knights D, Gale CA. Development of the Human Mycobiome over the First Month of Life and across Body Sites. mSystems. 2018 Jun 26;3(3):e00140-17. [article]

Shields-Cutler RR, Al-Ghalith GA, Yassour M, Knights D. SplinectomeR enables group comparisons in longitudinal microbiome studies. Frontiers in microbiology. 2018;9:785. [article]

Ward TL, Knights D, Gale CA. Infant fungal communities: current knowledge and research opportunities. BMC medicine. 2017 Dec 1;15(1):30. [article]

Clayton JB, Vangay P, Huang H, Ward T, Hillmann BM, Al-Ghalith GA, Travis DA, Long HT, Van Tuan B, Van Minh V, Cabana F. Captivity humanizes the primate microbiome. Proceedings of the National Academy of Sciences. 2016 Aug 29:201521835. [article]

Al-Ghalith GA, Montassier E, Ward HN, Knights D. NINJA-OPS: fast accurate marker gene alignment using concatenated ribosomes. PLoS computational biology. 2016 Jan 28;12(1):e1004658. [article]

Livanos AE, Greiner TU, Vangay P, Pathmasiri W, Stewart D, McRitchie S, Li H, Chung J, Sohn J, Kim S, Gao Z. Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice. Nature microbiology. 2016 Aug 22;1:16140. [article]

Maldonado-Gómez MX. Stable engraftment of Bifidobacterium longum AH1206 in the human gut depends on individualized features of the resident microbiome. Cell Host & Microbe. 2016 Oct 12;20(4):515-26. [article]

Knights D, et al. Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome.

Gut, 62 (10), 1505-1510 (2013). [ article ]


Smith MI, et al. Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor.

Science, published online January 30 2013; 10.1126/science.1229000. [ article ]


Huttenhower C, et al. Structure, Function and Diversity of the Healthy Human Microbiome.

Nature 486, 207--214 (2012). [ article ]


Yatsunenko T, et al. Human gut microbiome differentiation viewed across age and geography.

Nature 486 (7402), 222-227. [ article ]


Knights D, et al. Human-associated microbial signatures: examining their predictive value.

Cell Host & Microbe. 2011 Oct 4;10(4):292-6. [ article ]


Knights D, et al. Bayesian community-wide culture-independent microbial source tracking.

Nature Methods 2011 Jul 17;8(9):761-3. [ article ][ software ]


Wu GD, et al. Linking long-term dietary patterns with gut microbial enterotypes.

Science 2011 Oct 7;334(6052):105c8. [ article ]


Join us!


Interested in joining the lab? Contact Dan at dknights@umn.edu.

Want to support our research? Please contact the University of Minnesota Foundation, or give now.



Knights Lab

MCB 6-124

420 Washington Ave SE

Minneapolis, MN 55455

(612) 5-MICROB (612-564-2762)




Dr. Dan Knights is an Associate Professor in the Department of Computer Science and Engineering and the Biotechnology Institute at the University of Minnesota. The Knights lab models host-microbiome interactions in human disease, with labs in Minneapolis and Saint Paul. Knights is a PI with the Minnesota Supercomputing Institute.

© 2013-2014 Knights Lab, University of Minnesota