Kaitlin Flynn

Post-doctoral Research Fellow since 2015

Research areas

  • Colorectal cancer
  • Microbial ecology
  • F. nucleatum
  • C. difficile
  • Translational research


  • BA: Earlham College (2010)
  • PhD: University of Michigan (2015)
Kaitlin Flynn


My research is broadly focused on the gut microbiome and colorectal cancer. It is well-established that perturbances in gut microbial communities can promote tumorigenesis in the colon. My two main projects focus on both on a specific member of the tumor microbial community (Fusobacterium nucleatum) as well as examining the community as a whole spatially in the colon. For the latter project, I’ve teamed up with a gastroenterologist at UM and we are conducting a translational research project examining colonic mucosa microbial communities of the right and left colon. I’m excited by the power of sequencing technologies and bioinformatic tools to probe the microbial ecology of human health and disease.

Papers from time in Schloss lab

  1. Flynn KJ, Baxter NT, Schloss PD. 2016. Metabolic and community synergy of oral bacteria in colorectal cancer. mSphere. 1: e00102-16. DOI: 10.1128/mSphere.00102-16.
  2. Flynn KJ, Ruffin MT IV, Turgeon DK, Schloss PD. 2018. Spatial variation of the native colon microbiota in healthy adults. Cancer Prev Res (Phila). 11: 393-401. DOI: 10.1158/1940-6207.CAPR-17-0370.
  3. Hagan AK, Lesniak NA, Balunas MJ, Bishop L, Close WL, Doherty MD, Elmore AG, Flynn KJ, Hannigan GK, Koumpouras CC, Jenior ML, Kozik AJ, McBride K, Rifkin SB, Stough JMA, Sovacool KL, Sze MA, Tomkovich S, Topçuoğlu BD, Schloss PD. 2020. Ten simple rules to increase computational skills among biologists with Code Clubs. PLOS Computational Biology. 16: e1008119. DOI: 10.1371/journal.pcbi.1008119.
  4. Lesniak NA, Schubert AM, Flynn KJ, Leslie JL, Sinani H, Bergin IL, Young VB, Schloss PD. 2022. The gut bacterial community potentiates Clostridioides difficile infection severity. mBio. DOI: 10.1128/mbio.01183-22.