Joshua Stough

Post-doctoral Research Fellow since 2018

Research areas


  • BS: Auburn Univeristy (2011)
  • MS: Auburn University (2013)
  • PhD: University of Tennessee Knoxville (2017)
Joshua Stough


During my Master’s and PhD work, I trained amongst microbial ecologists in a broad variety of different environmental ecosystems. As such I have focused less on building expertise in an individual system, and more on developing my own unique approaches to analyzing large sequencing datasets in order to address fundamental ecological questions and propose novel hypotheses that can be tested experimentally. I am interested in the diversity and function of viruses, as well as their contribution the structure and function of microbial communities. I will be working in the Schloss lab to explore some of these ideas as they relate to recurrent Clostridium difficile infection.

Papers from time in Schloss lab

  1. Tomkovich S, Stough JMA, Bishop L, Schloss PD. 2020. The initial gut microbiota and response to antibiotic perturbation influence Clostridioides difficile colonization in mice. mSphere. 5: e00869-20. DOI: 10.1128/mSphere.00869-20.
  2. Stough JMA, Beaudoin AJ, Schloss PD. 2020. Coding-complete RNA virus genomes assembled from murine cecal metatranscriptomes. Microbiology Resource Announcements. 9: e00018-20. DOI: 10.1128/MRA.00018-20.
  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.