Program Outcomes

Of the 60 students who have entered the Microbiology and Immunology graduate program over the past 10 years;

  • 33 have graduated
  • 26 students are still in training and on track to finish with their degrees and one changed to another graduate program due to evolving interests

In the past 10 years

  • 100% of predoctoral trainees (39 total) funded by the T32 at least one year during their training in the M&I Program have graduated with a PhD (28), or are on track to complete their degree (11), a retention rate that speaks to the strength of our program
  • the mean time to graduation is 5.91 years and the median is 6.00

The success of the Training Program is evident in the number of students who have gone on to become leading scientists in academia and industry.

Of students who have completed their PhD in the past 10 years

  • 95% are working in STEM-related fields
  • 3 have co-founded successful biotechnology companies; several others are performing postdoctoral research
  • predoctoral graduates have gone on to pursue careers in academic research, consulting, industry, and business intelligence

Of the graduates

  • 30% have started their postdoctoral training after their PhDs
  • 15% have gone on to leadership roles in biotech
  • 50% went on to a career in industry
  • 5% went into regulatory compliance roles for clinical trials


Of the postdoctoral students who have competed their training in the past 10 years, all have been successful in the continuation of their research:

  • 18% have faculty positions
  • 45% have taken a job as scientists in industry
  • 32% are research leadership in industry (CEOs/VP/Director)
    9% are in related areas, such as research imaging

Thus, all of the of trainees are in positions consistent with the mission of our training program.

Accomplishments of Trainees

During the past five years, 20 graduate students and 14 postdocs were supported. The 34 trainees have all published, have manuscripts submitted, or are early in their training.

Overall, the trainees have published well:

  • 33 first-author publications and 117 publications in total
  • Average number of papers published per graduate student is 2.6 (range 0-8 papers); most of these students are still in training
  • Average number of papers published per postdoc is 6.6 (range 3-13 papers)
  • Average number of first author papers published per graduate student is 0.53 (range 0-4 papers) (notable due to the effects of the COVID-19 pandemic combined with 82% of these students still working toward their degree)
  • Average number of first author papers published per postdoc is 2.2(range 0-4 papers); most of these postdocs are still conducting their fellowships

Selected Publications

Our graduate trainees made significant, high impact contributions during the past five years. The following selected papers highlight a few of these important advances:

Shepherd ES, DeLoache WC, Pruss KM, Whitaker WR, Sonnenburg JL. An exclusive metabolic niche enables strain engraftment in the gut microbiota. Nature. 2018 May;557(7705):434-438. doi: 10.1038/s41586-018-0092-4. Epub 2018 May 9. PMID: 29743671; PMCID: PMC6126907.

Lissner MM, Cumnock K, Davis NM, Vilches-Moure JG, Basak P, Navarrete DJ, Allen JA, Schneider D. Metabolic profiling during malaria reveals the role of the aryl hydrocarbon receptor in regulating kidney injury. Elife. 2020 Oct 6;9:e60165. doi: 10.7554/eLife.60165. PMID: 33021470; PMCID: PMC7538157.

Cygan AM, Jean Beltran PM, Mendoza AG, Branon TC, Ting AY, Carr SA, Boothroyd JC. Proximity-Labeling Reveals Novel Host and Parasite Proteins at the Toxoplasma Parasitophorous Vacuole Membrane. mBio. 2021 Dec 21;12(6):e0026021. doi: 10.1128/mBio.00260-21. Epub 2021 Nov 9. PMID: 34749525; PMCID: PMC8576527.

Pruss KM, Sonnenburg JL. C. difficile exploits a host metabolite produced during toxin-mediated disease. Nature. 2021 May;593(7858):261-265. doi: 10.1038/s41586-021-03502-6. Epub 2021 Apr 28. PMID: 33911281; PMCID: PMC9067157.

Davis NM, Lissner MM, Richards CL, Chevée V, Gupta AS, Gherardini FC, Schneider DS. Metabolomic Analysis of Diverse Mice Reveals Hepatic Arginase-1 as Source of Plasma Arginase in Plasmodium chabaudi Infection. mBio. 2021 Oct 26;12(5):e0242421. doi: 10.1128/mBio.02424-21. Epub 2021 Oct 5. PMID: 34607466; PMCID: PMC8546868.

Han S*, Van Treuren W*, Fischer CR, Merrill BD, DeFelice BC, Sanchez JM, Higginbottom SK, Guthrie L, Fall LA, Dodd D, Fischbach MA, Sonnenburg JL. A metabolomics pipeline for the mechanistic interrogation of the gut microbiome. Nature. 2021 Jul;595(7867):415-420. doi: 10.1038/s41586-021-03707-9. PMCID: PMC8939302.

Brewer SM, Twittenhoff C, Kortmann J, Brubaker SW, Honeycutt J, Massis LM, Pham THM, Narberhaus F, Monack DM. A Salmonella Typhi RNA thermosensor regulates virulence factors and innate immune evasion in response to host temperature. PLoS Pathog. 2021 Mar 2;17(3):e1009345. doi: 10.1371/journal.ppat.1009345. PMID: 33651854; PMCID: PMC7954313.

Olm MR*, Dahan D*, Carter MM, Merrill BD, Yu FB, Jain S, Meng X, Tripathi S, Wastyk H, Neff N, Holmes S, Sonnenburg ED, Jha AR, Sonnenburg JL. Robust variation in infant gut microbiome assembly across a spectrum of lifestyles. Science. 2022 Jun 10;376(6598):1220-1223. doi: 10.1126/science.abj2972. Epub 2022 Jun 9. PMID: 35679413.

The following selected papers highlight a few of the important advances made by our postdoctoral trainees over the past five years:

Dovey CM, Diep J, Clarke BP, Hale AT, McNamara DE, Guo H, Brown NW Jr, Cao JY, Grace CR, Gough PJ, Bertin J, Dixon SJ, Fiedler D, Mocarski ES, Kaiser WJ, Moldoveanu T, York JD, Carette JE. MLKL Requires the Inositol Phosphate Code to Execute Necroptosis. Mol Cell. 2018 Jun 7;70(5):936-948.e7. doi: 10.1016/j.molcel.2018.05.010. Epub 2018 Jun 7. PMID: 29883610; PMCID: PMC5994928.

Hryckowian AJ, Van Treuren W, Smits SA, Davis NM, Gardner JO, Bouley DM, Sonnenburg JL. Microbiota-accessible carbohydrates suppress Clostridium difficile infection in a murine model. Nat Microbiol. 2018 Jun;3(6):662-669. doi: 10.1038/s41564-018-0150-6. Epub 2018 Apr 23. PMID: 29686297; PMCID: PMC6126909.

Co JY, Margalef-Català M, Li X, Mah AT, Kuo CJ, Monack DM, Amieva MR. Controlling Epithelial Polarity: A Human Enteroid Model for Host-Pathogen Interactions. Cell Rep. 2019 Feb 26;26(9):2509-2520.e4. doi: 10.1016/j.celrep.2019.01.108. PMID: 30811997; PMCID: PMC6391775.

Brubaker SW, Brewer SM, Massis LM, Napier BA, Monack DM. A Rapid Caspase-11 Response Induced by IFNγ Priming Is Independent of Guanylate Binding Proteins. iScience. 2020 Sep 29;23(10):101612. doi: 10.1016/j.isci.2020.101612. PMID: 33089101; PMCID: PMC7566093.

Davison LM, Alberto AA, Dand HA, Keller EJ, Patt M, Khan A, Dvorina N, White A, Sakurai N, Liegl LN, Vogl T, Jorgensen TN. S100a9 Protects Male Lupus-Prone NZBWF1 Mice From Disease Development. Front Immunol. 2021 Jun 17;12:681503. doi: 10.3389/fimmu.2021.681503. PMID: 34220829; PMCID: PMC8248531.

 Wastyk HC*, Fragiadakis GK*, Perelman D, Dahan D, Merrill BD, Yu FB, Topf M, Gonzalez CG, Van Treuren W, Han S, Robinson JL, Elias JE, Sonnenburg ED, Gardner CD, Sonnenburg JL. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021 Aug 5;184(16):4137-4153.e14. doi: 10.1016/j.cell.2021.06.019. Epub 2021 Jul 12. PMID: 34256014; PMCID: PMC9020749. 

Olm MR*, Dahan D*, Carter MM, Merrill BD, Yu FB, Jain S, Meng X, Tripathi S, Wastyk H, Neff N, Holmes S, Sonnenburg ED, Jha AR, Sonnenburg JL. Robust variation in infant gut microbiome assembly across a spectrum of lifestyles. Science. 2022 Jun 10;376(6598):1220-1223. doi: 10.1126/science.abj2972. Epub 2022 Jun 9. PMID: 35679413.

Guthrie L, Spencer SP, Perelman D, Van Treuren W, Han S, Yu FB, Sonnenburg ED, Fischbach MA, Meyer TW, Sonnenburg JL. Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes. Cell Host Microbe. 2022 Jun 8;30(6):863-874.e4. doi: 10.1016/j.chom.2022.05.003. Epub 2022 May 27. PMID: 35643079; PMCID: PMC9296065