Program Outcomes

Of the 61 students who have entered the Microbiology and Immunology graduate program over the past 10 years;

  • 28 have graduated and 3 others have successfully completed their oral defense and are completing their written dissertation during a writing quarter.
  • 28 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 (37 total) funded by the T32 at least one year during their training in the M&I Program have graduated with a PhD (24), or are on track to complete their degree (13), a retention rate that speaks to the strength of our program
  • the mean time to graduation is 5.91 years and the median is 5.00
  • indeed we have two eighth-year PhD students, which reflects exceptional personal difficulties during the pandemic. Both of these eighth-year students have successfully completed their oral defense and are completing dissertation writing this quarter. 

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

  • 96% are working in STEM-related fields
  • 2 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

  • 35% have started their postdoctoral training after their PhDs
  • 13% have gone on to leadership roles in biotech
  • 22% went on to a job in industry
  • 9% went into industry
  • 9% went on to an academic research position
  • 8% went on to scientific consulting roles
  • 4% went on to a business intelligence role

As a program and department we are committed to creating a communicative and nurturing environment that promotes kindness, diversity, equity, and inclusion.

The priority of mentors to actively promote a diverse and inclusive work environment and the commitment to fostering a diverse community in which all individuals are welcomed, respected, and supported to achieve their full potential.

We believe that training in science, specifically our network of Stanford Biosciences is the strongest when the trainees feel supported and included while immersed in diversity. We define diversity broadly, at all levels, spanning from ideas to disciplines to technology to, most importantly, people. Embedded firmly within our training program and embraced by all participating faculty are the values of justice, equity, diversity, and inclusion (JEDI). We share these values with the School of Medicine and Stanford University, as a whole. We recognize that to turn those values into practice requires action at every level and that every group, including students, postdoctoral fellows, and faculty must engage with conviction and energy. We, as a graduate program and department, are continually working to integrate culturally aware recruitment, training, mentoring, and career advancement that is individualized. Incoming students arrive with diverse backgrounds, education, and experience and we work to tailor the program outlined below to optimize the training of each student. 


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