Program Trainees

The M&I Training Program is comprised of research trainees across the microbiology and immunology department promoting excellence in scientific investigation. The program complements the training received by each graduate student and postdoctoral scholar in the department.

Current Trainees


Emma Esterman

Rotating Graduate Student

Miles Tuncel

Rotating Graduate Student

Emma Guiberson, PhD

  • Mentor: Justin Sonnenburg
  • Research: mechanisms of microbiota-host interaction using a variety of approaches including mass spectrometry

Melissa Steele-Ogus, PhD

  • Mentor: Ellen Yeh
  • Research: rhopalodiacean diatoms


Allison Dupzyk, PhD

  • Mentor: Jan Carette
  • Research:  adeno-associated virus (AAV) entry and AAV viral trafficking throughout the host cell

Savannah Lewis

Graduate Student

  • Mentor: Prasanna Jagannathan
  • Interest: development of natural immunity to malaria in individuals living in endemic areas

Nicole Tanenbaum

Graduate Student

  • Mentor: Jan Carette
  • Interest: identifying enterovirus host factors and characterizing the mechanism by which they promote infection

Benjamin Wang, PhD

  • Mentor: Denise Monack
  • Research: mechanisms of Salmonella persistence within macrophages in systemic mouse tissues


Elisa Caffrey

Graduate Student

  • Mentor: Justin Sonnenburg
  • Interest: gut-brain-axis, food fermentation and food-gut microbiome-host interactions

Elysse Grossi-Soyster

Graduate Student

Joy McKenna, PhD

  • Mentor: Denise Monack
  • Researchfocus on how bacterial pathogens, such as Salmonella and Shigella, interact with our cells to cause disease

Ben Waldman, PhD

  • Mentor: Jan Carette
  • Research: host-pathogen interactions, with a particular focus on species-specific defense systems and viral antagonism of those systems


Lily Xu

Graduate Student

  • Mentor: Jan Carette/Wah Chiu
  • Interest: the intersection of virology and structural biology, using single-particle cryo-EM to investigate viral processes in flaviviruses


Isabel Delwel

Graduate Student

  • Mentor: Erin Mordecai
  • Interest: evolution and host virus interactions of positive RNA viruses

Mary DeFeo

Graduate Student

  • Mentor: Dylan Dodd
  • Interest: host and microbial factors that affect heparan sulfate levels and neutrophil antifungal activity in vulvovaginal candidiasis

Leah Guthrie, PhD

  • Mentor: Justin Sonnenburg
  • Research: deciphering microbial hydroxycinnamate metabolism and impact on uremic illness

Youlim Kim

Graduate Student

  • Mentor: Manuel Amieva   
  • Interest: Helicobacter pylori colonization and migration in the gastric epithelium

Matt Olm, PhD

  • Mentor: Justin Sonnenburg
  • Research: the human microbiome and fine-scale microbial population genetics


Phylicia Aaron, PhD

  • Mentor: Elizabeth Egan
  • Research: salmonella enterica serovar-specific biology in the murine gastrointestinal tractRNA virology and disease tolerance and resistance

Oscar Diaz

Graduate Student

  • Mentor: Denise Monack
  • Interest: immune signaling and the bile acid landscape during Salmonella Typhimurium Infecto

Meagan Hamblin

Graduate Student

  • Mentor: Denise Monack
  • Interest: Salmonella enterica serovarspecific molecular host interactions

Alma Mendoza

Graduate Student

  • Mentor: John Boothroyd
  • Interest: translocation of folded proteins across the parasitophorous vacuole membrane

Kimberly Perez, PhD

  • Mentor: Juliana Idoyaga
  • Research: function of dendritic cell subsets during health and disease


Nicole Davis

Graduate Student

Sarah Ruddle

Graduate Student

  • Mentor: Denise Monack
  • Interest: Salmonella typhimurium host interaction

Krystal Thomas-White, PhD

  • Mentor: Denise Monack
  • Research: mechanisms of microbiome-host interactions

James Zengel, PhD

  • Mentor: Jan Carette
  • Research:  the role of host factors that affect the tropism and transduction efficiency of adeno-associated virus (AAV) in vivo, focusing on the role of the AAV receptor (AAVR)



Former Trainees




Kimberly Vasquez, PhD (2022)

Kerwyn Huang

Recent Graduate, currently interviewing

Abel Ferrel, PhD (2022)

John Boothroyd

Staff Research Scientist at Stanford University

Alicja Cygan, PhD (2021)

John Boothroyd

Senior Scientist at Merck

Terence Theisen, PhD (2021)

John Boothroyd

Scientist at Nanostring Technologies

Susan Brewer, PhD (2021)

Denise Monack

Postdoctoral Scholar at University of Washington

Kali Pruss, PhD (2020)

Justin Sonnenburg

Postdoctoral Researcher at Washington University

Michelle Lissner, PhD (2020)

David Schneider

Postdoctoral Researcher at Benaroya Research Institute

Will Van Treuren, PhD (2020)

Justin Sonnenburg

Chief Scientific Officer and Co-Founder at Interface Biosciences

Kyler Lugo, PhD (2020)

Denise Monack

Scientist at Assembly Biosciences

Rachel Hagey, PhD (2018)

Jeffrey Glenn

Research Scientist at Stanford University

Katherine Cumnock, PhD (2018)

David Schneider

Project Leader at Boston Consulting Group

Jillian Lund, PhD (2017)

Peter Sarnow


Caleb Marceau, PhD (2017)

Jan Carette

Sr Research Scientist, Clinical Virology at Gilead

Margaret Nakamoto, PhD (2017)

John Boothroyd

Early Access Program Leader at Scale Biosciences

Elizabeth Shepherd (Stanley), PhD (2017)

Justin Sonnenburg

Co-Founder, Head of People at Novome Biotechnologies

Dinah Proctor, PhD (2016)

David Relman

Postdoctoral Fellow at US National Institutes of Health

Julie Huang, PhD (2016)

Manuel Amieva

Research Scientist at Caribou Biosciences

Sarah Carden, PhD (2016)

Denise Monack

Sr Scientist, Immuno-oncology at Evelo Biosciences

Mara Pavel-Dinu, PhD (2015)

Helen Blau/Matthew Porteus

Instructor, Pediatrics Dept at Stanford University

Sara Bird, PhD (2015)

Karla Kirkegaard

Senior Product Manager at Natera

Harris Feinberg, PhD (2015)

Garry Nolan

President at EBSM Consulting

David Halladin, PhD (2014)

Julie Theriot

Business Intelligence Engineer at Third Sector Intelligence

Jonathan Lynch, PhD (2014)

Justin Sonnenburg

Assistant Project Scientist at UCLA

Jose Antonio Gomez, PhD (2013)

Karla Kirkegaard

Postdoctoral Researcher at UC Davis

Erica Cox, PhD (2013)

Peter Sarnow

Director at Denali Therapeutics

Justine Pompey, PhD (2012)

Upinder Singh

Laboratory Leadership Service Fellow at CDC

Moria Chambers, PhD (2012)

David Schneider

Assistant Professor of Biology at Bucknell University

Leigh Baxt, PhD (2010)

Upinder Singh

Sr Associate Director, Biology at Tri-Institutional Therapeutics Discovery Institute

Susan Vleck, PhD (2010)

Ann Arvin

Asst Director, EH&S Laboratory Chemical & Physical Safety Program at Stanford University

Gwen Liu, PhD (2010)

Chang-Zheng Chen

Sr Manager, Medical Writing at Vir Biotechnology

Robin Trujillo, PhD (2010)

Chang-Zheng Chen

COO at E and M Labs

Tamara Doukas, PhD (2009)

Peter Sarnow

Chief Scientific Officer at Lookout Health

Trever Burgon, PhD (2009)

Karla Kirkegaard

Vice President at QURE Healthcare

Janelle Ayres, PhD (2009)

David Schneider

Professor/Lab Head at Salk Institute for Biological Studies