Current Members



Susan Lynch, Ph.D.

Dr. Lynch is an Associate Professor of Medicine, at the University of California San Francisco, where she also Directs the Microbiome Research Core and acts as Associate Director of the Microbiome in Inflammatory Disease Program. Dr. Lynch graduated from University College Dublin and completed her postdoctoral studies at Stanford University. Her laboratory is located in the Division of Gastroenterology, at the University of California San Francisco, Parnassus Campus. 

Post-doctoral Scholars


Julia Durack, Ph.D.

Julia received her Ph.D. in 2010 from University of Tasmania, Australia, where she characterized stress responses  in multiple strains of Listeria monocytogenes; results of these studies have led to improved food preservation techniques in the Australian food industry.  Her  first postdoctoral fellowship with Dr. Daniel Portnoy  in the Department of Molecular and Cell Biology, University of California Berkeley elucidatated the function of the accessory cytosolic motor protein SecA2 in aiding intracellular virulence of L. monocytogenes. In 2013, she joined the Lynch Lab where her primary research focus is aimed at understanding the association of the airway and gastrointestinal microbiota to the pathogenesis of asthma.

Graduate Students


Aaron Chin, B.S.

Aaron is a MD candidate taking a one-year research fellowship funded by the UCSF RAPTR program. He is interested in the investigating the immunomodulatory effect of gut microbes in patients with inflammatory bowel disease.  A native of San Francisco,  Aaron completed his B.S. at UCSB in Molecular Biology/Biochemistry before returning home for medical school. Ultimately he hopes to incorporate microbiome research in his career in medicine.



Sophia Levan, B.A.

Sophia Levan is a MD/PhD candidate. She completed her B.A. at Wesleyan University where she majored in Chemistry and Molecular Biology with a concentration in Biophysics. Following her B.A., Sophia completed a year-long post-baccalaureate at the National Institute on Aging. She joined the MSTP at UCSF in 2013. Sophia’s research focuses on the neonatal gut microbiome,  specifically on identification of microbial products and the host signaling pathways that they modulate; these products may predispose neonates to allergic asthma development in childhood.


Ariane Panzer, B.A.

Ariane is from Austin, Texas, and attended Hampshire College in Amherst, MA where she completed a B.A. with a concentration in molecular biology, epigenetics, and health and society. After college, she worked at the Harvard School of Public Health for one year before moving to San Francisco where she worked in Dr. Lynch's research group for 2.5 years, prior to joining the Biomedical Science graduate program at UCSF. Now in her 2nd year of graduate studies, Ariane has returned to the Lynch lab for her thesis studies which focus on  early life development of the human microbiota and their impact on immune trajectories in the context of childhood allergic asthma.


Elze Rackaityte, B.A.

Elze graduated Wellesley College with a B.A. in Biological Sciences. She then trained at Institut Pasteur in the laboratory of Dr. Jean-Marc Ghigo, studying bacterial biofilms. Currently, she is a graduate student in Biomedical Sciences program at UCSF. Her project, which is co-mentored by Dr. Lynch and Dr. Trevor Burt,  investigates the convergence of gut microbiome and immune development in pre-natal life. In her free time, she enjoys various fermented goods. 


Meera Shenoy, B.S.

Meera completed her B.S. in Microbiology at the University of Washington in 2013, where she identified a single nucleotide polymorphism that regulates expression of the CD1A gene and is associated with active Mycobacterium tuberculosis infection. She also worked on the development of functional gold nanoprobes that assemble intracellularly for targeted bioimaging. Prior to her undergraduate work, she interned at Philips Medical Systems, where she examined the efficacy of cardiopulmonary resuscitation versus immediate automated external defribrillator shocks during cardiac arrest. Currently she is a Ph.D. candidate in the Biomedical Sciences Program at UCSF. Her project focuses on the relationship between airway and gut microbiota in HIV-infected patients with acute pneumonia, and their role in shaping host immune response and clinical outcomes. In her free time, she enjoys blatantly ignoring protocols, i.e. recipes, while cooking.


Germaine Yong, B.S.

Germaine completed her undergraduate studies in Biology at Duke University in 2014, where she investigated the role of microbial communities in marine biofouling. After graduation, she developed a method to measure in vivo growth rates of Candida albicans under the mentorship of Norman Pavelka at the Singapore Immunology Network. She also worked with Chong Yap Seng and Lynette Shek at the Singapore Institute of Clinical Sciences, where she investigated how polyunsaturated fatty acids influenced risk of infections in infants from the "Growing Up in Singapore Towards Health Outcomes" (GUSTO) birth cohort. Germaine joined the Lynch lab in 2016 as a UCSF Biomedical Sciences graduate student. She currently studies the role of the early life gut microbiome in the development of childhood obesity and is interested in using early life nutrition as an effective strategy to alleviate metabolic dysfunction.


Doug Fadrosh, M.S. - Lab Manager

Doug Fadrosh is a Specialist in the Lynch Lab who manages the Microbiome Profiling Services provided by the Lynch Lab and the lab itself.  Doug received his Masters degree in Biotechnology specializing in Biodefense from The Johns Hopkins University and a Bachelors degree in Molecular Biology from Juniata College. He has over 14 years of experience in molecular biology and DNA sequencing technologies settings from his time at The Institute for Genomic Research (TIGR), The J. Craig Venter Institute (JCVI), and the Institute for Genome Sciences (IGS).  Currently Doug is involved in a project that aims to characterize the mycobiota of paired infant gut and built environment (dust) samples and determine their relationships with atopy development at 2 years of age. Doug has been a part of the Lynch Lab since 2013 and his primary interests are DNA sequencing technologies, process optimization and research and development of new technologies. 


Kei Fujimura, Ph.D.

Kei completed her Ph.D. at the University of Northern British Columbia in Dr. Keith Egger's lab examining the effects of climate change on root-associated fungal communities in the Canadian High Arctic (Ellesmere Island). She joined the Lynch Lab in 2008 as a post-doctoral scholar and is now a staff researcher who leads studies focused on environmental and gut microbiota and how their association  with allergy and asthma development in children. She is involved in several birth cohort studies including the MAAP (Microbes, Allergy, Asthma and Pets) and URECA (Urban Environment and Childhood Asthma) studies.


Brandon LaMere, MPH

Brandon graduated from Michigan State in 1999 with a bachelor of science in medical technology and received his MPH in infectious disease from UC Berkeley in 2006. He works on a number of research projects focused on understanding the microbial ecology and molecular basis of immune dysfunction in patients with inflammatory bowel disease.


Din Lin, Ph.D.

Din is an immunologist with extensive experience in human immunology. He previously worked in the McCune lab examining whether induction of tolerance to SIV in utero and/or orally at birth impacts the course of SIV infection after birth in Rhesus macaques. He has also investigated efficacy of immunomodulatory drugs in SIV-infected Rhesus macaques. Most recently, he has developed an ex vivo  assay to test the immunostimulatory capacity of a microbial community. He currently examines immunomodulatory and epigenetic regulatory responses to microbiomes and their products in both humans and mice.


Kole Lynch, B.S.

Kole is originally from Gardnerville, Nevada and grew up skiing the Sierras, camping in the Nevada high desert, and fishing the Truckee River. He attended the University of Nevada, Reno where he completed a dual Bachelor’s of Science in Biochemistry and Microbiology. After graduation, he relocated to the Bay Area to further pursue his goal of applying to medical school. As a Research Associate in the Lynch lab, Kole supports the 16S rRNA sequencing Core where he manages sample processing from DNA extraction all the way to NextGen sequencing. More recently, he has been expanding his skill set by isolating a microbial consortium to investigate its role in chronic allergic disease.  Kole plans to study neurodegenerative disease and how the human microbiome influences the onset of synucleinopathies. 


Katie McCauley, MPH

Katie received her Masters of Public Health degree in Epidemiology/Biostatistics from UC Berkeley, where she focused on international, multi-center studies of childhood leukemia etiology.  She became fascinated by the role of the microbiome in health through her MPH coursework, and joined the Lynch Lab in February 2016. Her work now focuses primarily on longitudinal analyses of airway microbiota from children of diverse backgrounds. Katie also provides occasional statistical guidance for other projects throughout the group


Yvette Piceno, Ph.D.

Yvette obtained her doctoral degree in Biology, having studied the distribution of nitrogen-fixing bacteria in saltmarsh cordgrass rhizospheres along a tidal gradient and the response of the diazotrophs to altering plant resource allocation. She then joined Microbial Insights, Inc., a company specializing in microbial community profiling using molecular techniques, primarily focused within the environmental/bioremediation field. There she lead research for product and market development, as well as directed the molecular facilities. In 2004, Dr. Piceno joined Dr. Gary Andersen’s lab at the Lawrence Berkeley National Laboratory, working on numerous collaborative studies, ranging from ocean systems, oil reservoirs, and rock or agricultural soils, to human gut microbiome studies for chronic kidney disease patients. Yvette recently joined the Lynch Lab (July 2016) and will apply high-throughput sequencing techniques to examine the effects of fecal microbiota transplants for patients diagnosed with Clostridia difficile infections or pouchitis (an infectious state arising after a surgically-created pouch has been formed from ileal gut tissue as part of a treatment for ulcerative colitis or other diseases).



Elle Fukui, B.A.

Elle is a Bay Area native and recent graduate from UC Berkeley majoring in Molecular and Cell Biology with an emphasis in Cell and Developmental Biology. Elle previously worked at Lifelong Medical Care and Health Leads in San Pablo to empower patients from underserved communities to overcome the social barriers to healthcare. Elle joined the Lynch Lab in Spring 2017 due to her strong interest in the gut microbiome and its implications for human disease. She is conducting research under the mentorship of Elze Rackaityte examining the development of the gut microbiome and immune system in pre-natal life. Outside of the lab, Elle enjoys healthy cooking, hiking in redwood forests, listening to Spotify excessively, and reading magical realism novels while aiming for medical school in a few years.