Renuka Nayak, MD, PhD

Asst Professor in Residence
+1 415 221-4810 ext. 22398
Research Overview: 

The Nayak Lab studies the human gut microbiome and its impact on the treatment of autoimmune and rheumatic disease. We use cutting-edge technologies, such next-generation sequencing, anaerobic microbiology, metabolomics, gnotobiotics, single-cell phenotyping, and CRISPR to investigate the molecular mechanisms by which microbes impact human health and disease. We are also a translational research lab that obtains and studies patient samples; our goal is make discoveries with strong clinical implications. 

In the Nayak Lab, you can expect to become an expert on multiple of the following skills:

  • Analysis and visualization of large datasets using programming languages such as R
  • Generation and analysis of sequencing libraries, such as metagenomics, transcriptomics and transposon-sequencing libraries
  • In vitro anaerobic microbiology
  • Analytical chemistry, including HPLC, LC-MS, MALDI-TOF and qTOF
  • Gnotobiology and mouse models of autoimmunity
  • Single cell immune profiling
  • Analysis of patient specimens from observational cohorts and interventional studies

We seek to understand the mechanisms by which gut microbes impact the treatment of autoimmune disease using cutting-edge technologies. We strive to advance precision medicine for patients with rheumatic disease.

Primary Thematic Area: 
Secondary Thematic Area: 
Human Genetics
Research Summary: 
Elucidating the impact of the human gut microbiome on the treatment of autoimmune disease. Microbiology, translational studies with human samples, metagenomics, gnotobiotics, metabolomics, immunology.
Mentorship Development: 

2017 - Scientific Leadership and Laboratory Management Course, UCSF
1/2022 - DEI Champion Training
10/2022 - UCSF-TRAIN-UP program (now called Inclusive Research Mentor/Manager Training)
2/2022 - Raising a Resilient Researcher (NIH-OITE)


Simvastatin induces human gut bacterial cell surface genes.

Molecular microbiology

Escalante V, Nayak RR, Noecker C, Babdor J, Spitzer M, Deutschbauer AM, Turnbaugh PJ

Fanning the Flames of Autoimmunity: The Microbiome in Rheumatic Disease.

Arthritis & rheumatology (Hoboken, N.J.)

Nayak RR

Human gut bacterial metabolism drives Th17 activation and colitis.

Cell host & microbe

Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ

Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome.

Cell reports

Lam KN, Spanogiannopoulos P, Soto-Perez P, Alexander M, Nalley MJ, Bisanz JE, Nayak RR, Weakley AM, Yu FB, Turnbaugh PJ