Dr. Varun Aggarwala - Jio Institute Skip to main content

Dr. Varun Aggarwala

Assistant Professor, Jio Institute

Dr Varun Aggarwala is an Assistant Professor and Principal Investigator of the Microbiome Therapeutics laboratory at the Jio Institute. 

Varun performed his doctoral research at the Perelman School of Medicine of University of Pennsylvania, focusing on problems related to personalized medicine and genetics. He furthered his training in precision therapeutics at the Icahn School of Medicine of Mount Sinai Hospital, and identified therapeutically relevant commensal gut microbes in lieu of whole stool Facal Transplants for infectious and inflammatory bowel diseases, which are being evaluated in defined clinical trials. 

Previously Varun did his Masters in Computer Science from University of Pennsylvania and has a BTech in Computer Science and Engineering from IIT Guwahati. His honours include the prestigious DBT Ramalingaswami re-entry fellowship, IIT Silver medal and NTSE scholarship from MHRD. 

Now at the Jio Institute, Dr. Aggarwala’s laboratory is modelling microbiome dynamics and in-turn identifying reproducible live bacterial products, ranging from synbiotics to super-donor stool material, for robust and stable engineering of the human microbiome in both health and disease. Varun is committed towards the Atmanirbhar Bharat and Make in India mission, to realise our collective civilizational potential in this Amrit kaal.

  • PhD in Genomics and Computational Biology from University of Pennsylvania, 2016
  • Masters in Computer and Information Science from University of Pennsylvania, 2010
  • B.Tech in Computer Science and Engineering from Indian Institute of Technology Guwahati 2008


  • PI for DBT Ramalingaswami re-entry fellowship (2024-)
  • PI for Research fellowship award (175,500 USD, 2020-22) from Crohn’s and Colitis Foundation to study microbial strain dynamics in an FMT clinical trial for active Ulcerative Colitis
  • Co-PI on Pilot grant (50,000 USD, 2019-20) from Genetics and Genomics institute of Icahn School of Medicine at Mount Sinai, to study and design live biotherapeutic product for C. difficile infection
  • Awarded the 2nd prize for research talk at the Mount Sinai Inflammatory Bowel Disease retreat 2022
  • Awarded the best talk prize at Microbiome Virtual International Forum (MVIF) meeting in 2021
  • Selected as semifinalist for ASHG/Charles J Epstein Trainee award for excellence in human genetics research for year 2015
  • Awarded the Penn Center for Teaching and Learning certificate for excellence in teaching
  • Departmental Rank 1 and Institutional Rank 2, IIT Guwahati
  • Institute Silver Medal for being the topper of the Computer Science Department of IIT Guwahati
  • Recipient of Institute Merit Scholarship (full tuition waiver) for being the topper for years 2004-05 and 2006-07 in the entire institute
  • Recipient of N.T.S.E Scholarship (2002-2008) awarded by MHRD, Government of India


  • Jio Institute (March 2023-)
  • Department of Genetics and Genomic Sciences at the Icahn School of Medicine at Mount Sinai Hospital (May 2018-February 23)                          
  • Department of Microbiology at the Perelman School of Medicine of University of Pennsylvania (October 2016-April 18)                           



  • Faith JJ, Aggarwala V, Bethlehem L, Eggers JJ. “Compositions and Methods for Treating Infections of the Gastrointestinal Tract.” US20230310518A1


  • Chen-Liaw A, Aggarwala V, …, Faith JJ “Gut microbiota bacterial strain richness is species specific and limits therapeutic engraftment” bioRxiv 2022
  • Aggarwala V, Mogno I, Li Z, …, Faith JJ “Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes.” Nature Microbiology, 2021
  • Britton GJ, Contijoch EJ, Spindler MP, Aggarwala V, …, Faith JJ. “Defined microbiota transplant restores Th17/RORγt + regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas.” PNAS, 2020
  • Yang C, Mogno I, Contijoch EJ, Borgerding JN, Aggarwala V, …, Faith JJ. “Strain-level differences in gut microbiome composition determine fecal IgA levels and are modifiable by gut microbiota manipulation.” Cell Host and Microbe, 2020
  • Faith JJ, Chen-Liaw A, Aggarwala V, …, Mogno I. “Strain population structure varies widely across bacterial species and predicts strain colonization in unrelated individuals.” bioRxiv 2020
  • Aggarwala V, Liang G, Bushman FD. “Viral communities of the human gut: metagenomic analysis of composition and dynamics.” Mobile DNA, 2017
  • Aggarwala V, Ganguly A, Voight BF. “De novo mutational profile in RB1 clarified using a mutation rate modeling algorithm.” BMC Genomics, 2017
  • Aggarwala V, Voight BF. “An expanded sequence context model broadly explains variability in polymorphism levels across the human genome.” Nature Genetics, 2016
  • Shah PP, Donahue G, Otte GL, Capell BC, Nelson DM, Cao K, Aggarwala V, …, Berger SL. “Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape.” Genes and Development, 2013