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AI generated file to demonstrate microbiome engineering research in Varun Aggarwala's laboratory at the Jio Institute

Microbiota Therapeutics laboratory

(Page header is a generative AI image describing our laboratory mission) 

The overarching mission of our laboratory is to model microbiome dynamics (gut, skin, vaginal tract) and in-turn identify 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. Human body is colonized and is in a symbiotic relationship with trillions of  microorganisms (predominantly bacteria) which have a critical role in maintaining health and have been implicated across several diseases. The scientific community is actively perturbing the human microbial communities (probiotics, diet, synbiotics, stool transplant, xenobiotics) for desirable therapeutic outcomes with various degrees of success but several challenges remain: 

  1. We have not characterized the vast diversity of our commensal microbes
  2. Answered fundamental questions pertaining to their mechanism and modes of action 
  3. Barely understand the stability and structure of the complex microbial ecology and how it transforms under a homeostatic state and in presence of external perturbations (FMT, dietary changes, probiotics) 
  4. How to reproducibly engineer the microbiota? 

Microbiome Therapeutics laboratory (PI: Dr Varun Aggarwala) is addressing these open questions by integrating ideas from computational systems biology, ecology, genomics, & microbial culturing with fruitful collaborations from clinicians and public health researchers.

Course Facet

In November 2022, the FDA approved a specific C. difficile fecal microbiota treatment under the brand name Rebyota, administered rectally. 

Course Facet

In April 2023, the FDA approved a live spore capsule that can be taken by mouth, under the brand name Vowst.

Course Facet

In the United States, human feces has been regulated as an experimental drug since 2013.

Data and Compute Resources 

We collaborate extensively with clinicians and identify longitudinal microbiota samples (both in health and disease, with matched controls) to develop models and test our hypotheses. In our golden age of publicly available high-quality genomic datasets, we benefit tremendously from repurposing independent studies for our investigations. We also have access to high throughput sequencing and a biobanking facility for our projects. AWS and NSM Param are used for our high performance computing requirements. We will soon have a well-stocked laboratory for benchside research. 

Projects 

Our central theme is to engineer the microbiota but this is conditional on modeling and mechanistic understanding of underlying microbial dynamics Towards this, we are actively pursuing the following projects 

  1. Pangenomic representation of human commensal microbes to model microbiome dynamics in complex social settings (multiple donors, recipients or community with extensive sharing of microbes).
  2. Antibiotic resistance reservoirs: Modelling, stability and engineering techniques to reset it
  3. Microbiome for Age: Modelling, variation across lifespan, and engineering techniques for microbiome maturity. 
  4. Microbiome (im)maturity in children with undernutrition, and symbiotic interventions to reverse cognitive stunting.  
  5. Bacterial strain dynamics post Faecal Microbiota Transplants (FMT) for Ulcerative Colitis (UC). 
  6. Microbial Predictors for both clinical endpoint and longevity of response post-FMT for UC.
  7. Identification of super stool donors and superior interventional methodologies by integrating 1000s of FMT.
  8. Computational approaches to achieve actionable strain level resolution for commensal microbes.
  9. Core commensal microbiota in early childhood and its impact on the seeding of transient microbes.
  10. FMT registries, donor engraftment (urban vs rural), stool biobanks & hub for Indian microbiota therapeutics. 

Laboratory philosophy and culture 

We have an open non-hierarchical lab culture and encourage critical discussions and respect independent thoughts. The PI firmly believes that the success of trainees will be the true barometer of his own success and is committed to ensuring a productive environment that will benefit every stakeholder. We welcome creative ideas but insist on every project to make a positive impact on therapeutics, and thus contribute to the Atmanirbhar Bharat and Make in India mission to realise our collective civilizational potential in this Amrit kaal.

Programme Leadership

Dr. Varun Aggarwala, Microbiome Therapeutics, Jio Institute

Dr. Varun Aggarwala

Assistant Professor, Jio Institute

See Profile