Aiswarya Prasad

Aiswarya Prasad

PhD candidate in Quantitave biology studying gut microbiome evolution and ecology

Research Interest

My research focuses on understanding the bacterial diversity and ecology within the gut microbiome of animals. My work is driven by exciting, modern sequencing technologies and bioinformatic approaches to achieve in hours what once took months or was previously practically unachievable.

I am also keen on understanding how microbiomes operate at the strain-level which is an important open question given that the definition of strain has been a point of contention. It is especially important to understand strain-level patterns and interactions to enable engineering microbiomes towards the development of microbial consortia for specific applications. I have been using strain-level analysis approaches to understand the evolution and dynamics of bacterial communities in the gut microbiome of honeybees. I am also using synthetic gut microbial communities to address to understand how strains interact with each other in the context of a whole community of other microbes.

I am excited about applying cutting-edge approaches like high-throughput genome-resolved metagenomics, long-read sequencing, and strain-level analysis and manipulation to gain unprecedented insights into microbial diversity and interactions.

Apis species comparison

August 2020 --- October 2024

University of Lausanne, Switzerland

Honeybees serve as great model for studying gut microbiota evolution in the context of host ecology and evolution given their well-documented ecology and evolutionary history. Unlike the more diverse microbiomes of humans, primates, and mice, honeybees offer a more tractable system for understanding how gut microbiota are distributed and have evolved. This research is crucial for understanding how symbiotic interactions change and evolve across species but has been hindered by the lack of high-resolution genomic data.

Apis Profile Picture
Stinger of Apis Dorsata on a glove
Apis Profile Picture

Gut microbiome of wild and managed honeybees

August 2024 --- October 2024

University of Lausanne, Switzerland

Little is known about the gut microbiome of wild honeybees. Taking advantage of a large collection of wild honeybees of various subspecies from across Africa, painstakingly put together by our collaborators, we are investigating the differences in the gut microbiome of wild and managed honeybees. We are using shotgun metagenomics to resolve strain-level differences in the gut bacterial community and are currently analyzing the data to identify bacterial strains and species that are found in wild and managed honeybees and investigating their distribution across colonies of different subspecies.

Drawing of wild and managed honeybees
Drawing of honeybee gut microbiome research scheme

Priority Effects in the honeybee gut

August 2022 --- October 2024

University of Lausanne, Switzerland

In this ongoing study we aim to understand how bacterial strains in the gut microbiome interact with each other. I assemble synthetic microbial communities comprising honeybee-associated Lactobacillus and Bifidobacterium species and feed them to honeybees to study how strains of the same species compete with each other. We expect to see priority effects at the strain-level and that species will coexist by niche partitioning. We have developed a high-throughput compatible PacBio metagenomic approach to quantitatively detect strains in the gut. A pilot experiment points to clear signs of co-existance of strains between species but priority effects between strains of the same species. I carried out more replicates and combinations of strains and am currently analyzing the data to confirm the observations from the pilot experiment.

Aiswarya Prasad in microbiologist culturing bacteria

Gut Microbiome in Chronic Pancreatitis

August 2019 --- July 2020

Indian Institute of Science, Bengaluru, India

  • As a Master’s student ready to begin my thesis I was motivated to continue working on a project that would utilize a cutting-edge technology to study the gut microbiome which I was very excited about.
  • This excitement being contagious, I managed to convince my thesis supervisor to invest in a Nanopore sequencer for the lab.
  • I used this opportunity to optimize protocls and setup the Nanopore sequencer in the lab and developed my bioinformatic skills starting with setting up a Linux workstation for the lab and implementing a bioinformatic pipeline for metagenomics analysis.
  • I developed an end-to-end sampling and sequencing pipeline for metagenomics analysis of fecal samples using Nanopore sequencing in collaboration with a nearby hospital.
  • In collaboration with a gastroenterologist we analyzed the human gut microbiome in chronic pancreatitis patients and compared them with healthy samples to identify disease-related changes in the gut microbiome.

Gut Metaproteomics

August 2018 --- August 2019

Indian Institute of Science, Bengaluru, India

  • As a undergraduate student, I was excited to work on a project that would utilize cutting-edge technology to study the gut microbiome.
  • I surveyed and tested various approaches for sample preparation and metaproteomic analysis of fecal samples using LC-MS/MS.
  • Successfully detected proteins of microbiome origin but concluded that higher detection power eg. using a nano-LC MS/MS would be needed for fecal metaproteomics.

iGEM Project - Cellfiefuge

February 2016 --- October 2016

Indian Institute of Science, Bengaluru, India

  • The iGEM (International Genetically Engineered Machines) competition is an annual, worldwide synthetic biology event that brings together students from diverse backgrounds to design and build genetically engineered systems using standard biological parts. In 2016, I co-initiated the first iGEM team at the Indian Institute of Science (IISc), Bengaluru, India.
  • Our iGEM project aimed to cut infrastructure requirements for biomanufacturing initiatives by engineering bacteria that can autoinduce protein overexpression and autoaggregate when production is complete, replacing the need for centrifugation of large cultures.
  • More in our poster summarizing the project: iGEM Project Poster
  • An article summarizing our experience as the first team from the institute and how our efforts paved the way to future teams that have since won awards and special mentions for their work can be found here

Undergraduate students from the 2016 IISc iGEM team
Undergraduate students from the 2016 IISc iGEM team and SVCE team