Engineering immunity: Developing prophylactic probiotics from high-immunity individuals

Northeastern University
Roxbury Crossing, Massachusetts
Biology
$5,900
Pledged
35%
Funded
$17,000
Goal
41
Days Left
  • $5,900
    pledged
  • 35%
    funded
  • 41
    days left

About This Project

You know that friend who never gets sick? We do too, and we want to learn their secret. Our project is designed to create a powerful probiotic supplement by studying these ‘Resisters’ who have natural, above-average ability to fight off infections like the common cold or flu. We believe their superpower lies in their unique gut microbiome. We hypothesize that Resisters have distinctive gut microbiomes profiles containing bacterial strains that can enhance immune resilience.

Ask the Scientists

Join The Discussion

What is the context of this research?

Your gut is home to trillions of bacteria, and we're just learning its language. These microscopic allies—your microbiome—have a staggering impact on your immune, metabolic, and even mental health. In recent years, studies have directly linked gut bacteria to the severity of COVID-19 infections, the development of allergies, and even how well you respond to vaccines. While existing probiotics with bacteria like Lactiplantibacillus plantarum and Lactobacillus plantarum HEAL 9 offer a mild, but significant protection against colds, we're not aiming for "mild." We are expanding on this research to find the specific bacterial dream team that can dramatically upgrade your immune defenses against systemic infections. We hypothesize that by profiling the Resisters' microbiome, we can specifically identify bacteria which aid in host immune defense via bacterial derived metabolites and their interactions with the host's immune system.

What is the significance of this project?

The COVID-19 pandemic taught us a hard lesson: we need better, faster defenses. Imagine a general prophylactic that strengthens your immune system against future pandemics, buying the world precious time while vaccines are developed. By decoding the blood and gut microbiome signatures of people with naturally heightened immunity, we can pinpoint the exact microbes that grant this resistance. This technology can protect the public from common and costly infections, improving quality of life for millions and easing the massive financial burden on our healthcare system. The flu alone costs the US an estimated $90 billion annually. It’s time for a smarter defense. By profiling the Resister microbiome, we hope to create a general prophylactic probiotic to aid the general public's ability to fight off infections.

What are the goals of the project?

Our mission will follow a three-step process. First, we will recruit the elite by identifying and enrolling twelve “Resisters” to donate the blood and stool samples that hold their immunological secrets.

Second, we will decode the blueprint by fingerprinting their stool with next-generation sequencing to map their gut bacteria, while using cytokine multiplexing and untargeted metabolomics on their blood plasma to reveal the host–microbiome interactions that give them an edge.

Finally, we will build the shield by testing the identified bacteria—alone and in powerful consortia—in vitro using human-derived macrophage cell lines to assess their ability to help immune cells fend off infections and to build our prototype probiotic.

Budget

Please wait...

Resister stool collection will be performed to ensure both viability of bacteria isolated from stool and DNA integrity for downstream sequencing.

Nanopore long-read sequencing will allow us to identify the bacteria of interest within the Resister population and create Metagenome-Assembled Genomes (MAGs) for bacteria of interest.

Using plasma collected from Resisters, we can look at the cytokine distribution and metabolites present in blood to determine which signatures confer the Resister phenotype and what metabolites are microbial in origin.

Once we have identified the bacteria of interest, we must isolate them from stool using traditional culturomics methods to allow for further testing and DNA sequencing.

Finally, as a proof of concept that the Resister derived bacteria are able to improve the body's ability to fight infections, we will perform a THP-1 macrophage infection model to determine the bacteria's ability to aid in infection clearance.

Endorsed by

This project, aimed at characterizing the microbiome composition of individuals with exceptional resistance to common infections, has the potential to identify protective microbial communities and metabolites that could be leveraged for preventive therapeutics. The findings could revolutionize our approach to public health by enabling microbiome-based interventions that enhance natural immunity in vulnerable populations, thereby reducing antibiotic dependence and healthcare costs.

Project Timeline

Recruiting our twelve Resisters is estimated to take 3-6 months to ensure we find the right candidates for statistical power. The turnaround for our in-house nanopore sequencing is one week per donor so for all twelve donors a 3-month turnaround is expected. We will outsource metabolomics and cytokine analysis to General Metabolomics and Eve Biosciences, respectively, which will take 1-2 months. From start to finish, we anticipate this project will last one year.

Dec 01, 2025

Project Launched

Jan 31, 2026

Recruitment of 5 Resisters

Apr 30, 2026

Recruitment of all Resisters

May 31, 2026

Cytokine and Metabolomics Analysis

Jul 31, 2026

Finish Nanopore Sequencing

Meet the Team

Daniel Norment
Daniel Norment
PhD Student

Affiliates

Northeastern University
View Profile
Kim Lewis
Kim Lewis
University Distinguished Professor

Affiliates

Northeastern University
View Profile
Philip Strandwitz
Philip Strandwitz
CEO and co-founder

Affiliates

Holobiome, Inc Northeastern University
View Profile

Team Bio

This project brings together academic expertise and industry innovation through a collaboration between Northeastern University researchers and the biotechnology company Holobiome.

Daniel Norment

Daniel Norment, the PhD student investigator within the Lewis lab, has obtained his Master’s degree in biochemistry and molecular biology from the University of Massachusetts Amherst and has two years of industry experience working for Holobiome. Daniel specializes in working with human gut bacteria and translating DNA sequencing data into actionable insights.

Kim Lewis

Dr. Kim Lewis is a university distinguished professor and director of the Antimicrobial Discovery Center at Northeastern University in Boston Massachusetts. Dr. Lewis has authored over 100 papers, cofounded multiple biotechnology companies, and is an inventor on several patents. He has contributed to the development of general methods to grow previously uncultured bacteria, investigated drug-tolerant persister cells, and discovered several novel antibiotics. The Lewis lab has published high impact human microbiome papers in prestigious journals such as Nature Microbiology.

Philip Strandwitz

Dr. Strandwitz is a microbiome scientist turned entrepreneur. He was supported by one of the first grants in the Human Microbiome Project, and received his PhD in Biology in 2016 at Northeastern University in Dr. Kim Lewis' laboratory. His graduate work was focused on cultivating the "uncultured" members of the human microbiome, resulting in publications in top journals like Nature Microbiology and Microbiome. He is now CEO at Holobiome, a platform biotech company that’s mapping how our microbes impact our biology and developing solutions from that knowledge in the form of drugs and consumer products. He's brought in over $20M in capital to Holobiome, through non-dilutive grants, corporate partnerships, and venture capital. He’s also a Termeer Fellow, a mentorship network started by the founding CEO of Genzyme, Henri Termeer.

Lab Notes

Nothing posted yet.

Additional Information

Citations:

1. Lymberopoulos, E., Gentili, G. I., Budhdeo, S. & Sharma, N. COVID-19 severity is associated with population-level gut microbiome variations. Front Cell Infect Microbiol 12, 963338 (2022).

2. De Filippis, F. et al. Specific gut microbiome signatures and the associated pro-inflamatory functions are linked to pediatric allergy and acquisition of immune tolerance. Nat Commun 12, 5958 (2021).

3. Fonollá, J. et al. Effects of Lactobacillus coryniformis K8 CECT5711 on the immune response to influenza vaccination and the assessment of common respiratory symptoms in elderly subjects: a randomized controlled trial. Eur J Nutr 58, 83–90 (2019).

4. Ahrén, I. L., Hillman, M., Nordström, E. A., Larsson, N. & Niskanen, T. M. Fewer Community-Acquired Colds with Daily Consumption of Lactiplantibacillus plantarum HEAL9 and Lacticaseibacillus paracasei 8700:2. A Randomized, Placebo-Controlled Clinical Trial. The Journal of Nutrition 151, 214 (2020).

5. Damholt, A. et al. Lacticaseibacillus rhamnosus GG DSM 33156 effects on pathogen defence in the upper respiratory tract: a randomised, double-blind, placebo-controlled paediatric trial. (2022) doi:10.3920/BM2021.0065.

6. Dobson, R. Flu costs the US $90bn a year, report shows. BMJ 334, 1134 (2007).

7. Bramley, T. J., Lerner, D. & Sames, M. Productivity losses related to the common cold. J Occup Environ Med 44, 822–829 (2002).

8. Berggren, A. Randomised, double-blind and placebo-controlled study using new probiotic lactobacilli for strengthening the body immune defence against viral infections | European Journal of Nutrition. https://link.springer.com/article/10.1007/s00394-010-0127-6.


Project Backers

  • 5Backers
  • 35%Funded
  • $5,900Total Donations
  • $1,180.00Average Donation
Please wait...

See Your Scientific Impact

You can help a unique discovery by joining 5 other backers.
Fund This Project