Living Microbial Diagnostics to Enable Individualized Child Health Interventions

Microbiota in the gastrointestinal tract, or gut, often change in response to illness or disease in the body. Monitoring such changes could inform us about the current health status of the body. This research project aims to engineer bacteria to serve as a non-invasive living diagnostic to record these changes in the gut and thereby provide a basis for individualizing and improving health interventions for children and adolescents worldwide.

Millions of children annually do not reach their developmental potential predominantly due to infectious diseases as well as malnutrition and related disorders. A major challenge in diagnosing and treating these children in low-income settings lies in the lack of feasible options for objectively measuring individual nutritional, infection and inflammation status of the gastrointestinal tract.

To overcome this challenge, the consortium recently engineered a bacterium, using CRISPR1-based technology, capable of sensing, remembering, and reporting on the environment within the gastrointestinal tract of animals. These engineered bacteria can safely traverse the gastrointestinal tract and then be retrieved upon leaving the body, analysed in the laboratory, and enable predictive therapeutic interventions. The research project focuses on further developing these engineered bacteria and comprehensively testing their safety and capacity to reveal clinically-meaningful information. Initial preclinical studies will be complemented with a longitudinal analysis of samples from mothers and babies living in Zimbabwe in order to gain further insight into the impact of malnutrition and related disorders on gastrointestinal function in children.

The core objective is to develop the engineered bacteria technology into a non-invasive diagnostic tool to help predict individualised health interventions for use in at-risk children worldwide. In the future, the technology could be deployed throughout the world, in a sustainable and scalable fashion, and aid in improving child health and wellbeing overall.

1Clustered Regularly Interspaced Short Palindromic Repeats
Banner image above: A sample plate sits ready to be analysed in a DNA sequencer. 

Gel from an electrophoresis assay showing bands of DNA.

Researchers P. Munjoma (left) and P. Chandiwana (right), University of Zimbabwe, work on a longitudinal analysis of microbiota samples from mothers and babies living in Zimbabwe in order to gain further insight into the impact of malnutrition and related disorders on gastrointestinal function in children

Researcher M. Cherepkova, ETH Zurich, works on improving the efficiency of Record-seq technology to develop next-generation living microbial diagnostics.

    Additional Information


    • The research is part of the BRCCH Multi-Investigator Programme.
    • The consortium is led by investigators Prof Randall Platt.
    • Additional investigators and collaborators include Prof Dirk Bumann, Prof Kerina Duri, Prof Andrew Macpherson and Prof Uwe Sauer. Consortium members include Panashe Chandiwana, Masha Cherepkova, Dr Rick Farouni, Dr Daniela Ledezma Tejeida, Dr Benjamin Misselwitz, Privilege Munjoma, Raj Ramachanderan, Florian Schmidt, Tanmay Tanna and Dr Jakob Zimmerman.

    Consortium Members
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