# Defined microbial communities to prevent and eradicate infection by AMR pathogens

> **NIH NIH U19** · BAYLOR COLLEGE OF MEDICINE · 2021 · $533,331

## Abstract

Project Summary
Before the discovery of antibiotics, infectious diseases were the three leading causes of death in the United
States and constituted nearly 50% of the deaths annually. Today only one infectious disease, pneumonia, is
among the top 10 causes of death in the US, largely due to the success of antibiotics in treating bacterial
infections. Unfortunately, the public health benefits provided by antibiotics are at serious risk due to the
emergence of antibiotic resistant bacteria, an inevitable consequence of the evolutionary pressure exerted on
bacteria by these drugs. Eventually the bacterial pathogens we hope to keep at bay will become resistant to all
clinically relevant antibiotics, plunging humans back into a pre-antibiotic world in which infectious disease is the
leading cause of death. Therefore, we need to find innovative, and rapidly implementable, ways to reduce or
supplement antibiotics to preserve their utility in controlling bacterial infections. Many bacterial pathogens,
termed pathobionts, reside within the human microbiota in the absence of disease and only instigate
pathogenesis after disruption of the microbial community driven by abrupt environmental changes such as acute
inflammation. While there is general acceptance that the commensal microbes provide pathogen colonization
resistance and suppression of pathobiont virulence in a healthy state, the mechanistic understanding for how
they provide these benefits is lacking. In this project, we explore using the human microbiome to identify
ecological principles that allow for the design and implementation of microbial communities that suppress
bacterial pathogens. We have selected Clostridioides difficile and extraintestinal pathogenic E. coli (ExPEC) as
the two main pathogens to study as they are deemed antibiotic resistance threats by the CDC and necessitate
millions of antibiotic prescriptions each year. Even with antibiotic treatment, recurrent infections with both of
these pathogens is common, and there is currently a lack of long-lasting preventative strategies. Using a novel
method to simplify human microbiome communities and advanced in vitro human tissue culture and humanized
murine models, we seek to identify key microbial consortia for suppressing these pathogens. We ultimately
expect to optimize a small number of defined microbial communities that can be used to eradicate or prevent
these infections in people.

## Key facts

- **NIH application ID:** 10168134
- **Project number:** 1U19AI157981-01
- **Recipient organization:** BAYLOR COLLEGE OF MEDICINE
- **Principal Investigator:** ROBERT A BRITTON
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $533,331
- **Award type:** 1
- **Project period:** 2021-03-01 → 2026-02-28

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10168134

## Citation

> US National Institutes of Health, RePORTER application 10168134, Defined microbial communities to prevent and eradicate infection by AMR pathogens (1U19AI157981-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10168134. Licensed CC0.

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