# AN INTERBACTERIAL ADAPTIVE IMMUNE SYSTEM ENCODED BY BACTEROIDALES

> **NIH NIH R00** · DARTMOUTH COLLEGE · 2020 · $248,086

## Abstract

PROJECT SUMMARY / ABSTRACT
The composition of bacterial communities is paramount to their function. Intense competitive interactions
between bacteria can influence community composition by altering assembly or stability through the production
of anti-bacterial molecules. One such ecosystem rife with competitive interactions is the human gastrointestinal
microbiota, which harbors an abundance of bacteria from the order Bacteroidales. These bacteria encode the
type VI secretion system (T6SS), a contact-dependent toxin delivery pathway shown to mediate potent inter-
species competition. Bacteria that encode the T6SS also encode immunity proteins which bind to and
specifically inactivate toxins. I have found that Bacteroidales genomes possess arrays of “orphan immunity”
genes in the absence of the T6SS or corresponding toxin. These polyimmunity arrays are found associated
with xerD-like (PAX) recombinase genes that suggest an active mechanism of recruitment. I hypothesize that
genes within PAX clusters represent selective pressure from past episodes of direct interbacterial antagonism.
Therefore, characterization of the function, activity, and biogenesis of PAX clusters offers an avenue for the
identification of direct bacterial interactions in vivo and an understanding of their ecological consequences.
This proposal aims to augment my interdisciplinary background in cell biology, evolutionary biology, and
genetics with new training in germfree mouse experimentation to investigate this new mechanism of adaptation
to T6SS-mediated interbacterial antagonism within Bacteroidales and understand its impact on gut microbiome
assembly and dynamics. In Aim 1, I propose to characterize the function of genes within PAX clusters through
in vitro expression experiments in E. coli and growth competition experiments in vitro and in vivo under
conditions that promote contact-dependent interbacterial antagonism. In Aim 2, I will test the hypothesis that
the PAX recombinase mediates gene acquisition and excision from PAX clusters via tyrosine recombinase
activity in a manner analogous to integrons. In Aim 3, I will extend my characterization of PAX clusters to their
use as a new tool for deciphering interbacterial interactions by sequencing new gene insertions after exposure
of a PAX-containing strain to different bacterial communities in vivo. I will train with Dr. Lynn Hajjar at the
University of Washington Gnotobiotic Animal Core facility to gain experience in using germfree mice to study
the role of PAX clusters in the gut microbiota in vivo. Dr. Andrew Goodman at Yale University will collaborate
and provide advice and intellectual support. The proposed experiments will lay the foundation for my
independent research program, in which bioinformatics, bacterial genetics, and in vivo experimentation will be
combined to yield insight into direct interactions within the gut microbiota and the implications of these
interactions for human health and disease.

## Key facts

- **NIH application ID:** 10045595
- **Project number:** 4R00GM129874-03
- **Recipient organization:** DARTMOUTH COLLEGE
- **Principal Investigator:** Benjamin Davidson Ross
- **Activity code:** R00 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $248,086
- **Award type:** 4N
- **Project period:** 2018-09-10 → 2022-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10045595

## Citation

> US National Institutes of Health, RePORTER application 10045595, AN INTERBACTERIAL ADAPTIVE IMMUNE SYSTEM ENCODED BY BACTEROIDALES (4R00GM129874-03). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10045595. Licensed CC0.

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