# Systems-level perspectives of horizontal gene transfer within the human microbiome

> **NIH NIH DP2** · CORNELL UNIVERSITY · 2020 · $151,967

## Abstract

Project Summary:
Recent sequencing studies have suggested that the horizontal gene transfer (HGT) of plasmids, a possible
mechanism through which antimicrobial resistance (AMR) genes reach pathogens, is prevalent in the human
gut. Due to its prevalence in the community, it is possible to harness HGT as a method of manipulating the gut
microbiome by introducing plasmids. However, our knowledge of the conditions under which HGT occurs and
the rates of transfer between commensal bacteria and new species is lacking. In order to use HGT to perform
targeted manipulations of the gut microbiome, such as reducing the burden of AMR genes in the gut, it is
necessary to understand how plasmids are transferred throughout the community. In the Brito Lab, we
designed a HGT reporter plasmid that can track transfer events through gene edits created by a dCas9-
deaminase encoded in the plasmid. Using this reporter plasmid, I aim to determine the optimal parameters in
harnessing HGT for the in vivo delivery of plasmids to the gut microbial community. In my first aim, I will
optimize three parameters of conjugation-based plasmid delivery to the gut: donor species, donor dosage or
microbiota depletion by pre-treatment with antibiotics, in order to improve plasmid dispersal and persistence in
an in vivo mouse model. I will use the HGT reporter plasmid in conjunction with a single-cell sequencing
method optimized for bacterial communities to obtain taxonomic data of each cell that contains the plasmid
through various timepoints. This will allow me to determine which parameters increase dispersal and
persistence of the plasmid. In my second aim, I will compare conjugation to four different artificial
transformation methods to determine the most efficient plasmid delivery method. In order to determine
transformation efficiency for each method, I will deliver the HGT reporter plasmid to individual colonies of a
variety of gut commensal bacteria and use quantitative PCR of the plasmid and antibiotic selection to
determine the number of plasmid copies and transformants. Additionally, I will analyze how artificial
transformation affects dispersal by creating a mock gut community and use single-cell sequencing to
determine which species obtained the plasmid. Through the proposed experiments, I will determine the optimal
parameters for plasmid delivery to the gut, a necessary step for harnessing HGT for microbiome engineering.
The potential to engineer this community provides an opportunity to interrogate the specific host-microbiome
interactions that might underlie microbiome-associated diseases, as well as reducing AMR in the gut. I will also
gain valuable experience in microbiome research and single-cell sequencing technologies that will aid me in
my goal to become a professor in Puerto Rico and help train the next generation of Puerto Rican scientists.

## Key facts

- **NIH application ID:** 10157533
- **Project number:** 3DP2HL141007-01S1
- **Recipient organization:** CORNELL UNIVERSITY
- **Principal Investigator:** Ilana Lauren Brito
- **Activity code:** DP2 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $151,967
- **Award type:** 3
- **Project period:** 2017-09-30 → 2022-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10157533

## Citation

> US National Institutes of Health, RePORTER application 10157533, Systems-level perspectives of horizontal gene transfer within the human microbiome (3DP2HL141007-01S1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10157533. Licensed CC0.

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